Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
DVL1	1855	broad.mit.edu	37	1	1275504	1275504	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:1275504C>G	uc001aer.3	-	8	870	c.823G>C	c.(823-825)GAC>CAC	p.D275H	DVL1_uc002quu.2_5'UTR|DVL1_uc009vka.2_5'UTR|DVL1_uc001aeu.1_5'UTR	NM_004421	NP_004412	O14640	DVL1_HUMAN	dishevelled 1	275	PDZ.				canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway	cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome	frizzled binding|identical protein binding|protein kinase binding|signal transducer activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		ATGCCGCCGTCTCCACGGTCG	0.652													3	23	---	---	---	---	PASS
CAMTA1	23261	broad.mit.edu	37	1	7725174	7725174	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:7725174C>T	uc001aoi.2	+	9	2774	c.2567C>T	c.(2566-2568)TCG>TTG	p.S856L		NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	856					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TCGGCCGCCTCGGCCCAGGGC	0.677													7	27	---	---	---	---	PASS
PADI4	23569	broad.mit.edu	37	1	17690223	17690223	+	Silent	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:17690223C>A	uc001baj.2	+	16	1993	c.1965C>A	c.(1963-1965)TCC>TCA	p.S655S		NM_012387	NP_036519	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	655					chromatin modification|peptidyl-citrulline biosynthetic process from peptidyl-arginine|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	AGCCCTTCTCCTTCAAGTGGT	0.602													4	31	---	---	---	---	PASS
USP48	84196	broad.mit.edu	37	1	22033294	22033294	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:22033294C>A	uc001bfb.2	-	16	2269	c.2031G>T	c.(2029-2031)CAG>CAT	p.Q677H	USP48_uc001bfa.2_Missense_Mutation_p.Q215H|USP48_uc010odq.1_Missense_Mutation_p.Q689H|USP48_uc009vqc.2_Missense_Mutation_p.Q611H|USP48_uc001bfc.2_Missense_Mutation_p.Q677H|USP48_uc001bfd.1_5'Flank	NM_032236	NP_115612	Q86UV5	UBP48_HUMAN	ubiquitin specific protease 48 isoform a	677	DUSP 2.				ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		TTGGAAAGTACTGCTGCAGTT	0.403													18	65	---	---	---	---	PASS
DLGAP3	58512	broad.mit.edu	37	1	35351124	35351124	+	Silent	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:35351124C>G	uc001byc.2	-	5	1869	c.1869G>C	c.(1867-1869)CGG>CGC	p.R623R		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	623					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)				GCGCCAGGCTCCGCAGCTCCT	0.721													4	9	---	---	---	---	PASS
ZMYM1	79830	broad.mit.edu	37	1	35579229	35579229	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:35579229G>A	uc001bym.2	+	11	1946	c.1798G>A	c.(1798-1800)GAA>AAA	p.E600K	ZMYM1_uc001byn.2_Missense_Mutation_p.E600K|ZMYM1_uc010ohu.1_Missense_Mutation_p.E581K|ZMYM1_uc001byo.2_Missense_Mutation_p.E240K|ZMYM1_uc009vut.2_Missense_Mutation_p.E525K	NM_024772	NP_079048	Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM domain containing 1	600						nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TAAAGGAGAAGAAACATTTCG	0.318													6	27	---	---	---	---	PASS
CLSPN	63967	broad.mit.edu	37	1	36202137	36202137	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:36202137G>A	uc001bzi.2	-	25	4060	c.3980C>T	c.(3979-3981)TCA>TTA	p.S1327L	CLSPN_uc009vux.2_Missense_Mutation_p.S1263L	NM_022111	NP_071394	Q9HAW4	CLSPN_HUMAN	claspin	1327					activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CGTCAATCCTGAAGTGCTATC	0.443													9	64	---	---	---	---	PASS
EIF2C3	192669	broad.mit.edu	37	1	36479647	36479647	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:36479647G>C	uc001bzp.2	+	11	1660	c.1404G>C	c.(1402-1404)TTG>TTC	p.L468F	EIF2C3_uc001bzq.2_Missense_Mutation_p.L234F	NM_024852	NP_079128	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3	468					mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AAGAAATATTGAAGTAAGACA	0.378													6	91	---	---	---	---	PASS
FAM176B	55194	broad.mit.edu	37	1	36788602	36788602	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:36788602T>G	uc001cai.1	-	1	248	c.37A>C	c.(37-39)AAC>CAC	p.N13H	C1orf113_uc010oic.1_Intron|FAM176B_uc001caj.1_Missense_Mutation_p.N13H	NM_018166	NP_060636	Q9NVM1	F176B_HUMAN	hypothetical protein LOC55194	13						integral to membrane				pancreas(1)	1						GCCAGGCTGTTGCTGAGCAAC	0.667													9	21	---	---	---	---	PASS
ZSWIM5	57643	broad.mit.edu	37	1	45484503	45484503	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:45484503T>G	uc001cnd.2	-	14	3409	c.3181A>C	c.(3181-3183)ATC>CTC	p.I1061L		NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM domain containing 5	1061							zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)					ACCAGGGGGATGAGAGCTGCC	0.582											OREG0013450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	28	---	---	---	---	PASS
SPATA6	54558	broad.mit.edu	37	1	48771547	48771547	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:48771547C>A	uc001crr.1	-	12	1363	c.1198G>T	c.(1198-1200)GAG>TAG	p.E400*	SPATA6_uc001crs.1_Nonsense_Mutation_p.E384*|SPATA6_uc010omv.1_Nonsense_Mutation_p.E386*	NM_019073	NP_061946	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6 precursor	400					cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1						AGGTCTCTCTCATCCTGAAAA	0.368													19	53	---	---	---	---	PASS
NRD1	4898	broad.mit.edu	37	1	52266248	52266248	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:52266248G>C	uc001ctc.3	-	23	2947	c.2625C>G	c.(2623-2625)ATC>ATG	p.I875M	NRD1_uc009vzb.2_Missense_Mutation_p.I570M|NRD1_uc001ctd.3_Missense_Mutation_p.I807M|NRD1_uc001cte.2_Missense_Mutation_p.I743M|NRD1_uc001ctf.2_Missense_Mutation_p.I807M|NRD1_uc010ong.1_RNA	NM_002525	NP_002516	O43847	NRDC_HUMAN	nardilysin isoform a	806					cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0						TCTCGGGCTTGATGAGGATGT	0.428													5	114	---	---	---	---	PASS
CPT2	1376	broad.mit.edu	37	1	53676146	53676146	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:53676146C>G	uc001cvb.3	+	4	1315	c.800C>G	c.(799-801)TCG>TGG	p.S267W		NM_000098	NP_000089	P23786	CPT2_HUMAN	carnitine O-palmitoyltransferase precursor	267	Mitochondrial matrix (By similarity).				carnitine shuttle|fatty acid beta-oxidation|regulation of fatty acid oxidation	mitochondrial inner membrane	carnitine O-palmitoyltransferase activity				0					L-Carnitine(DB00583)|Perhexiline(DB01074)	GTGAGCCCCTCGGAAATCCAG	0.512													6	83	---	---	---	---	PASS
ALG6	29929	broad.mit.edu	37	1	63876833	63876833	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:63876833C>G	uc010oow.1	+	8	816	c.511C>G	c.(511-513)CTT>GTT	p.L171V	ALG6_uc001daz.2_RNA|ALG6_uc009waj.2_RNA|ALG6_uc010oox.1_5'UTR	NM_013339	NP_037471	Q9Y672	ALG6_HUMAN	dolichyl pyrophosphate Man9GlcNAc2	171					dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity				0						TTCTGTGAGTCTTGGCTTTGC	0.358													4	116	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70504896	70504896	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:70504896C>T	uc001dep.2	+	19	3305	c.3275C>T	c.(3274-3276)TCT>TTT	p.S1092F	LRRC7_uc009wbg.2_Missense_Mutation_p.S376F|LRRC7_uc001deq.2_Missense_Mutation_p.S333F	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1092						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						TCTCAGCCATCTGTGAATGAG	0.532													17	37	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70518754	70518754	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:70518754G>T	uc001dep.2	+	21	4072	c.4042G>T	c.(4042-4044)GTA>TTA	p.V1348L	LRRC7_uc009wbg.2_Missense_Mutation_p.V632L|LRRC7_uc001deq.2_Missense_Mutation_p.V542L	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1348						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						ACAAGAAGATGTATCTCCTAG	0.408													11	45	---	---	---	---	PASS
ASB17	127247	broad.mit.edu	37	1	76387905	76387905	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:76387905T>G	uc001dhe.1	-	2	681	c.541A>C	c.(541-543)ATT>CTT	p.I181L	ASB17_uc001dhf.1_RNA	NM_080868	NP_543144	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box-containing 17	181					intracellular signal transduction					ovary(1)	1						GTTAAGACAATGTTGATAGGG	0.363													10	36	---	---	---	---	PASS
LPHN2	23266	broad.mit.edu	37	1	82436211	82436211	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:82436211G>C	uc001dit.3	+	15	3077	c.2896G>C	c.(2896-2898)GAA>CAA	p.E966Q	LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Missense_Mutation_p.E966Q|LPHN2_uc001div.2_Missense_Mutation_p.E966Q|LPHN2_uc009wcd.2_Missense_Mutation_p.E966Q|LPHN2_uc001diw.2_Missense_Mutation_p.E550Q|LPHN2_uc009wce.1_Missense_Mutation_p.E52Q	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	979	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		CTATGGAACAGAAAAAGCGTA	0.373													9	27	---	---	---	---	PASS
COL24A1	255631	broad.mit.edu	37	1	86590590	86590590	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:86590590C>A	uc001dlj.2	-	3	1471	c.1429G>T	c.(1429-1431)GAT>TAT	p.D477Y	COL24A1_uc010osd.1_5'UTR|COL24A1_uc001dlk.2_RNA|COL24A1_uc010ose.1_RNA|COL24A1_uc010osf.1_RNA|COL24A1_uc009wcq.2_Missense_Mutation_p.D477Y	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	477					cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		GTATTTAGATCCTCATAATAA	0.338													9	27	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103461545	103461545	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:103461545C>G	uc001dul.2	-	27	2613	c.2295G>C	c.(2293-2295)AAG>AAC	p.K765N	COL11A1_uc001duk.2_5'UTR|COL11A1_uc001dum.2_Missense_Mutation_p.K777N|COL11A1_uc001dun.2_Missense_Mutation_p.K726N|COL11A1_uc009weh.2_Missense_Mutation_p.K649N	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	765	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTAACGTTACCTTTACTCCCC	0.398													3	33	---	---	---	---	PASS
CSDE1	7812	broad.mit.edu	37	1	115269613	115269613	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:115269613T>C	uc001efk.2	-	13	1921	c.1455A>G	c.(1453-1455)ATA>ATG	p.I485M	CSDE1_uc001efi.2_Missense_Mutation_p.I531M|CSDE1_uc001efj.2_RNA|CSDE1_uc001efl.2_Missense_Mutation_p.I454M|CSDE1_uc001efm.2_Missense_Mutation_p.I500M|CSDE1_uc009wgv.2_Missense_Mutation_p.I485M|CSDE1_uc001efn.2_Missense_Mutation_p.I454M	NM_001007553	NP_001007554	O75534	CSDE1_HUMAN	upstream of NRAS isoform 1	485	CSD 6.				male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCTTATCTCCTATTTGAGGAG	0.403													8	18	---	---	---	---	PASS
UBAP2L	9898	broad.mit.edu	37	1	154227733	154227733	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:154227733A>C	uc001fep.3	+	17	2182	c.2015A>C	c.(2014-2016)CAT>CCT	p.H672P	UBAP2L_uc009wot.2_Missense_Mutation_p.H672P|UBAP2L_uc010pek.1_Missense_Mutation_p.H664P|UBAP2L_uc010pel.1_Missense_Mutation_p.H682P|UBAP2L_uc010pen.1_Missense_Mutation_p.H586P|UBAP2L_uc001feq.2_5'UTR|UBAP2L_uc001fer.2_5'Flank	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a	672					binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			ACCAATCAGCATTCATCCTCC	0.502													10	68	---	---	---	---	PASS
UBAP2L	9898	broad.mit.edu	37	1	154227736	154227736	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:154227736C>T	uc001fep.3	+	17	2185	c.2018C>T	c.(2017-2019)TCA>TTA	p.S673L	UBAP2L_uc009wot.2_Missense_Mutation_p.S673L|UBAP2L_uc010pek.1_Missense_Mutation_p.S665L|UBAP2L_uc010pel.1_Missense_Mutation_p.S683L|UBAP2L_uc010pen.1_Missense_Mutation_p.S587L|UBAP2L_uc001feq.2_5'UTR|UBAP2L_uc001fer.2_5'Flank	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a	673					binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AATCAGCATTCATCCTCCTTG	0.507													9	71	---	---	---	---	PASS
CD5L	922	broad.mit.edu	37	1	157805709	157805709	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:157805709C>A	uc001frk.3	-	3	435	c.292G>T	c.(292-294)GGA>TGA	p.G98*		NM_005894	NP_005885	O43866	CD5L_HUMAN	CD5 molecule-like precursor	98	SRCR 1.				apoptosis|cellular defense response	extracellular space|membrane	scavenger receptor activity			ovary(1)	1	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TCTTCTGTTCCTGTGCAACTG	0.493													52	104	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158644424	158644424	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:158644424C>A	uc001fst.1	-	9	1353	c.1154G>T	c.(1153-1155)TGG>TTG	p.W385L		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	385	Spectrin 5.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					CTCGTTCATCCAGCCTGAGAG	0.468													6	124	---	---	---	---	PASS
FCER1G	2207	broad.mit.edu	37	1	161185114	161185114	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:161185114G>A	uc001fyz.1	+	1	28	c.3G>A	c.(1-3)ATG>ATA	p.M1I	FCER1G_uc001fza.1_Missense_Mutation_p.M1I	NM_004106	NP_004097	P30273	FCERG_HUMAN	Fc fragment of IgE, high affinity I, receptor	1					platelet activation	integral to plasma membrane					0	all_cancers(52;1.35e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Benzylpenicilloyl Polylysine(DB00895)	AGCCCAAGATGATTCCAGCAG	0.572													20	58	---	---	---	---	PASS
UHMK1	127933	broad.mit.edu	37	1	162468041	162468041	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:162468041A>T	uc001gcc.1	+	1	387	c.251A>T	c.(250-252)CAG>CTG	p.Q84L	UHMK1_uc001gcb.1_Intron|UHMK1_uc009wuu.1_Missense_Mutation_p.Q84L	NM_175866	NP_787062	Q8TAS1	UHMK1_HUMAN	kinase interacting stathmin	84	Protein kinase.				cell cycle arrest|neuron projection development|peptidyl-serine phosphorylation|positive regulation of translational initiation|protein autophosphorylation|regulation of protein export from nucleus	axon|dendrite cytoplasm|neuronal RNA granule|nucleus	protein binding|protein serine/threonine kinase activity|ribonucleoprotein binding|RNA binding				0	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			GAACAGTTGCAGGGTCACAGA	0.602													5	21	---	---	---	---	PASS
DDR2	4921	broad.mit.edu	37	1	162725039	162725039	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:162725039G>T	uc001gcf.2	+	7	976	c.511G>T	c.(511-513)GAC>TAC	p.D171Y	DDR2_uc001gcg.2_Missense_Mutation_p.D171Y	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2	171	Extracellular (Potential).|F5/8 type C.				cell adhesion	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			TCCAGTCACCGACCACTCCAT	0.478													12	48	---	---	---	---	PASS
TBX19	9095	broad.mit.edu	37	1	168260586	168260586	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:168260586T>G	uc001gfl.2	+	2	443	c.392T>G	c.(391-393)TTT>TGT	p.F131C	TBX19_uc001gfj.3_Missense_Mutation_p.F62C	NM_005149	NP_005140	O60806	TBX19_HUMAN	T-box 19	131	T-box.				anatomical structure morphogenesis	nucleus	DNA binding				0	all_hematologic(923;0.215)					TCCCCCAACTTTGGGGCCCAC	0.602													30	107	---	---	---	---	PASS
SERPINC1	462	broad.mit.edu	37	1	173873178	173873178	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:173873178G>T	uc001gjt.2	-	7	1363	c.1244C>A	c.(1243-1245)GCT>GAT	p.A415D		NM_000488	NP_000479	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C, member 1	415					blood coagulation|regulation of proteolysis	extracellular space|plasma membrane	heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(1)	1					Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)	GGTACTTGCAGCTGCTTCACT	0.463													7	42	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175362941	175362941	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:175362941C>A	uc001gkp.1	-	4	1412	c.1331G>T	c.(1330-1332)GGG>GTG	p.G444V	TNR_uc009wwu.1_Missense_Mutation_p.G444V|TNR_uc010pmz.1_3'UTR	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	444	Fibronectin type-III 2.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					GATTTCCCACCCATCGAAGGA	0.473													38	195	---	---	---	---	PASS
CEP350	9857	broad.mit.edu	37	1	179966134	179966134	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:179966134A>G	uc001gnt.2	+	6	1225	c.842A>G	c.(841-843)AAA>AGA	p.K281R	CEP350_uc001gnr.1_Missense_Mutation_p.K255R|CEP350_uc009wxl.2_Missense_Mutation_p.K280R|CEP350_uc001gnu.2_Missense_Mutation_p.K115R	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	281						centrosome|nucleus|spindle				ovary(4)	4						CATGATGTCAAACTGGAAAAA	0.423													30	97	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186017921	186017921	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:186017921C>T	uc001grq.1	+	42	6756	c.6527C>T	c.(6526-6528)GCA>GTA	p.A2176V		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	2176	Ig-like C2-type 19.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						ACTTGTGAAGCAACAAATGTT	0.358													17	28	---	---	---	---	PASS
TROVE2	6738	broad.mit.edu	37	1	193038725	193038725	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:193038725G>C	uc001gss.2	+	2	716	c.541G>C	c.(541-543)GAT>CAT	p.D181H	TROVE2_uc001gst.1_Intron|TROVE2_uc001gsu.1_Intron|TROVE2_uc001gsv.1_Missense_Mutation_p.D181H|TROVE2_uc001gsw.2_Missense_Mutation_p.D181H|TROVE2_uc009wyp.2_Missense_Mutation_p.D181H|TROVE2_uc009wyq.2_Missense_Mutation_p.D181H|TROVE2_uc001gsx.1_Missense_Mutation_p.D181H	NM_004600	NP_004591	P10155	RO60_HUMAN	TROVE domain family, member 2 isoform 2	181	TROVE.				transcription from RNA polymerase III promoter	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|RNA binding				0						GTCTCACAAAGATCTATTAAG	0.418													11	61	---	---	---	---	PASS
FAM58B	339521	broad.mit.edu	37	1	200183337	200183337	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:200183337G>C	uc009wzi.1	+	1	682	c.646G>C	c.(646-648)GAG>CAG	p.E216Q		NM_001105517	NP_001098987	P0C7Q3	FA58B_HUMAN	family with sequence similarity 58 member B	216					regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent		protein kinase binding				0	Prostate(682;0.19)					CGCCGAGGTCGAGGCTGAGAA	0.562													16	42	---	---	---	---	PASS
IKBKE	9641	broad.mit.edu	37	1	206664179	206664179	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:206664179A>G	uc001hdz.1	+	17	2089	c.1721A>G	c.(1720-1722)CAC>CGC	p.H574R	IKBKE_uc009xbv.1_Missense_Mutation_p.H574R|IKBKE_uc001hea.1_Missense_Mutation_p.H489R	NM_014002	NP_054721	Q14164	IKKE_HUMAN	IKK-related kinase epsilon	574					DNA damage response, signal transduction resulting in induction of apoptosis|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane|PML body	ATP binding|IkappaB kinase activity|NF-kappaB-inducing kinase activity|protein binding			ovary(3)|lung(3)|central_nervous_system(1)|skin(1)	8	Breast(84;0.137)					GAGCAGATTCACAAGCTGGAT	0.557											OREG0014171	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	33	---	---	---	---	PASS
CD34	947	broad.mit.edu	37	1	208072428	208072428	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:208072428G>A	uc001hgw.1	-	3	664	c.406C>T	c.(406-408)CCT>TCT	p.P136S	CD34_uc001hgx.1_Missense_Mutation_p.P136S|CD34_uc010psj.1_Intron	NM_001025109	NP_001020280	P28906	CD34_HUMAN	CD34 antigen isoform a	136	Extracellular (Potential).				cell-cell adhesion|leukocyte migration|regulation of immune response	integral to membrane	carbohydrate binding			ovary(1)	1						GACAGGCTAGGCTTCAAGGTT	0.463													5	177	---	---	---	---	PASS
ANGEL2	90806	broad.mit.edu	37	1	213186487	213186487	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:213186487G>A	uc001hjz.2	-	2	488	c.333C>T	c.(331-333)TAC>TAT	p.Y111Y	ANGEL2_uc010pto.1_Intron|ANGEL2_uc010ptp.1_Intron|ANGEL2_uc001hka.2_Intron|ANGEL2_uc010ptq.1_Intron|ANGEL2_uc001hkb.2_Silent_p.Y89Y	NM_144567	NP_653168	Q5VTE6	ANGE2_HUMAN	LOC90806 protein	111											0				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		CGTTCATGACGTAACTAGAGA	0.428													22	68	---	---	---	---	PASS
ESRRG	2104	broad.mit.edu	37	1	216850613	216850613	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:216850613C>A	uc001hkw.1	-	2	443	c.277G>T	c.(277-279)GGT>TGT	p.G93C	ESRRG_uc001hky.1_Missense_Mutation_p.G70C|ESRRG_uc009xdp.1_Missense_Mutation_p.G70C|ESRRG_uc001hkz.1_Missense_Mutation_p.G70C|ESRRG_uc010puc.1_Missense_Mutation_p.G70C|ESRRG_uc001hla.1_Missense_Mutation_p.G70C|ESRRG_uc001hlb.1_Missense_Mutation_p.G70C|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Missense_Mutation_p.G70C|ESRRG_uc001hld.1_Missense_Mutation_p.G70C|ESRRG_uc001hkx.1_Missense_Mutation_p.G98C|ESRRG_uc009xdo.1_Missense_Mutation_p.G70C|ESRRG_uc001hle.1_Missense_Mutation_p.G70C	NM_001438	NP_001429	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 1	93					positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	GGCCCACTACCTCCCAGGATA	0.527													16	62	---	---	---	---	PASS
RRP15	51018	broad.mit.edu	37	1	218480911	218480911	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:218480911G>T	uc001hlj.2	+	4	672	c.642G>T	c.(640-642)TTG>TTT	p.L214F		NM_016052	NP_057136	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog	214						mitochondrion|nucleolus	protein binding				0				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)		TCAGTGTTTTGAGAGGGATGG	0.368													13	36	---	---	---	---	PASS
ACTA1	58	broad.mit.edu	37	1	229568773	229568773	+	Missense_Mutation	SNP	C	A	A	rs113546590		TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:229568773C>A	uc001htm.2	-	2	195	c.90G>T	c.(88-90)AGG>AGT	p.R30S		NM_001100	NP_001091	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	30					muscle filament sliding|skeletal muscle fiber development|skeletal muscle thin filament assembly	actin filament|cytosol|stress fiber|striated muscle thin filament	ADP binding|ATP binding|myosin binding|structural constituent of cytoskeleton				0	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)			Dornase Alfa(DB00003)	GGAACACGGCCCTAGGGGCGT	0.692													7	29	---	---	---	---	PASS
COG2	22796	broad.mit.edu	37	1	230827305	230827305	+	Nonsense_Mutation	SNP	G	T	T	rs140155560		TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:230827305G>T	uc001htw.2	+	17	2261	c.2110G>T	c.(2110-2112)GAG>TAG	p.E704*	COG2_uc001htx.2_Nonsense_Mutation_p.E703*|COG2_uc010pwc.1_Nonsense_Mutation_p.E577*	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform	704					Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GTACTTGGGAGAGCAGGTAAC	0.587													10	42	---	---	---	---	PASS
OR2T4	127074	broad.mit.edu	37	1	248525700	248525700	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:248525700G>T	uc001ieh.1	+	1	818	c.818G>T	c.(817-819)TGC>TTC	p.C273F		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	273	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTTGCCACCTGCTCCTCCCAC	0.542													15	98	---	---	---	---	PASS
OR2G6	391211	broad.mit.edu	37	1	248685656	248685656	+	Missense_Mutation	SNP	G	A	A	rs147303796		TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr1:248685656G>A	uc001ien.1	+	1	709	c.709G>A	c.(709-711)GCC>ACC	p.A237T		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	237	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCGCCAAAAGGCCTTTGGGAC	0.453													10	50	---	---	---	---	PASS
ACP1	52	broad.mit.edu	37	2	277020	277020	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:277020G>C	uc002qwg.2	+	5	430	c.334G>C	c.(334-336)GCT>CCT	p.A112P	ACP1_uc002qwh.2_RNA|ACP1_uc002qwf.2_Missense_Mutation_p.A112P	NM_007099	NP_009030	P24666	PPAC_HUMAN	acid phosphatase 1, soluble isoform b	112						cytoplasm|internal side of plasma membrane|nucleus|soluble fraction	acid phosphatase activity|identical protein binding|non-membrane spanning protein tyrosine phosphatase activity			skin(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)		AACCTGCAAAGCTAAAATTGA	0.308													17	33	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15519752	15519752	+	Silent	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:15519752G>C	uc002rcc.1	-	30	3590	c.3564C>G	c.(3562-3564)CTC>CTG	p.L1188L	NBAS_uc010exl.1_Silent_p.L260L|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	1188										ovary(2)|liver(1)|skin(1)	4						AGCTATCAGTGAGGTTGGTAG	0.428													9	71	---	---	---	---	PASS
FAM179A	165186	broad.mit.edu	37	2	29240096	29240096	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:29240096G>T	uc010ezl.2	+	9	1472	c.1121G>T	c.(1120-1122)AGG>ATG	p.R374M	FAM179A_uc010ymm.1_Missense_Mutation_p.R374M|FAM179A_uc002rmr.3_Intron	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186	374							binding			ovary(3)|skin(1)	4						CTGCTTCGGAGGCTGGAGGAG	0.582													11	82	---	---	---	---	PASS
NRXN1	9378	broad.mit.edu	37	2	50280591	50280591	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:50280591C>T	uc010fbp.2	-	4	1558	c.751G>A	c.(751-753)GCC>ACC	p.A251T	NRXN1_uc002rxb.3_Missense_Mutation_p.A988T|NRXN1_uc010fbq.2_Missense_Mutation_p.A1356T|NRXN1_uc002rxe.3_Missense_Mutation_p.A1286T	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor	251	Extracellular (Potential).|Laminin G-like.				angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GCGATGTTGGCATCGTTTTCG	0.512													5	33	---	---	---	---	PASS
EFEMP1	2202	broad.mit.edu	37	2	56097912	56097912	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:56097912G>A	uc002rzh.2	-	10	1593	c.1263C>T	c.(1261-1263)AAC>AAT	p.N421N	EFEMP1_uc002rzi.2_Silent_p.N421N|EFEMP1_uc002rzj.2_Silent_p.N421N|EFEMP1_uc010ypc.1_Silent_p.N283N	NM_004105	NP_004096	Q12805	FBLN3_HUMAN	EGF-containing fibulin-like extracellular matrix	421	Mediates interaction with TIMP3.				negative regulation of chondrocyte differentiation|peptidyl-tyrosine phosphorylation|regulation of transcription, DNA-dependent|visual perception	extracellular space|proteinaceous extracellular matrix	calcium ion binding|epidermal growth factor receptor activity|epidermal growth factor receptor binding|growth factor activity			ovary(4)|pancreas(1)|skin(1)	6			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TATTGATGGTGTTGGCATAAA	0.413													7	62	---	---	---	---	PASS
COMMD1	150684	broad.mit.edu	37	2	62228088	62228088	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:62228088A>G	uc002sbp.2	+	2	444	c.433A>G	c.(433-435)ATA>GTA	p.I145V	COMMD1_uc002sbq.1_RNA	NM_152516	NP_689729	Q8N668	COMD1_HUMAN	MURR1	145	COMM.				copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			TGTTGCCATTATAGAGCTGGA	0.448													19	50	---	---	---	---	PASS
EDAR	10913	broad.mit.edu	37	2	109513383	109513383	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:109513383G>A	uc002teq.3	-	12	1758	c.1327C>T	c.(1327-1329)CAG>TAG	p.Q443*	EDAR_uc010fjn.2_Nonsense_Mutation_p.Q475*|EDAR_uc010yws.1_Nonsense_Mutation_p.Q475*	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor	443	Cytoplasmic (Potential).				apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1						GCATGTGGCTGGGAGGCAGGT	0.582													6	6	---	---	---	---	PASS
CBWD2	150472	broad.mit.edu	37	2	114195465	114195465	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:114195465C>G	uc002tju.2	+	1	198	c.20C>G	c.(19-21)TCT>TGT	p.S7C	CBWD2_uc002tjt.2_Missense_Mutation_p.S7C|CBWD2_uc010yxw.1_Translation_Start_Site|CBWD2_uc002tjv.2_Translation_Start_Site|CBWD2_uc010fkv.2_RNA	NM_172003	NP_742000	Q8IUF1	CBWD2_HUMAN	COBW domain-containing protein 2	7							ATP binding|protein binding				0						GCTGTTGGATCTGCGGATGAG	0.632													6	22	---	---	---	---	PASS
DPP10	57628	broad.mit.edu	37	2	115200401	115200401	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:115200401T>A	uc002tla.1	+	1	503	c.46T>A	c.(46-48)TCA>ACA	p.S16T		NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	16	Mediates effects on KCND2.|Cytoplasmic (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						GTGTCAACCCTCAAAAACAAT	0.468													11	46	---	---	---	---	PASS
CCDC93	54520	broad.mit.edu	37	2	118715998	118715998	+	Silent	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:118715998G>C	uc002tlj.2	-	12	1074	c.948C>G	c.(946-948)CGC>CGG	p.R316R	CCDC93_uc010fld.1_Silent_p.R316R	NM_019044	NP_061917	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	316	Potential.									large_intestine(1)|ovary(1)	2						TGACTTTCCGGCGATGTAGCT	0.403													7	30	---	---	---	---	PASS
PCDP1	200373	broad.mit.edu	37	2	120383210	120383210	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:120383210G>T	uc002tmb.2	+	16	1696	c.604G>T	c.(604-606)GAC>TAC	p.D202Y	PCDP1_uc010yyq.1_Missense_Mutation_p.D332Y	NM_001029996	NP_001025167	Q4G0U5	PCDP1_HUMAN	primary ciliary dyskinesia protein 1	488						cilium	calmodulin binding				0	Colorectal(110;0.196)					TCGTGAAATGGACAAAGAGAG	0.413													5	38	---	---	---	---	PASS
MKI67IP	84365	broad.mit.edu	37	2	122485356	122485356	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:122485356C>G	uc002tnk.2	-	7	903	c.826G>C	c.(826-828)GAG>CAG	p.E276Q	uc002tnj.1_Intron	NM_032390	NP_115766	Q9BYG3	MK67I_HUMAN	MKI67 interacting nucleolar phosphoprotein	276					protein complex assembly|rRNA metabolic process|rRNA transcription	condensed nuclear chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|protein binding|RNA binding				0						GTTTGAGTCTCTTGTATTTCT	0.308													5	55	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125547543	125547543	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:125547543G>A	uc002tno.2	+	18	3178	c.2814G>A	c.(2812-2814)CAG>CAA	p.Q938Q	CNTNAP5_uc010flu.2_Silent_p.Q939Q	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	938	Laminin G-like 3.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		TGAATGGACAGAAAATGGACC	0.522													15	63	---	---	---	---	PASS
SAP130	79595	broad.mit.edu	37	2	128775348	128775348	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:128775348T>A	uc002tpp.2	-	3	464	c.332A>T	c.(331-333)CAT>CTT	p.H111L	SAP130_uc002tpo.2_5'Flank|SAP130_uc010fmd.2_Missense_Mutation_p.H111L|SAP130_uc002tpq.1_Missense_Mutation_p.H85L	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b	111					histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		TGCGACAGCATGGTGTGTCGA	0.567													18	41	---	---	---	---	PASS
HS6ST1	9394	broad.mit.edu	37	2	129026380	129026380	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:129026380C>A	uc002tpt.3	-	2	626	c.592G>T	c.(592-594)GTG>TTG	p.V198L		NM_004807	NP_004798	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	198	Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process, enzymatic modification	integral to plasma membrane	sulfotransferase activity			pancreas(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		CCCCTCTGCACATGCCGCCAC	0.637													4	23	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141110606	141110606	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:141110606G>A	uc002tvj.1	-	76	12538	c.11566C>T	c.(11566-11568)CAT>TAT	p.H3856Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3856	Extracellular (Potential).|EGF-like 9.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATACATTGATGGGAACATGTG	0.363										TSP Lung(27;0.18)			12	52	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141113992	141113992	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:141113992A>G	uc002tvj.1	-	75	12421	c.11449T>C	c.(11449-11451)TAT>CAT	p.Y3817H		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3817	Extracellular (Potential).|EGF-like 8.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGATTACAATATGCATCATCT	0.323										TSP Lung(27;0.18)			3	17	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141294240	141294240	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:141294240A>T	uc002tvj.1	-	46	8524	c.7552T>A	c.(7552-7554)TGT>AGT	p.C2518S		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2518	Extracellular (Potential).|LDL-receptor class A 11.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCATTTCCACATTCAAACTCC	0.383										TSP Lung(27;0.18)			8	32	---	---	---	---	PASS
ZEB2	9839	broad.mit.edu	37	2	145158874	145158874	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:145158874G>T	uc002tvu.2	-	7	1288	c.808C>A	c.(808-810)CAC>AAC	p.H270N	ZEB2_uc002tvv.2_Missense_Mutation_p.H264N|ZEB2_uc010zbm.1_Missense_Mutation_p.H241N|ZEB2_uc010fnp.2_Missense_Mutation_p.H178N|ZEB2_uc010fnq.1_Missense_Mutation_p.H299N	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	270						cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)		AGCATTTGGTGCTATAAAAGG	0.393													9	53	---	---	---	---	PASS
GPD2	2820	broad.mit.edu	37	2	157436286	157436286	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:157436286A>C	uc002tzf.3	+	16	2404	c.2044A>C	c.(2044-2046)AAT>CAT	p.N682H	GPD2_uc010zch.1_Missense_Mutation_p.N455H|GPD2_uc002tzd.3_Missense_Mutation_p.N682H|GPD2_uc002tze.1_RNA	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,	682	EF-hand 2.|Potential.				cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1						GGTTGAACTCAATGAATTTTT	0.303													9	20	---	---	---	---	PASS
DPP4	1803	broad.mit.edu	37	2	162929976	162929976	+	Silent	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:162929976C>A	uc002ubz.2	-	2	588	c.27G>T	c.(25-27)CTG>CTT	p.L9L	DPP4_uc010fpb.2_5'UTR|DPP4_uc002uca.1_RNA|DPP4_uc002ucb.1_RNA	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV	9	Helical; Signal-anchor for type II membrane protein; (Potential).				cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	CCAGCAGTCCCAGAAGAACCT	0.542													12	28	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166856244	166856244	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:166856244C>G	uc010zcz.1	-	22	4312	c.4294G>C	c.(4294-4296)GAT>CAT	p.D1432H	SCN1A_uc002udo.3_Missense_Mutation_p.D1312H|SCN1A_uc010fpk.2_Missense_Mutation_p.D1284H	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1443	III.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	TTTCTGGAATCAACTGCTGCA	0.313													4	54	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168105057	168105057	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:168105057G>A	uc002udx.2	+	8	7173	c.7155G>A	c.(7153-7155)CCG>CCA	p.P2385P	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.P2210P|XIRP2_uc010fpq.2_Silent_p.P2163P|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2210					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						CCTCTGCTCCGGAAAAGCACA	0.453													15	51	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170177289	170177289	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:170177289C>A	uc002ues.2	-	2	398	c.185G>T	c.(184-186)TGC>TTC	p.C62F	LRP2_uc010zdf.1_Missense_Mutation_p.C62F	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	62	LDL-receptor class A 1.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	TCACTTACCGCAGCCAATTTC	0.493													4	39	---	---	---	---	PASS
KLHL23	151230	broad.mit.edu	37	2	170592730	170592730	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:170592730G>C	uc002ufh.1	+	4	1544	c.1206G>C	c.(1204-1206)ATG>ATC	p.M402I	KLHL23_uc002ufi.1_Missense_Mutation_p.M402I	NM_144711	NP_653312	Q8NBE8	KLH23_HUMAN	kelch-like 23	402	Kelch 3.										0						TTGCAAACATGATTAAAGGTA	0.388													23	66	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179396364	179396364	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:179396364G>A	uc010zfg.1	-	307	97498	c.97274C>T	c.(97273-97275)ACG>ATG	p.T32425M	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.T26120M|TTN_uc010zfi.1_Missense_Mutation_p.T26053M|TTN_uc010zfj.1_Missense_Mutation_p.T25928M|TTN_uc002umq.2_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33352							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GACTCCACTCGTGTTGGTGTA	0.453													12	47	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179396750	179396750	+	Silent	SNP	C	T	T	rs144094650	by1000genomes	TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:179396750C>T	uc010zfg.1	-	307	97112	c.96888G>A	c.(96886-96888)CCG>CCA	p.P32296P	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.P25991P|TTN_uc010zfi.1_Silent_p.P25924P|TTN_uc010zfj.1_Silent_p.P25799P|TTN_uc002umq.2_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33223							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTCCTCAGCCGGTTGTGGAC	0.532													9	29	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179611100	179611100	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:179611100T>C	uc002unb.2	-	46	16251	c.16027A>G	c.(16027-16029)ATG>GTG	p.M5343V	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCACAATCATACTTTTATGG	0.328													5	20	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179640092	179640092	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:179640092G>T	uc010zfg.1	-	28	6723	c.6499C>A	c.(6499-6501)CTT>ATT	p.L2167I	TTN_uc010zfh.1_Missense_Mutation_p.L2121I|TTN_uc010zfi.1_Missense_Mutation_p.L2121I|TTN_uc010zfj.1_Missense_Mutation_p.L2121I|TTN_uc002unb.2_Missense_Mutation_p.L2167I|uc002unc.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2167							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTTGGACAAGTAAGAATGCG	0.408													9	48	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179664420	179664420	+	Silent	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:179664420T>A	uc002und.2	-	6	933	c.708A>T	c.(706-708)ACA>ACT	p.T236T	TTN_uc010zfg.1_Silent_p.T236T|TTN_uc010zfh.1_Silent_p.T236T|TTN_uc010zfi.1_Silent_p.T236T|TTN_uc010zfj.1_Silent_p.T236T|TTN_uc002unb.2_Silent_p.T236T			Q8WZ42	TITIN_HUMAN	Homo sapiens cDNA FLJ32040 fis, clone NTONG2000858, highly similar to H.sapiens mRNA for titin protein.	236							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCATCTCAACTGTTGCAATTG	0.493													9	30	---	---	---	---	PASS
NEU2	4759	broad.mit.edu	37	2	233899557	233899557	+	Silent	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:233899557C>G	uc010zmn.1	+	2	933	c.933C>G	c.(931-933)CTC>CTG	p.L311L		NM_005383	NP_005374	Q9Y3R4	NEUR2_HUMAN	neuraminidase 2	311							exo-alpha-sialidase activity				0		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)		GTGCCTACCTCAACCCGCGAC	0.697													3	32	---	---	---	---	PASS
OXNAD1	92106	broad.mit.edu	37	3	16327951	16327951	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:16327951C>T	uc003caw.2	+	5	743	c.286C>T	c.(286-288)CAG>TAG	p.Q96*	OXNAD1_uc010her.1_RNA|OXNAD1_uc003cax.2_Nonsense_Mutation_p.Q96*|OXNAD1_uc011awb.1_Nonsense_Mutation_p.Q114*	NM_138381	NP_612390	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	96	FAD-binding FR-type.						oxidoreductase activity			skin(1)	1						TAAAGCTGGCCAGTGGTAAGT	0.463													12	31	---	---	---	---	PASS
EOMES	8320	broad.mit.edu	37	3	27758626	27758626	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:27758626C>T	uc003cdx.2	-	6	1996	c.1996G>A	c.(1996-1998)GAA>AAA	p.E666K	EOMES_uc003cdy.3_Missense_Mutation_p.E685K|EOMES_uc010hfn.2_3'UTR|EOMES_uc011axc.1_Missense_Mutation_p.E390K	NM_005442	NP_005433	O95936	EOMES_HUMAN	eomesodermin	666	Required for transcription activation (By similarity).				CD8-positive, alpha-beta T cell differentiation involved in immune response|cell differentiation involved in embryonic placenta development|endoderm formation|mesoderm formation|mesodermal to mesenchymal transition involved in gastrulation|positive regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|breast(1)	4						CTATACTCTTCAGCATTAATG	0.393													5	101	---	---	---	---	PASS
HEMK1	51409	broad.mit.edu	37	3	50617290	50617290	+	Silent	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:50617290G>T	uc003dau.2	+	9	1082	c.786G>T	c.(784-786)GCG>GCT	p.A262A	HEMK1_uc003dav.2_Silent_p.A262A|HEMK1_uc003daw.2_Silent_p.A262A	NM_016173	NP_057257	Q9Y5R4	HEMK1_HUMAN	HemK methyltransferase family member 1	262					DNA methylation		DNA binding|N-methyltransferase activity|protein methyltransferase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000283)|KIRC - Kidney renal clear cell carcinoma(197;0.0179)|Kidney(197;0.0212)		AAGACCCCGCGGCCCTGGATG	0.572													8	18	---	---	---	---	PASS
IFT57	55081	broad.mit.edu	37	3	107885739	107885739	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:107885739C>A	uc003dwx.3	-	8	1191	c.943G>T	c.(943-945)GTT>TTT	p.V315F		NM_018010	NP_060480	Q9NWB7	IFT57_HUMAN	estrogen-related receptor beta like 1	315	Potential.				activation of caspase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cilium|microtubule basal body	DNA binding|protein binding			ovary(1)|skin(1)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			TATTCTTGAACCAAATTCTCA	0.373													13	31	---	---	---	---	PASS
ARHGAP31	57514	broad.mit.edu	37	3	119134765	119134765	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:119134765C>T	uc003ecj.3	+	12	4521	c.3989C>T	c.(3988-3990)TCT>TTT	p.S1330F		NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein	1330					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2						GAGCGACCATCTGGGGGTTCT	0.522													7	105	---	---	---	---	PASS
GTF2E1	2960	broad.mit.edu	37	3	120500143	120500143	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:120500143G>T	uc003edz.3	+	5	1260	c.1146G>T	c.(1144-1146)GAG>GAT	p.E382D		NM_005513	NP_005504	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1,	382	Asp/Glu-rich (acidic).				interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.159)		AGGATGAAGAGGAAGATGACG	0.537													5	108	---	---	---	---	PASS
POLQ	10721	broad.mit.edu	37	3	121208732	121208732	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:121208732C>A	uc003eee.3	-	16	3175	c.3046G>T	c.(3046-3048)GTT>TTT	p.V1016F	POLQ_uc003eed.2_Missense_Mutation_p.V188F	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	1016					DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		AAAGTCTGAACAACTTTCTTA	0.363								DNA_polymerases_(catalytic_subunits)					11	73	---	---	---	---	PASS
NEK11	79858	broad.mit.edu	37	3	130871272	130871272	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:130871272C>G	uc003eny.2	+	8	1014	c.688C>G	c.(688-690)CAT>GAT	p.H230D	NEK11_uc003enx.2_Missense_Mutation_p.H230D|NEK11_uc003eoa.2_Missense_Mutation_p.H230D|NEK11_uc003enz.2_Missense_Mutation_p.H48D|NEK11_uc010htn.2_RNA|NEK11_uc011blk.1_Missense_Mutation_p.H82D|NEK11_uc011bll.1_Intron|NEK11_uc011blm.1_Missense_Mutation_p.H230D|NEK11_uc010hto.1_Missense_Mutation_p.H82D	NM_024800	NP_079076	Q8NG66	NEK11_HUMAN	NIMA-related kinase 11 isoform 1	230	Protein kinase.				cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|stomach(1)|central_nervous_system(1)	6						CTGCATGAATCATGCATTCGC	0.343													18	80	---	---	---	---	PASS
ATR	545	broad.mit.edu	37	3	142178212	142178212	+	Silent	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:142178212T>A	uc003eux.3	-	43	7328	c.7206A>T	c.(7204-7206)ACA>ACT	p.T2402T	ATR_uc003euy.1_Silent_p.T288T	NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	2402	PI3K/PI4K.				cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						GTTCTTTTCCTGTCATATACA	0.383								Other_conserved_DNA_damage_response_genes					9	21	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164756916	164756916	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:164756916C>A	uc003fei.2	-	20	2313	c.2251G>T	c.(2251-2253)GAT>TAT	p.D751Y		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	751	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	CTCACAGTATCTGCTCCCTAA	0.294										HNSCC(35;0.089)			4	6	---	---	---	---	PASS
BCHE	590	broad.mit.edu	37	3	165548739	165548739	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:165548739G>T	uc003fem.3	-	2	243	c.83C>A	c.(82-84)ACT>AAT	p.T28N	BCHE_uc003fen.3_Intron	NM_000055	NP_000046	P06276	CHLE_HUMAN	butyrylcholinesterase precursor	28					choline metabolic process|cocaine metabolic process|synaptic transmission, cholinergic	endoplasmic reticulum lumen|extracellular space|membrane	acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|enzyme binding			ovary(3)|pancreas(1)	4					Ambenonium(DB01122)|Atropine(DB00572)|Bambuterol(DB01408)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinnarizine(DB00568)|Demecarium bromide(DB00944)|Dibucaine(DB00527)|Donepezil(DB00843)|Echothiophate Iodide(DB01057)|Edrophonium(DB01010)|Ethopropazine(DB00392)|Etomidate(DB00292)|Galantamine(DB00674)|Hexafluronium bromide(DB00941)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Mivacurium(DB01226)|Neostigmine(DB01400)|Pancuronium(DB01337)|Pralidoxime(DB00733)|Procainamide(DB01035)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Terbutaline(DB00871)|Trimethaphan(DB01116)	GTCATCTTCAGTATGTGACTT	0.378													5	25	---	---	---	---	PASS
NDUFB5	4711	broad.mit.edu	37	3	179334808	179334808	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:179334808C>T	uc003fkc.2	+	4	347	c.318C>T	c.(316-318)GTC>GTT	p.V106V	NDUFB5_uc003fkd.2_RNA|NDUFB5_uc003fke.2_Silent_p.V54V	NM_002492	NP_002483	O43674	NDUB5_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta	106					mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			skin(1)	1	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)		NADH(DB00157)	AAGGCTATGTCCCAGAACACT	0.328													17	22	---	---	---	---	PASS
HTR3C	170572	broad.mit.edu	37	3	183770895	183770895	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:183770895G>A	uc003fmk.2	+	1	61	c.27G>A	c.(25-27)CAG>CAA	p.Q9Q		NM_130770	NP_570126	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine receptor 3 subunit C	9						integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			CTGCAAGGCAGAGTGCCCTCC	0.557													4	72	---	---	---	---	PASS
HTR3C	170572	broad.mit.edu	37	3	183777395	183777395	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:183777395G>A	uc003fmk.2	+	7	926	c.892G>A	c.(892-894)GAC>AAC	p.D298N		NM_130770	NP_570126	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine receptor 3 subunit C	298	Helical; Name=2; (Potential).					integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			CATGATGAATGACTTGCTCCC	0.572													8	136	---	---	---	---	PASS
SENP5	205564	broad.mit.edu	37	3	196612846	196612846	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:196612846G>A	uc003fwz.3	+	2	1043	c.794G>A	c.(793-795)CGA>CAA	p.R265Q	SENP5_uc011bty.1_Missense_Mutation_p.R265Q	NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	265					cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		AAAGCCCAGCGAAGCTGGGTA	0.483													13	46	---	---	---	---	PASS
SENP5	205564	broad.mit.edu	37	3	196654687	196654687	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr3:196654687G>A	uc003fwz.3	+	8	2292	c.2043G>A	c.(2041-2043)CTG>CTA	p.L681L	SENP5_uc011bty.1_Silent_p.L635L	NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	681	Protease.				cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		AGTATTTGCTGACTGAAGCCA	0.403													9	39	---	---	---	---	PASS
TADA2B	93624	broad.mit.edu	37	4	7056395	7056395	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:7056395C>T	uc003gjw.3	+	2	1028	c.877C>T	c.(877-879)CGG>TGG	p.R293W	TADA2B_uc010idi.2_Missense_Mutation_p.R218W	NM_152293	NP_689506	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2 (ADA2 homolog,	293					regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|zinc ion binding				0						AGAACTGCAGCGGTACCGGCG	0.522													4	32	---	---	---	---	PASS
SRP72	6731	broad.mit.edu	37	4	57361544	57361544	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:57361544G>A	uc003hbv.2	+	17	1702	c.1662G>A	c.(1660-1662)AAG>AAA	p.K554K	SRP72_uc010ihe.2_Silent_p.K493K	NM_006947	NP_008878	O76094	SRP72_HUMAN	signal recognition particle 72kDa	554	Poly-Lys.				response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)					TGAAAAAGAAGAAAAAGAAAA	0.254													3	14	---	---	---	---	PASS
UGT2B15	7366	broad.mit.edu	37	4	69512834	69512834	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:69512834C>T	uc011cal.1	-	6	1619	c.1581G>A	c.(1579-1581)AAG>AAA	p.K527K		NM_001076	NP_001067	P54855	UDB15_HUMAN	UDP glycosyltransferase 2B15 precursor	527					steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0						AATCTCTTTTCTTCTTCTTTC	0.388													19	80	---	---	---	---	PASS
SMR3A	26952	broad.mit.edu	37	4	71232643	71232643	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:71232643C>G	uc003hfg.1	+	3	418	c.337C>G	c.(337-339)CCA>GCA	p.P113A	SMR3B_uc011cas.1_Intron	NM_012390	NP_036522	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3	113	Pro-rich.					extracellular region					0		all_hematologic(202;0.196)				AAGACCCTATCCACCTGGACC	0.532													12	52	---	---	---	---	PASS
GK2	2712	broad.mit.edu	37	4	80328533	80328533	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:80328533T>A	uc003hlu.2	-	1	840	c.822A>T	c.(820-822)CAA>CAT	p.Q274H		NM_033214	NP_149991	Q14410	GLPK2_HUMAN	glycerol kinase 2	274					glycerol-3-phosphate metabolic process	mitochondrial outer membrane	ATP binding|glycerol kinase activity			ovary(2)|skin(2)	4						TGTTTTTGGCTTGTCCCTCCT	0.458													15	70	---	---	---	---	PASS
C4orf37	285555	broad.mit.edu	37	4	99064295	99064295	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:99064295C>T	uc003htt.1	-	1	97	c.7G>A	c.(7-9)GAT>AAT	p.D3N		NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555	3											0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)		GGAGCCCGATCATACATAGTG	0.577											OREG0016268	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	14	---	---	---	---	PASS
LRIT3	345193	broad.mit.edu	37	4	110791573	110791573	+	Silent	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:110791573A>T	uc003hzx.3	+	3	1726	c.1533A>T	c.(1531-1533)CCA>CCT	p.P511P	LRIT3_uc003hzw.3_Silent_p.P373P	NM_198506	NP_940908	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and	511	Fibronectin type-III.					integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		GTGTCTGTCCAAAAGGAGTGC	0.498													8	42	---	---	---	---	PASS
EGF	1950	broad.mit.edu	37	4	110865119	110865119	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:110865119G>C	uc003hzy.3	+	4	1083	c.631G>C	c.(631-633)GAT>CAT	p.D211H	EGF_uc011cfu.1_Missense_Mutation_p.D211H|EGF_uc011cfv.1_Missense_Mutation_p.D211H	NM_001963	NP_001954	P01133	EGF_HUMAN	epidermal growth factor precursor	211	LDL-receptor class B 3.|Extracellular (Potential).				angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)	GGATGTGCTTGATAAGCGGCT	0.443													10	22	---	---	---	---	PASS
TMEM155	132332	broad.mit.edu	37	4	122682747	122682747	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:122682747G>T	uc003idx.1	-	5	717	c.158C>A	c.(157-159)GCA>GAA	p.A53E	TMEM155_uc003idy.1_Missense_Mutation_p.A53E	NM_152399	NP_689612	Q4W5P6	TM155_HUMAN	transmembrane protein 155 precursor	53						extracellular region					0						CTGGCACCTTGCCATTCCCAG	0.413													4	42	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126328188	126328188	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:126328188C>T	uc003ifj.3	+	3	5461	c.5461C>T	c.(5461-5463)CAG>TAG	p.Q1821*	FAT4_uc011cgp.1_Nonsense_Mutation_p.Q119*	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	1821	Cadherin 17.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						TGATGGTCTTCAGTCCTCGGA	0.478													7	83	---	---	---	---	PASS
SORBS2	8470	broad.mit.edu	37	4	186545038	186545038	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:186545038G>A	uc003iyl.2	-	13	2391	c.1533C>T	c.(1531-1533)TCC>TCT	p.S511S	SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Silent_p.S611S|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cku.1_Intron|SORBS2_uc011ckv.1_Silent_p.S415S|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Silent_p.S625S|SORBS2_uc003iyf.2_Intron|SORBS2_uc003iyo.1_Intron	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2	511						actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TTTCGAATTCGGAGATGCGTG	0.572													5	61	---	---	---	---	PASS
KLKB1	3818	broad.mit.edu	37	4	187171402	187171402	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr4:187171402C>T	uc003iyy.2	+	7	675	c.604C>T	c.(604-606)CAC>TAC	p.H202Y	KLKB1_uc011clc.1_5'UTR|KLKB1_uc011cld.1_Missense_Mutation_p.H164Y	NM_000892	NP_000883	P03952	KLKB1_HUMAN	plasma kallikrein B1 precursor	202	Apple 3.				blood coagulation, intrinsic pathway|Factor XII activation|fibrinolysis|plasminogen activation|positive regulation of fibrinolysis	cytoplasm|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(1)	1		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		CACAGGTTGCCACATGAACAT	0.438													15	61	---	---	---	---	PASS
CLPTM1L	81037	broad.mit.edu	37	5	1341845	1341845	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:1341845T>C	uc003jch.2	-	3	440	c.394A>G	c.(394-396)ACC>GCC	p.T132A	CLPTM1L_uc003jcg.2_5'UTR	NM_030782	NP_110409	Q96KA5	CLP1L_HUMAN	CLPTM1-like	132	Extracellular (Potential).				apoptosis	integral to membrane				breast(1)|central_nervous_system(1)	2	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		ACCATGTAGGTGGTCAGAGGA	0.562													12	66	---	---	---	---	PASS
MARCH6	10299	broad.mit.edu	37	5	10410379	10410379	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:10410379G>C	uc003jet.1	+	18	1865	c.1682G>C	c.(1681-1683)GGA>GCA	p.G561A	MARCH6_uc011cmu.1_Missense_Mutation_p.G513A|MARCH6_uc003jeu.1_Missense_Mutation_p.G259A|MARCH6_uc011cmv.1_Missense_Mutation_p.G456A	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6	561	Cytoplasmic (Potential).				protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						GTGACCGCCGGATACTTGCTG	0.527													3	35	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16694532	16694532	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:16694532C>G	uc003jft.3	-	27	4216	c.3748G>C	c.(3748-3750)GAA>CAA	p.E1250Q	MYO10_uc011cnc.1_Missense_Mutation_p.E129Q|MYO10_uc011cnd.1_Missense_Mutation_p.E607Q|MYO10_uc011cne.1_Missense_Mutation_p.E607Q|MYO10_uc010itx.2_Missense_Mutation_p.E873Q	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1250	PH 1.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						CTGTCGTTTTCAAAGTACATC	0.552													9	145	---	---	---	---	PASS
SPEF2	79925	broad.mit.edu	37	5	35644570	35644570	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:35644570G>A	uc003jjo.2	+	4	639	c.528G>A	c.(526-528)GAG>GAA	p.E176E	SPEF2_uc003jjn.1_Silent_p.E176E|SPEF2_uc003jjq.3_Silent_p.E176E	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	176					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity	p.E176G(1)		skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGCATTTTGAGAAACTTGAAA	0.313													6	19	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45645292	45645292	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:45645292C>T	uc003jok.2	-	2	869	c.844G>A	c.(844-846)GAA>AAA	p.E282K		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	282	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						CTTACCTCTTCCCATTGATGT	0.333													3	8	---	---	---	---	PASS
PCSK1	5122	broad.mit.edu	37	5	95728791	95728791	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:95728791C>T	uc003kls.1	-	14	2382	c.2176G>A	c.(2176-2178)GAT>AAT	p.D726N	PCSK1_uc010jbi.1_Missense_Mutation_p.D416N	NM_000439	NP_000430	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	726					cell-cell signaling|cellular nitrogen compound metabolic process|energy reserve metabolic process|hormone biosynthetic process|peptide biosynthetic process|peptide hormone processing|regulation of insulin secretion	extracellular space|stored secretory granule|transport vesicle	serine-type endopeptidase activity			ovary(2)	2		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TAAAAAACATCAACATAGTCA	0.403													28	78	---	---	---	---	PASS
CHD1	1105	broad.mit.edu	37	5	98228350	98228350	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:98228350G>T	uc003knf.2	-	14	2207	c.2059C>A	c.(2059-2061)CAC>AAC	p.H687N		NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	687					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	AGCTCCTTGTGAAGGCTTGCA	0.383													13	32	---	---	---	---	PASS
SRFBP1	153443	broad.mit.edu	37	5	121356289	121356289	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:121356289A>G	uc003kst.1	+	6	931	c.859A>G	c.(859-861)ATT>GTT	p.I287V		NM_152546	NP_689759	Q8NEF9	SRFB1_HUMAN	serum response factor binding protein 1	287					regulation of transcription, DNA-dependent|transcription, DNA-dependent	perinuclear region of cytoplasm					0		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		CGACTTCTTCATTGGGAAAGT	0.383													17	43	---	---	---	---	PASS
ADAMTS19	171019	broad.mit.edu	37	5	128862084	128862084	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:128862084C>A	uc003kvb.1	+	4	1003	c.1003C>A	c.(1003-1005)CCA>ACA	p.P335T	ADAMTS19_uc003kvc.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	335	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GGTTGCAGACCCAGCAATGGT	0.393													10	33	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140208830	140208830	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:140208830T>C	uc003lho.2	+	1	1181	c.1154T>C	c.(1153-1155)GTG>GCG	p.V385A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Missense_Mutation_p.V385A|PCDHA6_uc011dab.1_Missense_Mutation_p.V385A	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	385	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACGGGCAGGTGAACTGCTCG	0.547													31	97	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140209110	140209110	+	Silent	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:140209110T>C	uc003lho.2	+	1	1461	c.1434T>C	c.(1432-1434)TCT>TCC	p.S478S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Silent_p.S478S|PCDHA6_uc011dab.1_Silent_p.S478S	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	478	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCACGGTGTCTGCGCGAGACG	0.647													8	21	---	---	---	---	PASS
CAMK2A	815	broad.mit.edu	37	5	149631622	149631622	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:149631622G>T	uc003lru.2	-	8	736	c.521C>A	c.(520-522)GCA>GAA	p.A174E	CAMK2A_uc003lrt.2_Missense_Mutation_p.A174E|CAMK2A_uc010jhe.2_Missense_Mutation_p.A154E|CAMK2A_uc010jhf.1_Missense_Mutation_p.Q12K	NM_171825	NP_741960	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II	174	Protein kinase.				interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission	cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGGAGTCCCTGCAAACCCTGC	0.552													7	20	---	---	---	---	PASS
ATP10B	23120	broad.mit.edu	37	5	160059368	160059368	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:160059368C>T	uc003lym.1	-	13	2235	c.1388G>A	c.(1387-1389)CGA>CAA	p.R463Q	ATP10B_uc003lyn.2_Missense_Mutation_p.R21Q	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	463	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGTCTCCAGTCGCTTAGCTGC	0.527													17	40	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12163563	12163563	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:12163563C>T	uc003nac.2	+	9	7205	c.7026C>T	c.(7024-7026)CCC>CCT	p.P2342P	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	2342					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				AGCACAGCCCCCAGACAGCAG	0.512													6	144	---	---	---	---	PASS
HLA-F	3134	broad.mit.edu	37	6	29695871	29695871	+	Silent	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:29695871T>C	uc011dlx.1	+	8	1420	c.1296T>C	c.(1294-1296)TCT>TCC	p.S432S	HLA-F_uc011dly.1_Intron|LOC285830_uc003nnp.2_Intron|LOC285830_uc011dlz.1_Intron	NM_018950	NP_061823	P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	Error:Variant_position_missing_in_P30511_after_alignment					antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity				0						taccagcatcttgtggggaat	0.000													7	17	---	---	---	---	PASS
COL11A2	1302	broad.mit.edu	37	6	33154404	33154404	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:33154404C>A	uc003ocx.1	-	5	1026	c.798G>T	c.(796-798)CAG>CAT	p.Q266H	COL11A2_uc003ocy.1_Missense_Mutation_p.Q266H|COL11A2_uc003ocz.1_Missense_Mutation_p.Q266H|COL11A2_uc003oda.2_Missense_Mutation_p.Q266H	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	266	Nonhelical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5						GCTCCCTCACCTGGCTCTGGG	0.577													17	45	---	---	---	---	PASS
EYS	346007	broad.mit.edu	37	6	66205243	66205243	+	Nonsense_Mutation	SNP	C	A	A	rs148294551		TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:66205243C>A	uc011dxu.1	-	4	599	c.61G>T	c.(61-63)GGA>TGA	p.G21*	EYS_uc003peq.2_Nonsense_Mutation_p.G21*|EYS_uc003per.1_Nonsense_Mutation_p.G21*|EYS_uc010kaj.1_RNA	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	21					response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						CATGTTTTTCCATTTATGAAA	0.373													7	22	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70866115	70866115	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:70866115G>T	uc003pfc.1	+	32	2293	c.2176G>T	c.(2176-2178)GCC>TCC	p.A726S	COL19A1_uc010kam.1_Missense_Mutation_p.A622S	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	726	Triple-helical region 4 (COL4).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						TGATTCCATGGCCCGGAAGGT	0.493													16	26	---	---	---	---	PASS
FILIP1	27145	broad.mit.edu	37	6	76022993	76022993	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:76022993A>G	uc003pia.2	-	5	2928	c.2555T>C	c.(2554-2556)GTT>GCT	p.V852A	FILIP1_uc003phy.1_Missense_Mutation_p.V852A|FILIP1_uc003phz.2_Missense_Mutation_p.V753A|FILIP1_uc010kbe.2_Missense_Mutation_p.V855A|FILIP1_uc003pib.1_Missense_Mutation_p.V604A	NM_015687	NP_056502	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	852										skin(3)|ovary(1)	4						CCTGTCTAGAACAGAAGATCT	0.458													20	60	---	---	---	---	PASS
MRAP2	112609	broad.mit.edu	37	6	84772654	84772654	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:84772654T>C	uc003pkg.3	+	3	360	c.170T>C	c.(169-171)GTG>GCG	p.V57A	MRAP2_uc010kbo.2_Intron	NM_138409	NP_612418	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	57					positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding			skin(2)	2						GCAGTCTTCGTGATTTTTATG	0.403													5	32	---	---	---	---	PASS
FHL5	9457	broad.mit.edu	37	6	97058603	97058603	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:97058603C>T	uc003pos.1	+	6	1065	c.660C>T	c.(658-660)AAC>AAT	p.N220N	FHL5_uc003pot.1_Silent_p.N220N	NM_020482	NP_065228	Q5TD97	FHL5_HUMAN	activator of cAMP-responsive element modulator	220	LIM zinc-binding 3.					nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		TTTATGCCAACAAGTGTGTAG	0.413													13	46	---	---	---	---	PASS
HACE1	57531	broad.mit.edu	37	6	105224980	105224980	+	Missense_Mutation	SNP	T	G	G	rs145211482	byFrequency	TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:105224980T>G	uc003pqu.1	-	16	1961	c.1684A>C	c.(1684-1686)ATT>CTT	p.I562L	HACE1_uc010kcy.1_Missense_Mutation_p.I44L|HACE1_uc010kcz.1_Intron|HACE1_uc010kcx.1_Intron|HACE1_uc003pqt.1_Missense_Mutation_p.I215L	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3	562					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		CTCCTAAAAATAGAATCTAAA	0.328													8	22	---	---	---	---	PASS
RTN4IP1	84816	broad.mit.edu	37	6	107050751	107050751	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:107050751G>C	uc003prj.2	-	5	1144	c.667C>G	c.(667-669)CAG>GAG	p.Q223E	RTN4IP1_uc010kdd.2_Intron|RTN4IP1_uc003prk.2_Missense_Mutation_p.Q123E	NM_032730	NP_116119	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1 precursor	223						mitochondrion	oxidoreductase activity|zinc ion binding				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		GGTTTTACCTGTATAGCAAAA	0.328													13	44	---	---	---	---	PASS
FYN	2534	broad.mit.edu	37	6	112017519	112017519	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:112017519C>G	uc003pvj.2	-	9	1343	c.1003G>C	c.(1003-1005)GAG>CAG	p.E335Q	FYN_uc003pvi.2_Missense_Mutation_p.E280Q|FYN_uc003pvk.2_Missense_Mutation_p.E335Q|FYN_uc003pvh.2_Missense_Mutation_p.E332Q|FYN_uc010kdy.1_Intron	NM_002037	NP_002028	P06241	FYN_HUMAN	protein-tyrosine kinase fyn isoform a	335	Protein kinase.				axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	ATGGGCTCCTCAGACACCACT	0.517													4	81	---	---	---	---	PASS
ROS1	6098	broad.mit.edu	37	6	117700284	117700284	+	Silent	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:117700284C>A	uc003pxp.1	-	17	2734	c.2535G>T	c.(2533-2535)CTG>CTT	p.L845L	ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	845	Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CCAACCAATACAGGAGCCCAT	0.393			T	GOPC|ROS1	glioblastoma|NSCLC								4	29	---	---	---	---	PASS
SLC35F1	222553	broad.mit.edu	37	6	118635205	118635205	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:118635205T>A	uc003pxx.3	+	8	1218	c.1017T>A	c.(1015-1017)TAT>TAA	p.Y339*	SLC35F1_uc003pxy.1_Nonsense_Mutation_p.Y144*	NM_001029858	NP_001025029	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	339	Helical; (Potential).				transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)		CAGGACTTTATCTCCTGTCTT	0.478													13	72	---	---	---	---	PASS
TNFAIP3	7128	broad.mit.edu	37	6	138202416	138202416	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:138202416A>G	uc003qhr.2	+	9	2399	c.2333A>G	c.(2332-2334)TAC>TGC	p.Y778C	TNFAIP3_uc003qhs.2_Missense_Mutation_p.Y778C	NM_006290	NP_006281	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	778	A20-type 7.				anti-apoptosis|apoptosis|B-1 B cell homeostasis|negative regulation of B cell activation|negative regulation of bone resorption|negative regulation of CD40 signaling pathway|negative regulation of endothelial cell apoptosis|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of interleukin-2 production|negative regulation of interleukin-6 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of osteoclast proliferation|negative regulation of protein ubiquitination|negative regulation of smooth muscle cell proliferation|negative regulation of toll-like receptor 2 signaling pathway|negative regulation of toll-like receptor 3 signaling pathway|negative regulation of tumor necrosis factor production|negative regulation of type I interferon production|positive regulation of protein catabolic process|protein K48-linked ubiquitination|protein K63-linked deubiquitination|protein oligomerization|regulation of defense response to virus by host|regulation of germinal center formation|regulation of vascular wound healing|tolerance induction to lipopolysaccharide	centrosome|cytosol|nucleus	caspase inhibitor activity|DNA binding|protease binding|protein self-association|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-protein ligase activity|ubiquitin-specific protease activity|zinc ion binding	p.0?(22)		haematopoietic_and_lymphoid_tissue(133)|lung(3)|ovary(1)	137	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		TGCAACGGCTACTGCAACGAA	0.607			D|N|F		marginal zone B-cell lymphomas|Hodgkin's lymphoma|primary mediastinal B cell lymphoma								24	74	---	---	---	---	PASS
ESR1	2099	broad.mit.edu	37	6	152163866	152163866	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:152163866A>G	uc003qom.3	+	4	957	c.587A>G	c.(586-588)CAT>CGT	p.H196R	ESR1_uc010kin.2_Missense_Mutation_p.H196R|ESR1_uc010kio.2_Missense_Mutation_p.H196R|ESR1_uc010kip.2_Missense_Mutation_p.H196R|ESR1_uc003qon.3_Missense_Mutation_p.H196R|ESR1_uc003qoo.3_Missense_Mutation_p.H196R|ESR1_uc010kiq.2_Intron|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_RNA|ESR1_uc011eeu.1_RNA|ESR1_uc011eev.1_Missense_Mutation_p.H23R|ESR1_uc011eew.1_Missense_Mutation_p.I28V	NM_001122742	NP_001116214	P03372	ESR1_HUMAN	estrogen receptor alpha isoform 4	196	NR C4-type.|Nuclear receptor.|Mediates interaction with DNTTIP2.				positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)	TCAGGCTACCATTATGGAGTC	0.453													11	37	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152725365	152725365	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:152725365T>C	uc010kiw.2	-	46	7410	c.6808A>G	c.(6808-6810)ACA>GCA	p.T2270A	SYNE1_uc003qot.3_Missense_Mutation_p.T2277A|SYNE1_uc003qou.3_Missense_Mutation_p.T2270A|SYNE1_uc010kjb.1_Missense_Mutation_p.T2253A	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2270	Potential.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TCTGGCGGTGTTTCTAGATTT	0.333										HNSCC(10;0.0054)			10	52	---	---	---	---	PASS
OPRM1	4988	broad.mit.edu	37	6	154360761	154360761	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:154360761C>T	uc003qpr.2	+	1	319	c.82C>T	c.(82-84)CCC>TCC	p.P28S	OPRM1_uc011efb.1_Missense_Mutation_p.P76S|OPRM1_uc011efc.1_Intron|OPRM1_uc011efd.1_Intron|OPRM1_uc011efe.1_Missense_Mutation_p.P121S|OPRM1_uc003qpn.2_Missense_Mutation_p.P28S|OPRM1_uc003qpo.1_Missense_Mutation_p.P28S|OPRM1_uc011eff.1_Missense_Mutation_p.P28S|OPRM1_uc011efg.1_Missense_Mutation_p.P28S|OPRM1_uc011efh.1_Missense_Mutation_p.P28S|OPRM1_uc003qpq.1_Missense_Mutation_p.P28S|OPRM1_uc003qpt.1_Missense_Mutation_p.P28S|OPRM1_uc011efi.1_Missense_Mutation_p.P28S|OPRM1_uc003qpp.2_RNA|OPRM1_uc003qps.2_RNA	NM_000914	NP_000905	P35372	OPRM_HUMAN	opioid receptor, mu 1 isoform MOR-1	28	Extracellular (Potential).				behavior|negative regulation of cell proliferation|sensory perception	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	mu-opioid receptor activity|protein binding			ovary(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tramadol(DB00193)	AGCACCCAGCCCCGGTTCCTG	0.652													5	12	---	---	---	---	PASS
SNX9	51429	broad.mit.edu	37	6	158358489	158358489	+	Silent	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:158358489G>C	uc003qqv.1	+	15	1640	c.1467G>C	c.(1465-1467)CTG>CTC	p.L489L		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	489	BAR.				cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		TCCATTTCCTGATGGAATGTA	0.373													4	75	---	---	---	---	PASS
MRPL18	29074	broad.mit.edu	37	6	160212095	160212095	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr6:160212095T>C	uc003qsw.3	+	2	304	c.176T>C	c.(175-177)TTA>TCA	p.L59S	TCP1_uc003qsr.2_5'Flank|TCP1_uc003qss.2_5'Flank|TCP1_uc010kjz.2_5'Flank|TCP1_uc003qst.2_5'Flank|TCP1_uc010kka.1_5'Flank|MRPL18_uc010kkb.2_RNA	NM_014161	NP_054880	Q9H0U6	RM18_HUMAN	mitochondrial ribosomal protein L18 precursor	59					rRNA transport|translation	mitochondrial ribosome	5S rRNA binding|structural constituent of ribosome				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.79e-06)		CTGGAGCTTTTATCTGTAGCC	0.562													4	16	---	---	---	---	PASS
ELMO1	9844	broad.mit.edu	37	7	37136261	37136261	+	Silent	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:37136261G>T	uc003tfk.1	-	15	1570	c.1263C>A	c.(1261-1263)ACC>ACA	p.T421T	ELMO1_uc011kbc.1_Silent_p.T325T|ELMO1_uc010kxg.1_Silent_p.T421T	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	421	ELMO.				actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						ATAGCATCTTGGTCAGCTCTA	0.468													10	43	---	---	---	---	PASS
GUSB	2990	broad.mit.edu	37	7	65429349	65429349	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:65429349C>A	uc003tun.2	-	11	1826	c.1750G>T	c.(1750-1752)GAG>TAG	p.E584*	GUSB_uc011kdt.1_Nonsense_Mutation_p.E438*	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor	584					glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0						CAAATGAGCTCTCCAACCACG	0.453													27	104	---	---	---	---	PASS
RABGEF1	27342	broad.mit.edu	37	7	66270167	66270167	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:66270167G>A	uc011kee.1	+	8	1067	c.903G>A	c.(901-903)AAG>AAA	p.K301K	RABGEF1_uc003tvf.2_Silent_p.K160K|RABGEF1_uc003tvg.2_Silent_p.K95K|RABGEF1_uc010lag.2_Silent_p.K287K|RABGEF1_uc003tvh.2_Silent_p.K287K|RABGEF1_uc003tvi.2_Silent_p.K121K	NM_014504	NP_055319	Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	504	VPS9.				endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1						CTCGAGACAAGCTGGCCTGCA	0.463													15	34	---	---	---	---	PASS
GNAI1	2770	broad.mit.edu	37	7	79846672	79846672	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:79846672C>G	uc003uhb.1	+	8	1265	c.928C>G	c.(928-930)CTC>GTC	p.L310V	GNAI1_uc011kgt.1_Missense_Mutation_p.L258V	NM_002069	NP_002060	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein),	310					cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						GTTTGAAGACCTCAATAAAAG	0.343													7	26	---	---	---	---	PASS
ZNF804B	219578	broad.mit.edu	37	7	88963668	88963668	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:88963668C>A	uc011khi.1	+	4	1910	c.1372C>A	c.(1372-1374)CCT>ACT	p.P458T		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	458						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TCTTCAATGGCCTACGGAACT	0.418										HNSCC(36;0.09)			14	57	---	---	---	---	PASS
PIK3CG	5294	broad.mit.edu	37	7	106508577	106508577	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:106508577C>A	uc003vdv.3	+	2	656	c.571C>A	c.(571-573)CGC>AGC	p.R191S	PIK3CG_uc003vdu.2_Missense_Mutation_p.R191S|PIK3CG_uc003vdw.2_Missense_Mutation_p.R191S	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	191					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						GGTGGCCAGCCGCGACCCCAA	0.612													14	24	---	---	---	---	PASS
LAMB1	3912	broad.mit.edu	37	7	107572753	107572753	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:107572753C>T	uc003vew.2	-	28	4593	c.4258G>A	c.(4258-4260)GAA>AAA	p.E1420K	LAMB1_uc003vev.2_Missense_Mutation_p.E1444K|LAMB1_uc003veu.2_5'Flank	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	1420	Domain alpha.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CTCTCTCCTTCGTCAGTTCTG	0.572													9	54	---	---	---	---	PASS
LAMB4	22798	broad.mit.edu	37	7	107743501	107743501	+	Missense_Mutation	SNP	A	T	T	rs140607116	by1000genomes	TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:107743501A>T	uc010ljo.1	-	10	1252	c.1168T>A	c.(1168-1170)TAC>AAC	p.Y390N	LAMB4_uc003vey.2_Missense_Mutation_p.Y390N	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	390	Laminin EGF-like 2.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						ATGCACGCGTAGGGATCTGAG	0.587													7	27	---	---	---	---	PASS
LAMB4	22798	broad.mit.edu	37	7	107743502	107743502	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:107743502G>A	uc010ljo.1	-	10	1251	c.1167C>T	c.(1165-1167)CCC>CCT	p.P389P	LAMB4_uc003vey.2_Silent_p.P389P	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	389	Laminin EGF-like 2.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						TGCACGCGTAGGGATCTGAGA	0.592													7	27	---	---	---	---	PASS
C7orf60	154743	broad.mit.edu	37	7	112472715	112472715	+	Silent	SNP	T	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:112472715T>G	uc003vgo.1	-	4	616	c.489A>C	c.(487-489)TCA>TCC	p.S163S	C7orf60_uc011kms.1_Silent_p.S189S	NM_152556	NP_689769	Q1RMZ1	CG060_HUMAN	hypothetical protein LOC154743	163										ovary(2)|skin(1)	3						TGATTTTTCCTGAGGCTTGTA	0.294													16	44	---	---	---	---	PASS
ZNF777	27153	broad.mit.edu	37	7	149129570	149129570	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:149129570A>T	uc003wfv.2	-	6	1956	c.1793T>A	c.(1792-1794)GTG>GAG	p.V598E		NM_015694	NP_056509	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	598					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			GCCTCCGCGCACGCGGTGGAT	0.672													10	35	---	---	---	---	PASS
GIMAP7	168537	broad.mit.edu	37	7	150217426	150217426	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:150217426T>A	uc003whk.2	+	2	494	c.364T>A	c.(364-366)TCA>ACA	p.S122T		NM_153236	NP_694968	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	122							GTP binding			pancreas(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTTTGGGAAGTCAGCCATGAA	0.527													5	43	---	---	---	---	PASS
GIMAP4	55303	broad.mit.edu	37	7	150269977	150269977	+	Silent	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr7:150269977A>G	uc003whl.2	+	3	901	c.819A>G	c.(817-819)GAA>GAG	p.E273E	GIMAP4_uc011kuu.1_Silent_p.E134E|GIMAP4_uc011kuv.1_Silent_p.E287E	NM_018326	NP_060796	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	273	Potential.						GTP binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGGAGCAGGAAAAGAGAAAGA	0.468													8	44	---	---	---	---	PASS
CDCA2	157313	broad.mit.edu	37	8	25317909	25317909	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:25317909C>G	uc003xep.1	+	3	550	c.71C>G	c.(70-72)TCT>TGT	p.S24C	PPP2R2A_uc003xek.2_Intron|KCTD9_uc003xeo.2_5'Flank|CDCA2_uc011lae.1_Missense_Mutation_p.S24C|CDCA2_uc003xeq.1_Missense_Mutation_p.S9C	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	24					cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		GGAAATGCCTCTTTCATTTTG	0.428													28	116	---	---	---	---	PASS
ADAM18	8749	broad.mit.edu	37	8	39466640	39466640	+	Splice_Site	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:39466640G>T	uc003xni.2	+	4	267	c.267_splice	c.e4+1	p.M89_splice	ADAM18_uc003xnh.2_Splice_Site_p.M89_splice|ADAM18_uc010lww.2_Splice_Site|ADAM18_uc010lwx.2_Splice_Site_p.M89_splice	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18						cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			ATATTTTATGGTAAAGTAAGA	0.269													4	7	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55542146	55542146	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:55542146C>T	uc003xsd.1	+	4	5852	c.5704C>T	c.(5704-5706)CAG>TAG	p.Q1902*	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1902					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TGGTACACTTCAGGAAGCTGA	0.398													6	52	---	---	---	---	PASS
FAM110B	90362	broad.mit.edu	37	8	59058961	59058961	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:59058961A>T	uc003xtj.1	+	5	1052	c.172A>T	c.(172-174)AAG>TAG	p.K58*		NM_147189	NP_671722	Q8TC76	F110B_HUMAN	hypothetical protein LOC90362	58						microtubule organizing center|mitochondrion|nucleus				large_intestine(1)	1		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)				GGAGGCCGACAAGGCCAAGTA	0.677													8	15	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72951230	72951230	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:72951230T>C	uc003xza.2	-	19	2340	c.2165A>G	c.(2164-2166)AAT>AGT	p.N722S	uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	722	Helical; Name=1; (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	AGATCCTAAATTCATCATATG	0.348													9	45	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72963055	72963055	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:72963055A>T	uc003xza.2	-	15	2038	c.1863T>A	c.(1861-1863)TGT>TGA	p.C621*	uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	621	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	CTGTAATTGGACATTTATTGC	0.328													5	32	---	---	---	---	PASS
GDAP1	54332	broad.mit.edu	37	8	75275277	75275277	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:75275277A>G	uc003yah.2	+	5	762	c.683A>G	c.(682-684)GAA>GGA	p.E228G	GDAP1_uc011lfj.1_Missense_Mutation_p.E113G|GDAP1_uc003yai.2_Missense_Mutation_p.E160G	NM_018972	NP_061845	Q8TB36	GDAP1_HUMAN	ganglioside-induced differentiation-associated	228	GST C-terminal.					cytoplasm					0	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			AGAAGAAATGAAGAAACCCCA	0.348													15	63	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77761266	77761266	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:77761266G>T	uc003yav.2	+	7	3799	c.3412G>T	c.(3412-3414)GTG>TTG	p.V1138L	ZFHX4_uc003yau.1_Missense_Mutation_p.V1183L|ZFHX4_uc003yaw.1_Missense_Mutation_p.V1138L	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1138						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAAAGTTAGTGTGGCAGGGGG	0.388										HNSCC(33;0.089)			4	10	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77765710	77765710	+	Silent	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:77765710C>A	uc003yav.2	+	10	6805	c.6418C>A	c.(6418-6420)CGA>AGA	p.R2140R	ZFHX4_uc003yau.1_Silent_p.R2185R|ZFHX4_uc003yaw.1_Silent_p.R2140R	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2140	Homeobox 1.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TTTTAAGGAACGACAGAGAAA	0.378										HNSCC(33;0.089)			8	107	---	---	---	---	PASS
CNGB3	54714	broad.mit.edu	37	8	87679237	87679237	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:87679237C>T	uc003ydx.2	-	6	814	c.768G>A	c.(766-768)GCG>GCA	p.A256A	CNGB3_uc010maj.2_Silent_p.A118A	NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	256	Helical; Name=H2; (Potential).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						ATATGATGTCCGCAATAAGCC	0.438													7	42	---	---	---	---	PASS
TM7SF4	81501	broad.mit.edu	37	8	105361034	105361034	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:105361034T>C	uc003ylx.1	+	2	303	c.254T>C	c.(253-255)GTC>GCC	p.V85A		NM_030788	NP_110415	Q9H295	TM7S4_HUMAN	dendritic cell-specific transmembrane protein	85					osteoclast differentiation	cell surface|integral to membrane|plasma membrane				pancreas(2)|large_intestine(1)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			ATTCTTCTTGTCTTTCTCTCT	0.473													12	28	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113246625	113246625	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:113246625A>G	uc003ynu.2	-	68	10868	c.10709T>C	c.(10708-10710)ATG>ACG	p.M3570T	CSMD3_uc003yns.2_Missense_Mutation_p.M2772T|CSMD3_uc003ynt.2_Missense_Mutation_p.M3530T|CSMD3_uc011lhx.1_Missense_Mutation_p.M3401T	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3570	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TTCTTCCTTCATTTTCTTCAC	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			16	53	---	---	---	---	PASS
ADCY8	114	broad.mit.edu	37	8	131812807	131812807	+	Silent	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:131812807A>T	uc003ytd.3	-	15	3181	c.2925T>A	c.(2923-2925)TCT>TCA	p.S975S	ADCY8_uc010mds.2_Silent_p.S844S	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	975	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CATAGGATTGAGAATACAGCT	0.502										HNSCC(32;0.087)			12	48	---	---	---	---	PASS
TG	7038	broad.mit.edu	37	8	134042191	134042191	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:134042191G>C	uc003ytw.2	+	41	7203	c.7162G>C	c.(7162-7164)GGG>CGG	p.G2388R	TG_uc010mdw.2_Missense_Mutation_p.G1147R|TG_uc011ljb.1_Missense_Mutation_p.G757R|TG_uc011ljc.1_Missense_Mutation_p.G521R	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	2388					hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AGACCGTGGCGGGGCTGATGT	0.642													7	9	---	---	---	---	PASS
CYP11B2	1585	broad.mit.edu	37	8	143996220	143996220	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:143996220T>G	uc003yxk.1	-	4	703	c.700A>C	c.(700-702)ACC>CCC	p.T234P		NM_000498	NP_000489	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B,	234					aldosterone biosynthetic process|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|potassium ion homeostasis|regulation of blood volume by renal aldosterone|sodium ion homeostasis|xenobiotic metabolic process		corticosterone 18-monooxygenase activity|electron carrier activity|steroid 11-beta-monooxygenase activity				0	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Candesartan(DB00796)|Metyrapone(DB01011)	AGCTGGACGGTGGATTTGAAC	0.582									Familial_Hyperaldosteronism_type_I				10	10	---	---	---	---	PASS
OPLAH	26873	broad.mit.edu	37	8	145109735	145109735	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:145109735C>G	uc003zar.3	-	18	2573	c.2491G>C	c.(2491-2493)GAC>CAC	p.D831H	OPLAH_uc003zas.1_Missense_Mutation_p.D80H	NM_017570	NP_060040	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	831							5-oxoprolinase (ATP-hydrolyzing) activity|ATP binding				0	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		L-Glutamic Acid(DB00142)	ACAGTCAGGTCTGGCAGGTGG	0.652													3	12	---	---	---	---	PASS
ZNF251	90987	broad.mit.edu	37	8	145947489	145947489	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr8:145947489C>T	uc003zdv.3	-	5	1812	c.1556G>A	c.(1555-1557)AGA>AAA	p.R519K		NM_138367	NP_612376	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	519					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		ACCATGTTTTCTGCACTTACG	0.527													5	93	---	---	---	---	PASS
JAK2	3717	broad.mit.edu	37	9	5066761	5066761	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr9:5066761A>G	uc010mhm.2	+	9	1411	c.1298A>G	c.(1297-1299)AAT>AGT	p.N433S	JAK2_uc003ziw.2_Missense_Mutation_p.N433S	NM_004972	NP_004963	O60674	JAK2_HUMAN	Janus kinase 2	433	SH2; atypical.				actin filament polymerization|activation of caspase activity by protein phosphorylation|activation of JAK2 kinase activity|blood coagulation|cellular component movement|erythrocyte differentiation|interferon-gamma-mediated signaling pathway|interleukin-12-mediated signaling pathway|JAK-STAT cascade involved in growth hormone signaling pathway|mammary gland epithelium development|mesoderm development|negative regulation of cell proliferation|negative regulation of DNA binding|positive regulation of apoptosis|positive regulation of cell-substrate adhesion|positive regulation of growth hormone receptor signaling pathway|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|protein autophosphorylation|regulation of inflammatory response|regulation of interferon-gamma-mediated signaling pathway|response to antibiotic|response to lipopolysaccharide|STAT protein import into nucleus|tumor necrosis factor-mediated signaling pathway|tyrosine phosphorylation of STAT protein	caveola|cytoskeleton|cytosol|endomembrane system|nucleus	ATP binding|growth hormone receptor binding|heme binding|histone binding|histone kinase activity (H3-Y41 specific)|interleukin-12 receptor binding|non-membrane spanning protein tyrosine kinase activity|protein kinase binding|SH2 domain binding		PCM1/JAK2(30)|PAX5/JAK2(18)|ETV6/JAK2(11)|BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)	haematopoietic_and_lymphoid_tissue(28629)|lung(5)|breast(5)|ovary(1)|liver(1)	28641	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)		AAGGACTTTAATAAATATTTT	0.328		1	T|Mis|O	ETV6|PCM1|BCR	ALL|AML|MPD| CML				Polycythemia_Vera_Familial				5	9	---	---	---	---	PASS
NFIB	4781	broad.mit.edu	37	9	14307382	14307382	+	Silent	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr9:14307382T>A	uc003zle.2	-	2	603	c.168A>T	c.(166-168)GCA>GCT	p.A56A	NFIB_uc003zlf.2_Silent_p.A56A|NFIB_uc011lmo.1_Silent_p.A56A	NM_005596	NP_005587	O00712	NFIB_HUMAN	nuclear factor I/B	56	CTF/NF-I.				anterior commissure morphogenesis|chondrocyte differentiation|Clara cell differentiation|commissural neuron axon guidance|DNA replication|glial cell differentiation|lung ciliated cell differentiation|negative regulation of DNA binding|negative regulation of epithelial cell proliferation involved in lung morphogenesis|negative regulation of mesenchymal cell proliferation involved in lung development|positive regulation of transcription from RNA polymerase II promoter|principal sensory nucleus of trigeminal nerve development|Type I pneumocyte differentiation|Type II pneumocyte differentiation	cerebellar mossy fiber|nucleolus|nucleus	RNA polymerase II transcription corepressor activity|sequence-specific DNA binding RNA polymerase II transcription factor activity				0				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)		CATCTTTGACTGCTCTTTCTT	0.453			T	MYB|HGMA2	adenoid cystic carcinoma|lipoma								10	28	---	---	---	---	PASS
TEK	7010	broad.mit.edu	37	9	27206656	27206656	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr9:27206656C>A	uc003zqi.3	+	15	2883	c.2441C>A	c.(2440-2442)ACA>AAA	p.T814K	TEK_uc011lno.1_Missense_Mutation_p.T771K|TEK_uc011lnp.1_Missense_Mutation_p.T666K|TEK_uc003zqj.1_Missense_Mutation_p.T748K	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	814	Cytoplasmic (Potential).				angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)		CCAGATCCTACAATTTATCCA	0.438													15	11	---	---	---	---	PASS
PAX5	5079	broad.mit.edu	37	9	36846882	36846882	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr9:36846882A>T	uc003zzo.1	-	9	1505	c.1057T>A	c.(1057-1059)TCG>ACG	p.S353T	PAX5_uc011lpt.1_Missense_Mutation_p.S149T|PAX5_uc011lpu.1_RNA|PAX5_uc011lpv.1_Intron|PAX5_uc011lpw.1_Intron|PAX5_uc011lpx.1_Missense_Mutation_p.S253T|PAX5_uc011lpy.1_Intron|PAX5_uc010mls.1_Intron|PAX5_uc011lpz.1_Missense_Mutation_p.S310T|PAX5_uc011lqa.1_Missense_Mutation_p.S245T|PAX5_uc010mlq.1_RNA|PAX5_uc011lqb.1_RNA|PAX5_uc010mlo.1_Missense_Mutation_p.S319T|PAX5_uc010mlp.1_Intron|PAX5_uc011lqc.1_Intron|PAX5_uc010mlr.1_Silent_p.P275P	NM_016734	NP_057953	Q02548	PAX5_HUMAN	paired box 5	353					cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter	nucleus	DNA binding	p.?(11)	PAX5/JAK2(18)	haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2)	147		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		TCGTTGTACGAGGAATACTGA	0.592			T|Mis|D|F|S	IGH@|ETV6|PML|FOXP1|ZNF521|ELN	NHL|ALL|B-ALL								10	19	---	---	---	---	PASS
FOXB2	442425	broad.mit.edu	37	9	79635629	79635629	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr9:79635629C>T	uc004ako.1	+	1	1059	c.1059C>T	c.(1057-1059)CAC>CAT	p.H353H		NM_001013735	NP_001013757	Q5VYV0	FOXB2_HUMAN	forkhead box B2	353					brain development|embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0						CCCTGTGCCACTCGGCAAGCC	0.602													3	3	---	---	---	---	PASS
NCBP1	4686	broad.mit.edu	37	9	100433431	100433431	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr9:100433431G>C	uc004axq.2	+	23	2782	c.2323G>C	c.(2323-2325)GAC>CAC	p.D775H		NM_002486	NP_002477	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa	775					gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA cleavage|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of mRNA 3'-end processing|positive regulation of viral transcription|regulation of translational initiation|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm|ribonucleoprotein complex	protein binding|RNA cap binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.158)				TGCTGAATTAGACCCTCATAT	0.438													13	50	---	---	---	---	PASS
TMEFF1	8577	broad.mit.edu	37	9	103261052	103261052	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr9:103261052A>G	uc004baz.1	+	2	312	c.202A>G	c.(202-204)AAT>GAT	p.N68D	TMEFF1_uc004bay.1_Missense_Mutation_p.N142D	NM_003692	NP_003683	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two	68	Extracellular (Potential).				multicellular organismal development	integral to membrane|plasma membrane					0		Acute lymphoblastic leukemia(62;0.0452)				TGCAGAATTAAATGTGAGGGA	0.269													3	41	---	---	---	---	PASS
OR13C9	286362	broad.mit.edu	37	9	107380010	107380010	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr9:107380010T>C	uc011lvr.1	-	1	476	c.476A>G	c.(475-477)CAA>CGA	p.Q159R		NM_001001956	NP_001001956	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C,	159	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						AAATGTAGTTTGTACTGCAGA	0.438													22	47	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	16893354	16893354	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr10:16893354C>A	uc001ioo.2	-	60	9595	c.9543G>T	c.(9541-9543)AAG>AAT	p.K3181N	CUBN_uc009xjq.1_RNA	NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	3181	CUB 24.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGTTTAAATTCTTGTCATACA	0.408													21	22	---	---	---	---	PASS
ST8SIA6	338596	broad.mit.edu	37	10	17363099	17363099	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr10:17363099C>T	uc001ipd.2	-	8	975	c.975G>A	c.(973-975)TTG>TTA	p.L325L	ST8SIA6_uc010qce.1_RNA	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide	325	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						TTGTGATCATCAAGCCGGTGG	0.443													47	71	---	---	---	---	PASS
MTPAP	55149	broad.mit.edu	37	10	30602551	30602551	+	Missense_Mutation	SNP	C	G	G	rs148562969	by1000genomes	TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr10:30602551C>G	uc001iva.3	-	9	1799	c.1736G>C	c.(1735-1737)AGT>ACT	p.S579T	MTPAP_uc001ivb.3_Missense_Mutation_p.S709T	NM_018109	NP_060579	Q9NVV4	PAPD1_HUMAN	PAP associated domain containing 1 precursor	579					cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1						TGTCTGAGTACTAATTGTTCT	0.358													35	61	---	---	---	---	PASS
ZNF33A	7581	broad.mit.edu	37	10	38344864	38344864	+	Silent	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr10:38344864A>T	uc001izh.2	+	5	1987	c.1809A>T	c.(1807-1809)ACA>ACT	p.T603T	ZNF33A_uc001izg.2_Silent_p.T604T|ZNF33A_uc010qev.1_Silent_p.T610T|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	603						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3						GAACACATACAGGGGAGAAAC	0.373													14	25	---	---	---	---	PASS
SLC18A3	6572	broad.mit.edu	37	10	50819812	50819812	+	Silent	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr10:50819812C>G	uc001jhw.2	+	1	1466	c.1026C>G	c.(1024-1026)GTC>GTG	p.V342V	CHAT_uc001jhv.1_Intron|CHAT_uc001jhx.1_5'Flank|CHAT_uc001jhy.1_5'Flank|CHAT_uc001jia.2_5'Flank|CHAT_uc001jhz.2_5'Flank|CHAT_uc010qgs.1_5'Flank	NM_003055	NP_003046	Q16572	VACHT_HUMAN	vesicular acetylcholine transporter	342	Helical; (Potential).				neurotransmitter secretion	clathrin sculpted acetylcholine transport vesicle membrane|integral to plasma membrane|membrane fraction	acetylcholine transmembrane transporter activity			ovary(2)	2						TGCTGGGCGTCTACCTCACCG	0.672													16	30	---	---	---	---	PASS
SORCS3	22986	broad.mit.edu	37	10	106983002	106983002	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr10:106983002A>G	uc001kyi.1	+	20	3090	c.2863A>G	c.(2863-2865)ACA>GCA	p.T955A	SORCS3_uc010qqz.1_RNA	NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	955	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CGGCAATAGCACAAAGGTTTG	0.453													41	77	---	---	---	---	PASS
HSPA12A	259217	broad.mit.edu	37	10	118451864	118451864	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr10:118451864G>T	uc001lct.2	-	6	766	c.661C>A	c.(661-663)CAG>AAG	p.Q221K	HSPA12A_uc001lcu.2_Missense_Mutation_p.Q138K	NM_025015	NP_079291	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	221							ATP binding			ovary(1)	1				all cancers(201;0.0158)		ACCCTCACCTGGTAGGCAGCT	0.597													5	122	---	---	---	---	PASS
PRLHR	2834	broad.mit.edu	37	10	120354611	120354611	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr10:120354611G>T	uc001ldp.1	-	2	285	c.146C>A	c.(145-147)CCC>CAC	p.P49H		NM_004248	NP_004239	P49683	PRLHR_HUMAN	G protein-coupled receptor 10	49	Extracellular (Potential).				female pregnancy	integral to plasma membrane	neuropeptide Y receptor activity				0		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)		GCTCTGGAAGGGCGTGACGGC	0.697													4	15	---	---	---	---	PASS
C10orf90	118611	broad.mit.edu	37	10	128153547	128153547	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr10:128153547T>C	uc001ljq.2	-	4	1373	c.1252A>G	c.(1252-1254)AAA>GAA	p.K418E	C10orf90_uc001ljp.2_Intron|C10orf90_uc010qum.1_Missense_Mutation_p.K515E|C10orf90_uc009yao.2_3'UTR|C10orf90_uc001ljo.2_5'Flank	NM_001004298	NP_001004298	Q96M02	CJ090_HUMAN	hypothetical protein LOC118611	418										ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		GAAAATACTTTTGTGTGTACT	0.423													15	21	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093094	1093094	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:1093094T>G	uc001lsx.1	+	31	12026	c.11999T>G	c.(11998-12000)GTG>GGG	p.V4000G		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4000						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accactacggtgaccccaacc	0.000													3	8	---	---	---	---	PASS
OR52A4	390053	broad.mit.edu	37	11	5142713	5142713	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:5142713C>T	uc001lzz.1	-	1	96	c.96G>A	c.(94-96)GGG>GGA	p.G32G	OR52A4_uc001maa.2_RNA	NM_001005222	NP_001005222			olfactory receptor, family 52, subfamily A,											ovary(2)	2		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.7e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		AGAATGGAATCCCAATCCAGC	0.423													6	145	---	---	---	---	PASS
ZNF214	7761	broad.mit.edu	37	11	7021527	7021527	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:7021527C>A	uc001mfa.2	-	3	1690	c.1387G>T	c.(1387-1389)GTC>TTC	p.V463F	ZNF214_uc010ray.1_Missense_Mutation_p.V463F|ZNF214_uc009yfh.1_Missense_Mutation_p.V463F	NM_013249	NP_037381	Q9UL59	ZN214_HUMAN	zinc finger protein 214	463	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		CCTGTATGGACTCTCTGATGA	0.423													12	43	---	---	---	---	PASS
RIC3	79608	broad.mit.edu	37	11	8132433	8132433	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:8132433G>A	uc001mgd.2	-	6	976	c.922C>T	c.(922-924)CAT>TAT	p.H308Y	RIC3_uc001mgb.2_Missense_Mutation_p.H146Y|RIC3_uc001mgc.2_Missense_Mutation_p.H307Y|RIC3_uc001mge.2_Missense_Mutation_p.H126Y|RIC3_uc010rbl.1_Missense_Mutation_p.H258Y|RIC3_uc010rbm.1_Missense_Mutation_p.H336Y|RIC3_uc009yfm.2_Missense_Mutation_p.H227Y|RIC3_uc009yfn.2_Missense_Mutation_p.H111Y	NM_024557	NP_078833	Q7Z5B4	RIC3_HUMAN	resistance to inhibitors of cholinesterase 3	308	Cytoplasmic (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				large_intestine(1)|ovary(1)|pancreas(1)	3				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		TCGTCTTCATGAAAACAGCAG	0.493													5	68	---	---	---	---	PASS
INSC	387755	broad.mit.edu	37	11	15243165	15243165	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:15243165G>A	uc001mly.2	+	8	1149	c.1103G>A	c.(1102-1104)AGC>AAC	p.S368N	INSC_uc001mlz.2_Missense_Mutation_p.S321N|INSC_uc001mma.2_Missense_Mutation_p.S321N|INSC_uc010rcs.1_Missense_Mutation_p.S356N|INSC_uc001mmb.2_Missense_Mutation_p.S321N|INSC_uc001mmc.2_Missense_Mutation_p.S279N	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a	368					cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5						TTCCTGGAGAGCATGGAGGAG	0.632													6	21	---	---	---	---	PASS
OR4X2	119764	broad.mit.edu	37	11	48266676	48266676	+	Silent	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:48266676G>T	uc001ngs.1	+	1	21	c.21G>T	c.(19-21)CTG>CTT	p.L7L		NM_001004727	NP_001004727	Q8NGF9	OR4X2_HUMAN	olfactory receptor, family 4, subfamily X,	7	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TCATTTTTCTGGTACTTTCTC	0.418													5	68	---	---	---	---	PASS
APLNR	187	broad.mit.edu	37	11	57004291	57004291	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:57004291G>A	uc001njo.2	-	1	637	c.188C>T	c.(187-189)TCA>TTA	p.S63L	APLNR_uc001njn.3_RNA	NM_005161	NP_005152	P35414	APJ_HUMAN	apelin receptor	63	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			lung(5)|ovary(1)	6						GATATCAGCTGAGCGCCTCTT	0.612													10	38	---	---	---	---	PASS
CCDC86	79080	broad.mit.edu	37	11	60609992	60609992	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:60609992G>A	uc001nqa.2	+	1	564	c.395G>A	c.(394-396)GGA>GAA	p.G132E	CCDC86_uc001nqb.2_Intron	NM_024098	NP_077003	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	132	Pro-rich.				interspecies interaction between organisms	nucleus					0						CAGGACCAGGGAGTACTGGCC	0.617													13	58	---	---	---	---	PASS
DDB1	1642	broad.mit.edu	37	11	61070589	61070589	+	Silent	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:61070589C>A	uc001nrc.3	-	23	3097	c.2871G>T	c.(2869-2871)GTG>GTT	p.V957V	DDB1_uc010rle.1_Silent_p.V268V|DDB1_uc010rlf.1_Silent_p.V957V	NM_001923	NP_001914	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1	957	Interaction with CDT1 and CUL4A.				cell cycle checkpoint|interspecies interaction between organisms|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytoplasm|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4						CCAAGATTTCCACAGCACTCA	0.438								NER					6	106	---	---	---	---	PASS
LRP5	4041	broad.mit.edu	37	11	68191058	68191058	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:68191058G>A	uc001ont.2	+	14	3204	c.3129G>A	c.(3127-3129)GAG>GAA	p.E1043E	LRP5_uc009ysg.2_Silent_p.E453E	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	1043	LDL-receptor class B 17.|Beta-propeller 4.|Extracellular (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7						GGACGTGCGAGGCCACCAATA	0.622													9	37	---	---	---	---	PASS
NUMA1	4926	broad.mit.edu	37	11	71740319	71740319	+	Silent	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:71740319C>A	uc001orl.1	-	4	232	c.60G>T	c.(58-60)GTG>GTT	p.V20V	NUMA1_uc001ork.1_Silent_p.V20V|NUMA1_uc001orm.1_Silent_p.V20V|NUMA1_uc009ysx.1_Silent_p.V20V|NUMA1_uc001oro.1_Silent_p.V20V|NUMA1_uc009ysy.1_Silent_p.V20V|NUMA1_uc001orp.2_Silent_p.V20V|NUMA1_uc001orq.2_Silent_p.V20V	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	20					G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8						CAGGGTCAGCCACGTGTAGAC	0.498			T	RARA	APL								3	14	---	---	---	---	PASS
ELMOD1	55531	broad.mit.edu	37	11	107524922	107524922	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:107524922G>T	uc010rvs.1	+	10	1076	c.672G>T	c.(670-672)GAG>GAT	p.E224D	ELMOD1_uc001pjm.2_Missense_Mutation_p.E216D|ELMOD1_uc010rvt.1_Missense_Mutation_p.E218D	NM_018712	NP_061182	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1 isoform 1	224	ELMO.				phagocytosis	cytoskeleton	GTPase activator activity				0		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		CAGAATGGGAGAAGAAAAGGA	0.373													4	23	---	---	---	---	PASS
FAM55A	120400	broad.mit.edu	37	11	114393009	114393009	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:114393009A>C	uc001ppa.2	-	6	1316	c.899T>G	c.(898-900)TTT>TGT	p.F300C	FAM55A_uc010rxd.1_Missense_Mutation_p.F149C	NM_152315	NP_689528	Q8N323	FA55A_HUMAN	hypothetical protein LOC120400	442						extracellular region					0		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;3.02e-06)|Epithelial(105;0.000144)|all cancers(92;0.00106)		AAATGGTCTAAAGTGCTGGCC	0.438													13	44	---	---	---	---	PASS
TECTA	7007	broad.mit.edu	37	11	121028813	121028813	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:121028813C>T	uc010rzo.1	+	13	4569	c.4569C>T	c.(4567-4569)ATC>ATT	p.I1523I		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	1523	VWFD 4.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGCCCGACATCTCCTTCCAGC	0.577													12	38	---	---	---	---	PASS
OR8A1	390275	broad.mit.edu	37	11	124440189	124440189	+	Silent	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:124440189C>G	uc010san.1	+	1	225	c.225C>G	c.(223-225)CCC>CCG	p.P75P		NM_001005194	NP_001005194	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A,	75	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		TGCACACCCCCATGTACTACT	0.488													9	68	---	---	---	---	PASS
AKAP3	10566	broad.mit.edu	37	12	4736450	4736450	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:4736450C>A	uc001qnb.3	-	4	1847	c.1618G>T	c.(1618-1620)GCC>TCC	p.A540S		NM_006422	NP_006413	O75969	AKAP3_HUMAN	A-kinase anchor protein 3	540					acrosome reaction|cellular component movement	acrosomal vesicle	protein kinase A binding			skin(3)|large_intestine(1)|ovary(1)|kidney(1)	6						CCTCCCTGGGCCAGGTGATAT	0.517													6	26	---	---	---	---	PASS
AKAP3	10566	broad.mit.edu	37	12	4736451	4736451	+	Silent	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:4736451C>A	uc001qnb.3	-	4	1846	c.1617G>T	c.(1615-1617)CTG>CTT	p.L539L		NM_006422	NP_006413	O75969	AKAP3_HUMAN	A-kinase anchor protein 3	539					acrosome reaction|cellular component movement	acrosomal vesicle	protein kinase A binding			skin(3)|large_intestine(1)|ovary(1)|kidney(1)	6						CTCCCTGGGCCAGGTGATATT	0.522													6	26	---	---	---	---	PASS
GNB3	2784	broad.mit.edu	37	12	6952169	6952169	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:6952169G>A	uc001qrd.2	+	5	537	c.132G>A	c.(130-132)CAG>CAA	p.Q44Q	GNB3_uc001qrc.2_5'UTR|GNB3_uc009zfe.2_Silent_p.Q44Q	NM_002075	NP_002066	P16520	GBB3_HUMAN	guanine nucleotide-binding protein, beta-3	44					cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of blood pressure|synaptic transmission	plasma membrane	GTPase activity|GTPase binding|signal transducer activity				0						GACGAGTCCAGATGCGGACGC	0.597													7	24	---	---	---	---	PASS
C1R	715	broad.mit.edu	37	12	7187907	7187907	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:7187907C>A	uc010sfy.1	-	10	2106	c.2047G>T	c.(2047-2049)GGC>TGC	p.G683C		NM_001733	NP_001724	P00736	C1R_HUMAN	complement component 1, r subcomponent	683	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AAGCCATAGCCCCTGCTGCAC	0.572													6	41	---	---	---	---	PASS
CD163L1	283316	broad.mit.edu	37	12	7528090	7528090	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:7528090C>A	uc001qsy.2	-	11	2814	c.2788G>T	c.(2788-2790)GAC>TAC	p.D930Y	CD163L1_uc010sge.1_Missense_Mutation_p.D940Y	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	930	SRCR 9.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|skin(2)|central_nervous_system(1)	11						TCTTCTGGGTCCCAGTGGGTG	0.512													6	24	---	---	---	---	PASS
A2M	2	broad.mit.edu	37	12	9243921	9243921	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:9243921G>C	uc001qvk.1	-	19	2458	c.2345C>G	c.(2344-2346)TCC>TGC	p.S782C	A2M_uc009zgk.1_Missense_Mutation_p.S632C	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	782					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	AGAGGCAGTGGAAGAGATACC	0.562													21	99	---	---	---	---	PASS
RAPGEF3	10411	broad.mit.edu	37	12	48142237	48142237	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:48142237C>A	uc009zkp.2	-	11	1557	c.1117G>T	c.(1117-1119)GAG>TAG	p.E373*	RAPGEF3_uc010sln.1_5'Flank|RAPGEF3_uc001rpy.2_5'Flank|RAPGEF3_uc009zkq.2_Nonsense_Mutation_p.E373*|RAPGEF3_uc001rpz.3_Nonsense_Mutation_p.E415*|RAPGEF3_uc001rqa.2_5'Flank|RAPGEF3_uc009zkr.2_RNA|RAPGEF3_uc009zks.2_Nonsense_Mutation_p.E427*	NM_001098532	NP_001092002	A8K2G5	A8K2G5_HUMAN	Rap guanine nucleotide exchange factor 3 isoform	373					regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex	cAMP-dependent protein kinase regulator activity|guanyl-nucleotide exchange factor activity			lung(2)|skin(1)|pancreas(1)	4	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		TTGCCCTTACCTGTTGGGTCA	0.532													4	31	---	---	---	---	PASS
KRT2	3849	broad.mit.edu	37	12	53038841	53038841	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:53038841C>G	uc001sat.2	-	9	1915	c.1882G>C	c.(1882-1884)GAA>CAA	p.E628Q		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	628	Tail.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.19)		CCAAAAGCTTCACCTGAGCTA	0.537													6	88	---	---	---	---	PASS
LRP1	4035	broad.mit.edu	37	12	57594585	57594585	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:57594585C>T	uc001snd.2	+	64	10678	c.10212C>T	c.(10210-10212)GAC>GAT	p.D3404D		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	3404	Extracellular (Potential).|LDL-receptor class A 22.				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	ACAACAGTGACGAGGCCAACT	0.597													5	53	---	---	---	---	PASS
MON2	23041	broad.mit.edu	37	12	62887715	62887715	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:62887715G>T	uc001sre.2	+	3	587	c.196G>T	c.(196-198)GAG>TAG	p.E66*	MON2_uc009zqj.2_Nonsense_Mutation_p.E66*|MON2_uc010ssl.1_5'UTR|MON2_uc010ssm.1_Nonsense_Mutation_p.E66*|MON2_uc010ssn.1_Nonsense_Mutation_p.E66*|MON2_uc001srd.1_Intron	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	66					Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		GAACAGCTCAGAGGTTGTACA	0.328													3	11	---	---	---	---	PASS
UTP20	27340	broad.mit.edu	37	12	101680199	101680199	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:101680199G>C	uc001tia.1	+	5	583	c.427G>C	c.(427-429)GAG>CAG	p.E143Q	UTP20_uc009ztz.1_Missense_Mutation_p.E143Q	NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	143					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4						TCAGGACACAGAGTTGTTAGA	0.433													6	113	---	---	---	---	PASS
IGF1	3479	broad.mit.edu	37	12	102811758	102811758	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:102811758C>G	uc001tjp.3	-	4	645	c.426G>C	c.(424-426)AAG>AAC	p.K142N	IGF1_uc001tjn.2_Intron|IGF1_uc001tjm.2_Missense_Mutation_p.K142N|IGF1_uc001tjo.2_Intron	NM_001111285	NP_001104755	P05019	IGF1_HUMAN	insulin-like growth factor 1 isoform 3	142					anti-apoptosis|bone mineralization involved in bone maturation|cellular component movement|DNA replication|glycolate metabolic process|muscle hypertrophy|myoblast differentiation|myoblast proliferation|myotube cell development|negative regulation of smooth muscle cell apoptosis|phosphatidylinositol-mediated signaling|platelet activation|platelet degranulation|positive regulation of activated T cell proliferation|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis|positive regulation of osteoblast differentiation|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of Ras protein signal transduction|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat5 protein|Ras protein signal transduction|regulation of multicellular organism growth|satellite cell maintenance involved in skeletal muscle regeneration	platelet alpha granule lumen	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|integrin binding			central_nervous_system(1)|pancreas(1)	2						ACTTCGTGTTCTTGTTGGTAG	0.468													10	115	---	---	---	---	PASS
RPH3A	22895	broad.mit.edu	37	12	113307828	113307828	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:113307828C>T	uc010syl.1	+	10	1142	c.780C>T	c.(778-780)TCC>TCT	p.S260S	RPH3A_uc001ttz.2_Silent_p.S260S|RPH3A_uc001tty.2_Silent_p.S256S|RPH3A_uc009zwe.1_Silent_p.S256S|RPH3A_uc010sym.1_Silent_p.S211S|RPH3A_uc001tua.2_Silent_p.S20S	NM_001143854	NP_001137326	Q9Y2J0	RP3A_HUMAN	rabphilin 3A homolog isoform 1	260	Pro-rich.				intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(2)|skin(2)	7				BRCA - Breast invasive adenocarcinoma(302;0.00453)		CTGGAGACTCCAGCCGGAGCC	0.542													4	16	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117669887	117669887	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:117669887G>A	uc001twm.1	-	22	3971	c.3285C>T	c.(3283-3285)ATC>ATT	p.I1095I		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	1095	FAD-binding FR-type.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	AGGCCTGGAAGATGGTGCAGG	0.597													5	20	---	---	---	---	PASS
B3GNT4	79369	broad.mit.edu	37	12	122691663	122691663	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:122691663C>T	uc001ubx.2	+	3	1083	c.865C>T	c.(865-867)CGG>TGG	p.R289W	B3GNT4_uc001uby.2_Missense_Mutation_p.R264W	NM_030765	NP_110392	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal	289	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		AGCCACAGTGCGGCGCCTCCA	0.557													8	35	---	---	---	---	PASS
ATP6V0A2	23545	broad.mit.edu	37	12	124220151	124220151	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:124220151C>G	uc001ufr.2	+	8	1053	c.805C>G	c.(805-807)CGC>GGC	p.R269G	ATP6V0A2_uc001ufq.1_Missense_Mutation_p.R269G	NM_012463	NP_036595	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	269	Cytoplasmic (Potential).				ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|immune response|insulin receptor signaling pathway|transferrin transport	endosome membrane|integral to membrane|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		GCTGAACACCCGCATCCAGGA	0.493													5	12	---	---	---	---	PASS
ANKLE2	23141	broad.mit.edu	37	12	133312095	133312095	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr12:133312095C>T	uc001ukx.2	-	9	1664	c.1597G>A	c.(1597-1599)GAA>AAA	p.E533K	ANKLE2_uc009zyw.1_5'Flank|ANKLE2_uc001uky.3_Missense_Mutation_p.E471K	NM_015114	NP_055929	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	533						cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		CGAAAATCTTCTGCCTATGAA	0.527													11	39	---	---	---	---	PASS
COL4A2	1284	broad.mit.edu	37	13	111134895	111134895	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr13:111134895C>A	uc001vqx.2	+	32	3080	c.2791C>A	c.(2791-2793)CAA>AAA	p.Q931K		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	931	Triple-helical region.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GGATGGTTTCCAAGGCATGCC	0.522													5	140	---	---	---	---	PASS
OR4Q3	441669	broad.mit.edu	37	14	20216239	20216239	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:20216239C>T	uc010tkt.1	+	1	653	c.653C>T	c.(652-654)TCT>TTT	p.S218F		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	218	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTACTATTCTCTTATGCTATC	0.507													11	63	---	---	---	---	PASS
FLJ10357	55701	broad.mit.edu	37	14	21548879	21548879	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:21548879G>T	uc001vzp.2	+	12	2463	c.2434G>T	c.(2434-2436)GAC>TAC	p.D812Y	FLJ10357_uc001vzo.1_5'UTR|FLJ10357_uc010aij.2_RNA|FLJ10357_uc010tln.1_Missense_Mutation_p.D98Y	NM_018071	NP_060541	Q8TER5	ARH40_HUMAN	hypothetical protein LOC55701	812					regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;5.79e-11)|Epithelial(56;8.35e-09)|all cancers(55;4.23e-08)	GBM - Glioblastoma multiforme(265;0.0197)		TATGCCTGGGGACACCTTGTC	0.647													10	34	---	---	---	---	PASS
MYH7	4625	broad.mit.edu	37	14	23889431	23889431	+	Nonsense_Mutation	SNP	C	A	A	rs141735183		TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:23889431C>A	uc001wjx.2	-	27	3455	c.3349G>T	c.(3349-3351)GAG>TAG	p.E1117*	MIR208B_hsa-mir-208b|MI0005570_5'Flank	NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1117	Potential.				adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		tcctccagctcctcGATGCGT	0.562													9	22	---	---	---	---	PASS
FOXG1	2290	broad.mit.edu	37	14	29237714	29237714	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:29237714T>G	uc001wqe.2	+	1	1428	c.1229T>G	c.(1228-1230)CTC>CGC	p.L410R		NM_005249	NP_005240	P55316	FOXG1_HUMAN	forkhead box G1	410					axon midline choice point recognition|central nervous system neuron development|dorsal/ventral pattern formation|embryo development ending in birth or egg hatching|hindbrain development|inner ear morphogenesis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|nonmotile primary cilium assembly|nose development|positive regulation of cell cycle|positive regulation of neuroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of mitotic cell cycle|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)|lung(2)	4			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		GTCAACCTGCTCGCGGGCCAG	0.687													4	27	---	---	---	---	PASS
EGLN3	112399	broad.mit.edu	37	14	34400377	34400377	+	Silent	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:34400377G>C	uc001wsa.3	-	2	728	c.402C>G	c.(400-402)CGC>CGG	p.R134R	EGLN3_uc001wry.2_Silent_p.R40R|EGLN3_uc001wrz.2_Silent_p.R134R	NM_022073	NP_071356	Q9H6Z9	EGLN3_HUMAN	egl nine homolog 3	134	Fe2OG dioxygenase.				apoptosis	cytoplasm|nucleus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding				0	Breast(36;0.0303)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.000246)|Lung(238;0.000959)|Epithelial(34;0.155)	GBM - Glioblastoma multiforme(112;0.0118)	Vitamin C(DB00126)	TGTCCACGTGGCGAACATAAC	0.473													14	43	---	---	---	---	PASS
FOXA1	3169	broad.mit.edu	37	14	38061517	38061517	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:38061517C>T	uc001wuf.2	-	2	784	c.472G>A	c.(472-474)GAC>AAC	p.D158N	FOXA1_uc010tpz.1_Missense_Mutation_p.D125N	NM_004496	NP_004487	P55317	FOXA1_HUMAN	forkhead box A1	158					chromatin remodeling|embryo development|epithelial cell maturation involved in prostate gland development|epithelial tube branching involved in lung morphogenesis|epithelial-mesenchymal signaling involved in prostate gland development|glucose homeostasis|lung epithelial cell differentiation|negative regulation of survival gene product expression|neuron fate specification|pattern specification process|positive regulation of estrogen receptor signaling pathway|positive regulation of mitotic cell cycle|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|prostate gland epithelium morphogenesis|prostate gland stromal morphogenesis|response to estradiol stimulus|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|protein domain specific binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding				0	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		GTCTTGGCGTcgccgccgccg	0.557													13	31	---	---	---	---	PASS
RPL10L	140801	broad.mit.edu	37	14	47120615	47120615	+	Missense_Mutation	SNP	C	G	G	rs11557561		TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:47120615C>G	uc001wwg.2	-	1	414	c.325G>C	c.(325-327)GAC>CAC	p.D109H		NM_080746	NP_542784	Q96L21	RL10L_HUMAN	ribosomal protein L10-like protein	109					spermatogenesis|translation	cytosolic large ribosomal subunit|nucleus	structural constituent of ribosome			ovary(1)	1						TGGAGCCTGTCAGCCCCAGCA	0.547													9	45	---	---	---	---	PASS
SIPA1L1	26037	broad.mit.edu	37	14	72190544	72190544	+	Silent	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:72190544G>C	uc001xms.2	+	16	4800	c.4452G>C	c.(4450-4452)CTG>CTC	p.L1484L	SIPA1L1_uc001xmt.2_Silent_p.L1463L|SIPA1L1_uc001xmu.2_Silent_p.L1463L|SIPA1L1_uc001xmv.2_Silent_p.L1484L|SIPA1L1_uc010ttm.1_Silent_p.L938L|SIPA1L1_uc001xmw.2_Silent_p.L249L	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	1484	Ser-rich.				actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GCAAGTACCTGATTGGATGGA	0.428													10	131	---	---	---	---	PASS
ANGEL1	23357	broad.mit.edu	37	14	77272759	77272759	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:77272759C>T	uc001xsv.2	-	5	1493	c.1380G>A	c.(1378-1380)AAG>AAA	p.K460K	ANGEL1_uc010tvf.1_Intron	NM_015305	NP_056120	Q9UNK9	ANGE1_HUMAN	angel homolog 1	460										ovary(2)|central_nervous_system(1)|skin(1)	4			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		CCCATTTCACCTTCCAGGCTG	0.532													5	37	---	---	---	---	PASS
CPSF2	53981	broad.mit.edu	37	14	92622903	92622903	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:92622903A>G	uc001yah.1	+	12	1760	c.1523A>G	c.(1522-1524)GAT>GGT	p.D508G		NM_017437	NP_059133	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2	508					histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		ACAAATGGAGATGAACCTATG	0.323													15	74	---	---	---	---	PASS
C14orf177	283598	broad.mit.edu	37	14	99183521	99183521	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:99183521A>G	uc001yfz.1	+	4	707	c.288A>G	c.(286-288)ATA>ATG	p.I96M		NM_182560	NP_872366	Q52M58	CN177_HUMAN	hypothetical protein LOC283598	96											0		Melanoma(154;0.128)				ATCACCAAATAATGTCTGCTT	0.423													17	68	---	---	---	---	PASS
ASPG	374569	broad.mit.edu	37	14	104559906	104559906	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:104559906C>T	uc001yoq.1	+	3	330	c.270C>T	c.(268-270)ATC>ATT	p.I90I	ASPG_uc001yoo.1_Silent_p.I118I|ASPG_uc001yop.1_Silent_p.I90I|ASPG_uc001yor.1_Silent_p.I90I	NM_001080464	NP_001073933	Q86U10	LPP60_HUMAN	60 kDa lysophospholipase	90	Asparaginase.				lipid catabolic process		1-alkyl-2-acetylglycerophosphocholine esterase activity|asparaginase activity|lysophospholipase activity				0						ACATGACCATCGCTGAGTGGG	0.408													20	79	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105411849	105411849	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:105411849G>A	uc010axc.1	-	7	10059	c.9939C>T	c.(9937-9939)TTC>TTT	p.F3313F	AHNAK2_uc001ypx.2_Silent_p.F3213F	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3313						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ACGGCATCTTGAATTTGGGCA	0.622													14	352	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106209343	106209343	+	RNA	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr14:106209343T>A	uc010tyt.1	-	3625		c.58380A>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_5'UTR|uc001ysf.2_5'UTR|uc001ysg.1_RNA					Parts of antibodies, mostly variable regions.												0						CCAGGGCTGCTGTGCCCCCAG	0.672													5	19	---	---	---	---	PASS
OR4N4	283694	broad.mit.edu	37	15	22382701	22382701	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr15:22382701G>T	uc001yuc.1	+	7	1210	c.229G>T	c.(229-231)GTG>TTG	p.V77L	LOC727924_uc001yub.1_RNA|OR4N4_uc010tzv.1_Missense_Mutation_p.V77L	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	77	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CTCCTTCATTGTGGCTCCCAG	0.493													18	190	---	---	---	---	PASS
INO80	54617	broad.mit.edu	37	15	41280040	41280040	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr15:41280040G>A	uc001zni.2	-	30	3916	c.3703C>T	c.(3703-3705)CTG>TTG	p.L1235L	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	1235	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.|Helicase C-terminal.				cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						GCTCTTTGCAGAATGCGTTCT	0.502													12	214	---	---	---	---	PASS
MGA	23269	broad.mit.edu	37	15	42042356	42042356	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr15:42042356G>T	uc010ucy.1	+	17	6732	c.6551G>T	c.(6550-6552)AGG>ATG	p.R2184M	MGA_uc010ucz.1_Missense_Mutation_p.R1975M|MGA_uc010uda.1_Missense_Mutation_p.R800M|MGA_uc001zoi.2_Missense_Mutation_p.R398M	NM_001164273	NP_001157745	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 1	2145	Basic motif.					MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)		CCCTTAACCAGGAAATGTGTT	0.428													22	75	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54685268	54685268	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr15:54685268G>C	uc002ack.2	+	16	4736	c.4736G>C	c.(4735-4737)CGT>CCT	p.R1579P	UNC13C_uc002acl.2_Missense_Mutation_p.R409P	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1579					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GATATTCCTCGTGAAGATCAG	0.388													12	54	---	---	---	---	PASS
SIN3A	25942	broad.mit.edu	37	15	75684849	75684849	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr15:75684849G>C	uc002bai.2	-	15	2844	c.2585C>G	c.(2584-2586)CCT>CGT	p.P862R	SIN3A_uc002baj.2_Missense_Mutation_p.P862R|SIN3A_uc010uml.1_Missense_Mutation_p.P862R	NM_015477	NP_056292	Q96ST3	SIN3A_HUMAN	transcriptional co-repressor Sin3A	862					blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5						CTTGGACTTAGGGGGACTGCC	0.428													5	87	---	---	---	---	PASS
ST20	400410	broad.mit.edu	37	15	80191279	80191279	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr15:80191279G>C	uc002bez.3	-	3	914	c.234C>G	c.(232-234)TAC>TAG	p.Y78*	ST20_uc002bfa.3_Nonsense_Mutation_p.Y78*|MTHFS_uc002bex.3_5'Flank	NM_001100879	NP_001094349	Q9HBF5	ST20_HUMAN	cervical cancer suppressor-1	78											0						TTATTTAAAAGTAGAAGTATG	0.338													3	62	---	---	---	---	PASS
C15orf51	196968	broad.mit.edu	37	15	100341295	100341295	+	RNA	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr15:100341295C>A	uc010urx.1	-	3		c.352G>T			C15orf51_uc010ury.1_RNA|uc002bvp.2_5'Flank|C15orf51_uc010urz.1_RNA|C15orf51_uc010bow.2_RNA	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0						AGGAGTCCACCAGGTTCTGGG	0.547													4	50	---	---	---	---	PASS
E4F1	1877	broad.mit.edu	37	16	2282275	2282275	+	Silent	SNP	C	G	G	rs149258624		TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:2282275C>G	uc002cpm.2	+	4	567	c.519C>G	c.(517-519)CTC>CTG	p.L173L	E4F1_uc010bsi.2_Silent_p.L173L|E4F1_uc010bsj.2_Silent_p.L173L	NM_004424	NP_004415	Q66K89	E4F1_HUMAN	p120E4F	173					cell division|cell proliferation|interspecies interaction between organisms|mitosis|regulation of growth	cytoplasm|nucleoplasm	DNA binding|ligase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)	1						GGCTGGGGCTCGCAGGGGAGG	0.667													9	28	---	---	---	---	PASS
ZNF434	54925	broad.mit.edu	37	16	3434852	3434852	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:3434852G>C	uc002cuz.2	-	5	1007	c.205C>G	c.(205-207)CAG>GAG	p.Q69E	ZNF434_uc002cux.3_Missense_Mutation_p.Q280E|ZNF434_uc010uwx.1_5'UTR|ZNF434_uc002cuy.3_5'UTR|ZNF434_uc010uwy.1_5'UTR|ZNF434_uc010uwz.1_Missense_Mutation_p.Q280E|ZNF434_uc010uxa.1_Missense_Mutation_p.Q69E	NM_017810	NP_060280	Q9NX65	ZN434_HUMAN	zinc finger protein 434	69					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						CTGTTCTGCTGACAGGTCTGG	0.527													4	112	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9862740	9862740	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:9862740C>G	uc002czo.3	-	12	3111	c.2563G>C	c.(2563-2565)GAC>CAC	p.D855H	GRIN2A_uc010uym.1_Missense_Mutation_p.D855H|GRIN2A_uc010uyn.1_Missense_Mutation_p.D698H|GRIN2A_uc002czr.3_Missense_Mutation_p.D855H	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	855	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	CCAGGCCGGTCGGAGCACACG	0.567													15	79	---	---	---	---	PASS
ACSM5	54988	broad.mit.edu	37	16	20422839	20422839	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:20422839G>A	uc002dhe.2	+	2	180	c.33G>A	c.(31-33)CAG>CAA	p.Q11Q	ACSM5_uc002dhd.1_Silent_p.Q11Q	NM_017888	NP_060358	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	11					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2						TAGTCCTCCAGGCACTGAGGA	0.557													7	21	---	---	---	---	PASS
TBX6	6911	broad.mit.edu	37	16	30100411	30100411	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:30100411C>T	uc010veh.1	-	4	534	c.474G>A	c.(472-474)TGG>TGA	p.W158*	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TBX6_uc002dwk.1_Nonsense_Mutation_p.W158*	NM_004608	NP_004599	O95947	TBX6_HUMAN	T-box 6	158	T-box.				anatomical structure morphogenesis|mesoderm development|multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2						CGCTGGGCTCCCAGCGCCGGC	0.647													4	27	---	---	---	---	PASS
TBX6	6911	broad.mit.edu	37	16	30102165	30102165	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:30102165C>T	uc010veh.1	-	3	327	c.267G>A	c.(265-267)CCG>CCA	p.P89P	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TBX6_uc002dwk.1_Silent_p.P89P	NM_004608	NP_004599	O95947	TBX6_HUMAN	T-box 6	89					anatomical structure morphogenesis|mesoderm development|multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2						GGCTGACCCCCGGGAGGGAAT	0.662													5	17	---	---	---	---	PASS
SLC12A3	6559	broad.mit.edu	37	16	56906359	56906359	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:56906359T>A	uc010ccm.2	+	7	978	c.949T>A	c.(949-951)TTC>ATC	p.F317I	SLC12A3_uc002ekd.3_Missense_Mutation_p.F317I|SLC12A3_uc010ccn.2_Missense_Mutation_p.F316I	NM_001126108	NP_001119580	P55017	S12A3_HUMAN	solute carrier family 12, member 3 isoform 3	317					sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CTCCAAAGGCTTCTTCAGCTA	0.567													6	32	---	---	---	---	PASS
MIR328	442901	broad.mit.edu	37	16	67236282	67236282	+	RNA	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:67236282C>G	hsa-mir-328|MI0000804	-			c.17C>G			ELMO3_uc002esa.2_Intron|ELMO3_uc002esb.2_Intron|ELMO3_uc002esc.2_Intron|uc010vjf.1_RNA																	0						CTGAGCCCCTCCTGCCCCCCC	0.632													4	59	---	---	---	---	PASS
ZFHX3	463	broad.mit.edu	37	16	72821790	72821790	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:72821790T>C	uc002fck.2	-	10	11058	c.10385A>G	c.(10384-10386)CAG>CGG	p.Q3462R	ZFHX3_uc002fcl.2_Missense_Mutation_p.Q2548R	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	3462					muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				CAACTTGTACTGCACCTTTGG	0.597													13	50	---	---	---	---	PASS
GLG1	2734	broad.mit.edu	37	16	74497334	74497334	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:74497334A>C	uc002fcy.3	-	20	2761	c.2711T>G	c.(2710-2712)TTG>TGG	p.L904W	GLG1_uc002fcx.2_Missense_Mutation_p.L904W|GLG1_uc002fcw.3_Missense_Mutation_p.L893W|GLG1_uc002fcz.3_Missense_Mutation_p.L321W	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3	904	Cys-rich GLG1 13.|Extracellular (Potential).					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						ATTTTGCTTCAAGCACTGCAA	0.413													12	33	---	---	---	---	PASS
DEF8	54849	broad.mit.edu	37	16	90015915	90015915	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr16:90015915G>A	uc002fpn.1	+	2	131	c.42G>A	c.(40-42)GCG>GCA	p.A14A	DEF8_uc002fpl.2_5'UTR|DEF8_uc002fpm.2_Intron|DEF8_uc002fpo.1_5'UTR|DEF8_uc002fpp.1_5'UTR|DEF8_uc010vpq.1_5'UTR|DEF8_uc010vpr.1_5'UTR	NM_207514	NP_997397	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 isoform 1	14					intracellular signal transduction		zinc ion binding			central_nervous_system(1)	1		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		CCTGGCAGGCGATGCAGGTAT	0.662													10	44	---	---	---	---	PASS
AMAC1L3	643664	broad.mit.edu	37	17	7386197	7386197	+	Silent	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr17:7386197T>C	uc010cmj.1	+	2	1009	c.894T>C	c.(892-894)TAT>TAC	p.Y298Y	ZBTB4_uc002ghd.3_Intron|POLR2A_uc002ghe.2_5'Flank|POLR2A_uc002ghf.3_5'Flank	NM_001102614	NP_001096084	P0C7Q6	AMCL3_HUMAN	acyl-malonyl condensing enzyme 1-like 3	298	DUF6 2.|Helical; (Potential).					integral to membrane					0		Prostate(122;0.173)				TACTGCAGTATTATATGCTCC	0.572													7	89	---	---	---	---	PASS
UBB	7314	broad.mit.edu	37	17	16285361	16285361	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr17:16285361G>T	uc002gpx.2	+	2	278	c.140G>T	c.(139-141)GGC>GTC	p.G47V	UBB_uc010vwe.1_Missense_Mutation_p.G47V	NM_018955	NP_061828	P0CG47	UBB_HUMAN	ubiquitin B precursor	47	Ubiquitin-like 1.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			skin(3)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		ATCTTTGCAGGCAAGCAGCTG	0.547													11	72	---	---	---	---	PASS
FLJ40504	284085	broad.mit.edu	37	17	26603835	26603835	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr17:26603835C>T	uc002has.3	-	3	736	c.640G>A	c.(640-642)GAG>AAG	p.E214K		NM_173624	NP_775895			SubName: Full=Putative uncharacterized protein FLJ40504; SubName: Full=cDNA FLJ40504 fis, clone TESTI2045509, highly similar to KERATIN, TYPE I CYTOSKELETAL 18;												0	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		ATGTCACTCTCCACAGACTGG	0.517													12	29	---	---	---	---	PASS
COASY	80347	broad.mit.edu	37	17	40717709	40717709	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr17:40717709C>T	uc002hzz.2	+	9	1675	c.1518C>T	c.(1516-1518)CTC>CTT	p.L506L	COASY_uc010cyj.2_Silent_p.L535L|COASY_uc002iab.2_Silent_p.L211L|COASY_uc002iad.2_Silent_p.L506L|COASY_uc002iac.2_Silent_p.L506L|COASY_uc002iae.2_Silent_p.L301L|MLX_uc002iaf.2_5'Flank|MLX_uc002iag.2_5'Flank|MLX_uc002iah.2_5'Flank	NM_001042529	NP_001035994	Q13057	COASY_HUMAN	coenzyme A synthase isoform a	506	DPCK.				coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial outer membrane	ATP binding|dephospho-CoA kinase activity|pantetheine-phosphate adenylyltransferase activity				0		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		GGGATGGCCTCAGTGAAGCCG	0.577													4	29	---	---	---	---	PASS
PPP1R9B	84687	broad.mit.edu	37	17	48212999	48212999	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr17:48212999C>T	uc002iqh.3	-	11	2322	c.2319G>A	c.(2317-2319)CTG>CTA	p.L773L		NM_032595	NP_115984	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B	771	Potential.|Interacts with TGN38 (By similarity).				cell cycle arrest|cell differentiation|cell migration|filopodium assembly|negative regulation of cell growth|nervous system development|regulation of cell growth by extracellular stimulus|regulation of cell proliferation|regulation of exit from mitosis|RNA splicing	adherens junction|cytoskeleton|dendritic spine|filopodium|lamellipodium|nucleoplasm|protein phosphatase type 1 complex|ruffle membrane|synapse	actin binding|protein phosphatase 1 binding|protein phosphatase inhibitor activity				0						TCTCCTTTTTCAGGAACTCGA	0.602													4	12	---	---	---	---	PASS
RSAD1	55316	broad.mit.edu	37	17	48559474	48559474	+	Missense_Mutation	SNP	G	A	A	rs138384713		TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr17:48559474G>A	uc002iqw.1	+	4	553	c.497G>A	c.(496-498)CGG>CAG	p.R166Q	RSAD1_uc010wmq.1_RNA	NM_018346	NP_060816	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing	166					porphyrin biosynthetic process	mitochondrion	4 iron, 4 sulfur cluster binding|coproporphyrinogen oxidase activity|metal ion binding				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			ACTGAGCTCCGGCTGTTGGGA	0.612											OREG0024567	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	27	83	---	---	---	---	PASS
CSNK1D	1453	broad.mit.edu	37	17	80211007	80211007	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr17:80211007G>T	uc002kej.2	-	4	766	c.450C>A	c.(448-450)TTC>TTA	p.F150L	SLC16A3_uc002kee.2_Intron|CSNK1D_uc002kef.2_Missense_Mutation_p.F150L|CSNK1D_uc002kei.2_Missense_Mutation_p.F150L|CSNK1D_uc010wvj.1_Intron|CSNK1D_uc010dil.2_5'Flank|CSNK1D_uc002keh.2_Missense_Mutation_p.F15L|CSNK1D_uc010dim.1_5'Flank	NM_001893	NP_001884	P48730	KC1D_HUMAN	casein kinase 1, delta isoform 1	150	Protein kinase.				circadian regulation of gene expression|DNA repair|G2/M transition of mitotic cell cycle|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|regulation of circadian rhythm|Wnt receptor signaling pathway	centrosome|cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			breast(2)	2	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)			TGGCCAGCCCGAAGTCGATGA	0.552													4	88	---	---	---	---	PASS
TMEM200C	645369	broad.mit.edu	37	18	5891854	5891854	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr18:5891854G>A	uc002kmx.1	-	1	250	c.209C>T	c.(208-210)GCG>GTG	p.A70V		NM_001080209	NP_001073678	A6NKL6	T200C_HUMAN	transmembrane protein 200C	70	Helical; (Potential).					integral to membrane					0						GCCCACCACCGCCATGGCTAT	0.662													11	12	---	---	---	---	PASS
LAMA1	284217	broad.mit.edu	37	18	7014032	7014032	+	Missense_Mutation	SNP	C	A	A	rs138476816		TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr18:7014032C>A	uc002knm.2	-	23	3239	c.3145G>T	c.(3145-3147)GTG>TTG	p.V1049L	LAMA1_uc010wzj.1_Missense_Mutation_p.V525L	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1049	Laminin EGF-like 12.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GTCGACCCCACGAGACTGCAA	0.483													5	14	---	---	---	---	PASS
LAMA3	3909	broad.mit.edu	37	18	21494522	21494522	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr18:21494522A>T	uc002kuq.2	+	57	7564	c.7478A>T	c.(7477-7479)CAG>CTG	p.Q2493L	LAMA3_uc002kur.2_Missense_Mutation_p.Q2437L|LAMA3_uc002kus.3_Missense_Mutation_p.Q884L|LAMA3_uc002kut.3_Missense_Mutation_p.Q828L	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	2493	Laminin G-like 1.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GTGAAATTTCAGAGGTACAAG	0.458													6	26	---	---	---	---	PASS
OSBPL1A	114876	broad.mit.edu	37	18	21921529	21921529	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr18:21921529T>A	uc002kve.2	-	5	550	c.376A>T	c.(376-378)ATC>TTC	p.I126F		NM_080597	NP_542164	Q9BXW6	OSBL1_HUMAN	oxysterol-binding protein-like 1A isoform B	126					cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding			ovary(4)	4	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					ATGCTTCTGATTTCTTCAGCA	0.343													6	43	---	---	---	---	PASS
MEX3C	51320	broad.mit.edu	37	18	48703809	48703809	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr18:48703809C>T	uc002lfc.3	-	2	892	c.892G>A	c.(892-894)GAG>AAG	p.E298K		NM_016626	NP_057710	Q5U5Q3	MEX3C_HUMAN	ring finger and KH domain containing 2	298						cytoplasm|nucleus	RNA binding|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		GAGAAGTGCTCTGCAGCTGAG	0.483													4	45	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56202164	56202164	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr18:56202164G>C	uc002lhj.3	-	5	5469	c.5255C>G	c.(5254-5256)TCA>TGA	p.S1752*	ALPK2_uc002lhk.1_Nonsense_Mutation_p.S1083*	NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	1752							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						AAGAAAGGCTGAGTTCTTTCT	0.413													6	47	---	---	---	---	PASS
SALL3	27164	broad.mit.edu	37	18	76754570	76754570	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr18:76754570C>G	uc002lmt.2	+	2	2579	c.2579C>G	c.(2578-2580)ACC>AGC	p.T860S	SALL3_uc010dra.2_Missense_Mutation_p.T467S	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	860					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CAGCAGCTGACCGGCCTCAAG	0.682													9	17	---	---	---	---	PASS
ELAVL1	1994	broad.mit.edu	37	19	8032655	8032655	+	Silent	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:8032655C>A	uc002mjb.2	-	5	617	c.450G>T	c.(448-450)GCG>GCT	p.A150A		NM_001419	NP_001410	Q15717	ELAV1_HUMAN	ELAV-like 1	150	RRM 2.				3'-UTR-mediated mRNA stabilization|multicellular organismal development	cytoplasm|nucleoplasm	identical protein binding|mRNA binding|nucleotide binding				0						ACCGGATAAACGCAACCCCTC	0.453													5	45	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8181625	8181625	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:8181625C>T	uc002mjf.2	-	28	3666	c.3645G>A	c.(3643-3645)ATG>ATA	p.M1215I		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1215	EGF-like 17.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						GACCCCCTGGCATGTTGGTGC	0.632													9	37	---	---	---	---	PASS
MARCH2	51257	broad.mit.edu	37	19	8491686	8491686	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:8491686G>A	uc002mjv.2	+	4	811	c.370G>A	c.(370-372)GAG>AAG	p.E124K	MARCH2_uc002mjw.2_Missense_Mutation_p.E124K|MARCH2_uc002mjx.2_Missense_Mutation_p.E124K	NM_016496	NP_057580	Q9P0N8	MARH2_HUMAN	membrane-associated ring finger (C3HC4) 2	124					endocytosis	cytoplasmic vesicle|endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						ACCCCTCACAGAGGTACCCTT	0.592													6	18	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9072126	9072126	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:9072126G>T	uc002mkp.2	-	3	15524	c.15320C>A	c.(15319-15321)ACT>AAT	p.T5107N		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5109	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GTCTTTAGAAGTGGCCAGTAT	0.423													11	86	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9087486	9087486	+	Silent	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:9087486C>A	uc002mkp.2	-	1	4533	c.4329G>T	c.(4327-4329)CTG>CTT	p.L1443L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	1443	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GAGCAAGGACCAGGGGTTCCC	0.512													5	96	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9088466	9088466	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:9088466C>G	uc002mkp.2	-	1	3553	c.3349G>C	c.(3349-3351)GAA>CAA	p.E1117Q		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	1117	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						ATTGTAATTTCTCTGGATGTT	0.468													5	70	---	---	---	---	PASS
ZNF559	84527	broad.mit.edu	37	19	9453519	9453519	+	Silent	SNP	A	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:9453519A>C	uc002mlg.2	+	7	2039	c.1392A>C	c.(1390-1392)CCA>CCC	p.P464P	ZNF559_uc002mlf.2_Silent_p.P233P|ZNF559_uc010dwl.1_Silent_p.P233P|ZNF559_uc010xkn.1_Silent_p.P456P|ZNF559_uc010dwm.1_3'UTR|ZNF559_uc002mle.3_Silent_p.P528P|ZNF559_uc010dwk.1_Silent_p.P233P|ZNF559_uc002mld.2_3'UTR|ZNF559_uc010dwo.1_Intron|ZNF177_uc002mli.2_Intron|ZNF177_uc002mlj.2_Intron	NM_032497	NP_115886	Q9BR84	ZN559_HUMAN	zinc finger protein 559	464					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GGGAGAGGCCATATAAATGTC	0.443													11	32	---	---	---	---	PASS
FBXW9	84261	broad.mit.edu	37	19	12807343	12807343	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:12807343G>C	uc010dyx.2	-	1	53	c.53C>G	c.(52-54)TCG>TGG	p.S18W	FBXW9_uc010xmp.1_RNA|FBXW9_uc002mum.1_Missense_Mutation_p.S18W|FBXW9_uc002mun.1_5'UTR	NM_032301	NP_115677	Q5XUX1	FBXW9_HUMAN	F-box and WD-40 domain protein 9	18							protein binding			ovary(1)	1						CTCTGGGTCCGAGTCATCGTC	0.677													3	38	---	---	---	---	PASS
KCNN1	3780	broad.mit.edu	37	19	18092701	18092701	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:18092701G>T	uc002nht.2	+	5	992	c.682G>T	c.(682-684)GTG>TTG	p.V228L	KCNN1_uc010xqa.1_Missense_Mutation_p.V228L	NM_002248	NP_002239	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance	228	Helical; Name=Segment S4; (Potential).				synaptic transmission	voltage-gated potassium channel complex	calmodulin binding|small conductance calcium-activated potassium channel activity				0						CGACGTGGACGTGCTGCTGTC	0.672													4	15	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	31038893	31038893	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:31038893G>A	uc002nsu.1	+	4	2505	c.2367G>A	c.(2365-2367)ACG>ACA	p.T789T	ZNF536_uc010edd.1_Silent_p.T789T	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	789	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					ATGCCGGCACGCAGTCAGCAT	0.507													6	58	---	---	---	---	PASS
DPY19L3	147991	broad.mit.edu	37	19	32971362	32971362	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:32971362T>A	uc002ntg.2	+	18	2064	c.1888T>A	c.(1888-1890)TTC>ATC	p.F630I	DPY19L3_uc002nth.1_Missense_Mutation_p.F630I|DPY19L3_uc002nti.1_RNA|DPY19L3_uc002ntj.1_Missense_Mutation_p.F52I	NM_207325	NP_997208	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3	630						integral to membrane				ovary(4)	4	Esophageal squamous(110;0.162)					CCTAAGGTCCTTCGGCACTGA	0.532													8	19	---	---	---	---	PASS
TMEM147	10430	broad.mit.edu	37	19	36037609	36037609	+	Silent	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:36037609G>C	uc002oaj.1	+	4	340	c.243G>C	c.(241-243)CTG>CTC	p.L81L	uc010eec.1_5'Flank|uc002oag.2_5'Flank|TMEM147_uc002oai.1_Silent_p.L32L|TMEM147_uc002oak.1_5'UTR	NM_032635	NP_116024	Q9BVK8	TM147_HUMAN	transmembrane protein 147	81						endoplasmic reticulum membrane|integral to membrane	protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			TGGCAGACCTGATAGGTCTAA	0.562													12	44	---	---	---	---	PASS
MLL4	9757	broad.mit.edu	37	19	36210823	36210823	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:36210823G>T	uc010eei.2	+	3	574	c.574G>T	c.(574-576)GCA>TCA	p.A192S		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	192					chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GATGGTGCAGGCACTGACTGA	0.701													4	33	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40363021	40363021	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:40363021C>A	uc002omp.3	-	32	15057	c.15049G>T	c.(15049-15051)GCG>TCG	p.A5017S		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	5017	VWFD 12.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GAGCCGGGCGCCCGCCATGCA	0.647													6	6	---	---	---	---	PASS
PSG6	5675	broad.mit.edu	37	19	43585368	43585368	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:43585368G>A	uc002ovi.2	-	2	188	c.95C>T	c.(94-96)ACC>ATC	p.T32I	PSG6_uc010xwk.1_Intron|PSG2_uc002ovr.2_Missense_Mutation_p.T32I|PSG2_uc002ovq.3_Missense_Mutation_p.T32I|PSG2_uc010eiq.1_Missense_Mutation_p.T32I|PSG2_uc002ovs.3_Missense_Mutation_p.T32I|PSG2_uc002ovt.3_Missense_Mutation_p.T32I			Q00889	PSG6_HUMAN	SubName: Full=Putative uncharacterized protein PSG6;	32					female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)				TTGGGCAGTGGTGGGCAGGTT	0.493													13	111	---	---	---	---	PASS
SIGLEC6	946	broad.mit.edu	37	19	52034461	52034461	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:52034461C>T	uc002pwy.2	-	2	542	c.380G>A	c.(379-381)TGG>TAG	p.W127*	SIGLEC6_uc002pwz.2_Nonsense_Mutation_p.W127*|SIGLEC6_uc002pxa.2_Nonsense_Mutation_p.W127*|SIGLEC6_uc010ydb.1_Nonsense_Mutation_p.W80*|SIGLEC6_uc010ydc.1_Nonsense_Mutation_p.W116*|SIGLEC6_uc010eoz.1_Nonsense_Mutation_p.W116*|SIGLEC6_uc010epb.1_Nonsense_Mutation_p.W80*|SIGLEC6_uc010epa.1_Nonsense_Mutation_p.W116*	NM_001245	NP_001236	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6 isoform 1	127	Extracellular (Potential).				cell adhesion|cell-cell signaling	cytoplasm|extracellular region|integral to plasma membrane|membrane fraction|nucleus				ovary(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GTATTTCATCCATTTGGACTT	0.537													14	74	---	---	---	---	PASS
ZNF761	388561	broad.mit.edu	37	19	53959080	53959080	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:53959080G>C	uc010eqp.2	+	7	1777	c.1319G>C	c.(1318-1320)TGT>TCT	p.C440S	ZNF761_uc010ydy.1_Missense_Mutation_p.C386S|ZNF761_uc002qbt.1_Missense_Mutation_p.C386S	NM_001008401	NP_001008401	Q86XN6	ZN761_HUMAN	zinc finger protein 761	440	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00786)		GCTTACAAGTGTAATGAGTGT	0.378													23	87	---	---	---	---	PASS
ZNF813	126017	broad.mit.edu	37	19	53994939	53994939	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:53994939C>G	uc002qbu.2	+	4	1581	c.1453C>G	c.(1453-1455)CAT>GAT	p.H485D	ZNF813_uc010eqq.1_Intron	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	485	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		CCTCGTAATTCATACGGCAAT	0.398													7	41	---	---	---	---	PASS
CNOT3	4849	broad.mit.edu	37	19	54657541	54657541	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:54657541C>G	uc002qdj.1	+	17	2438	c.2127C>G	c.(2125-2127)CAC>CAG	p.H709Q	CNOT3_uc010yel.1_3'UTR|CNOT3_uc002qdi.2_3'UTR|CNOT3_uc002qdk.1_Missense_Mutation_p.H709Q|CNOT3_uc010ere.1_RNA|CNOT3_uc002qdl.2_Missense_Mutation_p.H164Q	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	709					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					TCCAGAGGCACGAGGAGCCCA	0.602													4	77	---	---	---	---	PASS
ZFP28	140612	broad.mit.edu	37	19	57065985	57065985	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:57065985C>T	uc002qnj.2	+	8	1902	c.1831C>T	c.(1831-1833)CAT>TAT	p.H611Y	uc002qnk.1_Intron	NM_020828	NP_065879	Q8NHY6	ZFP28_HUMAN	zinc finger protein 28	611	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		TTTAAGGATTCATACTGGGGA	0.428													5	94	---	---	---	---	PASS
ZIM2	23619	broad.mit.edu	37	19	57293432	57293432	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:57293432C>G	uc002qnr.2	-	9	917	c.535G>C	c.(535-537)GAG>CAG	p.E179Q	uc010ygp.1_Intron|uc002qnp.1_Intron|ZIM2_uc010ygq.1_5'UTR|ZIM2_uc010ygr.1_5'UTR|ZIM2_uc002qnq.2_Missense_Mutation_p.E179Q|ZIM2_uc010etp.2_Missense_Mutation_p.E179Q|ZIM2_uc010ygs.1_Missense_Mutation_p.E179Q	NM_015363	NP_056178	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	179	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		AGCACATCCTCGAAGGTCACC	0.498													7	159	---	---	---	---	PASS
VN1R1	57191	broad.mit.edu	37	19	57967431	57967431	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr19:57967431G>T	uc002qos.1	-	1	424	c.424C>A	c.(424-426)CTC>ATC	p.L142I	ZNF547_uc002qpm.3_Intron	NM_020633	NP_065684	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	142	Helical; Name=3; (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		AATCCATTGAGAAGGCAGATG	0.428													9	48	---	---	---	---	PASS
TMC2	117532	broad.mit.edu	37	20	2591070	2591070	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr20:2591070G>C	uc002wgf.1	+	12	1434	c.1419G>C	c.(1417-1419)GAG>GAC	p.E473D	TMC2_uc002wgg.1_Missense_Mutation_p.E457D|TMC2_uc010zpw.1_Missense_Mutation_p.E305D|TMC2_uc010zpx.1_Missense_Mutation_p.E304D	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2	473	Extracellular (Potential).					integral to membrane				ovary(3)	3						CTCAGGTAGAGATCGTGATGT	0.512													4	101	---	---	---	---	PASS
CDH26	60437	broad.mit.edu	37	20	58545157	58545157	+	Silent	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr20:58545157A>T	uc002ybe.2	+	3	447	c.147A>T	c.(145-147)CTA>CTT	p.L49L	CDH26_uc010zzy.1_RNA	NM_177980	NP_817089	Q8IXH8	CAD26_HUMAN	cadherin-like 26 isoform a	49	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			ACCAGCCTCTACGGCGATCCA	0.502													22	60	---	---	---	---	PASS
NRIP1	8204	broad.mit.edu	37	21	16337633	16337633	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr21:16337633T>C	uc002yjx.2	-	4	3479	c.2881A>G	c.(2881-2883)AAA>GAA	p.K961E		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	961					androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		CCTTTCTTTTTACTGTCAGCC	0.418													12	43	---	---	---	---	PASS
KRTAP27-1	643812	broad.mit.edu	37	21	31709628	31709628	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr21:31709628C>G	uc002ynx.1	-	1	385	c.359G>C	c.(358-360)AGC>ACC	p.S120T		NM_001077711	NP_001071179	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	120						intermediate filament				ovary(2)	2						CTGCTGAGTGCTTTCTGATTG	0.493													9	129	---	---	---	---	PASS
KCNJ6	3763	broad.mit.edu	37	21	39086590	39086590	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr21:39086590C>A	uc011aej.1	-	3	923	c.870G>T	c.(868-870)TGG>TGT	p.W290C	KCNJ6_uc002ywo.2_Missense_Mutation_p.W290C	NM_002240	NP_002231	P48051	IRK6_HUMAN	potassium inwardly-rectifying channel J6	290	Cytoplasmic (By similarity).				synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)	TGGAGATCTCCCAGAAAGGAC	0.483													5	99	---	---	---	---	PASS
POFUT2	23275	broad.mit.edu	37	21	46702293	46702293	+	Silent	SNP	C	G	G			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr21:46702293C>G	uc002zhc.2	-	4	634	c.609G>C	c.(607-609)GCG>GCC	p.A203A	POFUT2_uc002zhb.2_RNA|POFUT2_uc002zhd.2_Silent_p.A203A|POFUT2_uc011afp.1_Silent_p.A203A	NM_133635	NP_598368	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2 isoform C	203					fucose metabolic process	endoplasmic reticulum	peptide-O-fucosyltransferase activity				0				Colorectal(79;0.243)		GCAGCAGGGGCGCCACGATGG	0.632													8	17	---	---	---	---	PASS
SFI1	9814	broad.mit.edu	37	22	31927072	31927072	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr22:31927072T>C	uc003ale.2	+	4	688	c.295T>C	c.(295-297)TGG>CGG	p.W99R	SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Missense_Mutation_p.W99R|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	99					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						CTTATATTTATGGATTCGAAT	0.338													15	35	---	---	---	---	PASS
SMC1B	27127	broad.mit.edu	37	22	45768156	45768156	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr22:45768156A>T	uc003bgc.2	-	13	2127	c.2075T>A	c.(2074-2076)CTC>CAC	p.L692H	SMC1B_uc003bgd.2_Missense_Mutation_p.L692H|SMC1B_uc003bge.1_Missense_Mutation_p.L475H	NM_148674	NP_683515	Q8NDV3	SMC1B_HUMAN	SMC1 structural maintenance of chromosomes	692	Potential.				chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TTCTTTGCGGAGTGTCTTCAT	0.318													6	17	---	---	---	---	PASS
BMX	660	broad.mit.edu	37	X	15565027	15565027	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:15565027C>T	uc004cww.2	+	17	1966	c.1778C>T	c.(1777-1779)TCA>TTA	p.S593L	BMX_uc004cwx.3_Missense_Mutation_p.S593L|BMX_uc004cwy.3_Missense_Mutation_p.S593L	NM_203281	NP_975010	P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	593	Protein kinase.				cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)					AGCAGCAAGTCAGACGTATGG	0.448													10	45	---	---	---	---	PASS
ZFX	7543	broad.mit.edu	37	X	24197618	24197618	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:24197618C>A	uc004dbf.2	+	4	635	c.377C>A	c.(376-378)TCA>TAA	p.S126*	ZFX_uc004dbd.1_Nonsense_Mutation_p.S126*|ZFX_uc010nfx.1_Intron|ZFX_uc004dbe.2_Nonsense_Mutation_p.S126*|ZFX_uc011mjv.1_Nonsense_Mutation_p.S165*|ZFX_uc010nfy.1_Nonsense_Mutation_p.S126*	NM_003410	NP_003401	P17010	ZFX_HUMAN	zinc finger protein, X-linked	126					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(2)	2						ACTTCAGCCTCAATGTCTATG	0.348													15	88	---	---	---	---	PASS
FTSJ1	24140	broad.mit.edu	37	X	48340063	48340063	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:48340063C>T	uc004djo.1	+	9	938	c.615C>T	c.(613-615)TTC>TTT	p.F205F	FTSJ1_uc004djl.2_Silent_p.F205F|FTSJ1_uc004djm.2_Silent_p.F205F|FTSJ1_uc004djn.1_Silent_p.F205F|FTSJ1_uc004djp.1_Silent_p.F205F|FTSJ1_uc011mlw.1_Silent_p.F68F	NM_012280	NP_036412	Q9UET6	RRMJ1_HUMAN	FtsJ homolog 1 isoform a	205					RNA methylation|rRNA processing		methyltransferase activity|nucleic acid binding				0						CCGAGGGCTTCATCCCGGACC	0.622													6	4	---	---	---	---	PASS
TRO	7216	broad.mit.edu	37	X	54957228	54957228	+	Silent	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:54957228C>T	uc004dtq.2	+	12	4178	c.4071C>T	c.(4069-4071)TTC>TTT	p.F1357F	TRO_uc004dts.2_Intron|TRO_uc004dtr.2_Intron|TRO_uc004dtt.2_RNA|TRO_uc004dtu.2_RNA|TRO_uc004dtv.2_Intron|TRO_uc011mok.1_Silent_p.F888F|TRO_uc004dtw.2_Silent_p.F960F|TRO_uc004dtx.2_Silent_p.F740F	NM_001039705	NP_001034794	Q12816	TROP_HUMAN	trophinin isoform 5	1357	55; approximate.|62 X 10 AA approximate tandem repeats.				embryo implantation|homophilic cell adhesion	integral to plasma membrane				ovary(1)	1						GCACGGGCTTCAGTAGTGGAC	0.567													18	24	---	---	---	---	PASS
HEPH	9843	broad.mit.edu	37	X	65417698	65417698	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:65417698G>A	uc011moz.1	+	10	1744	c.1684G>A	c.(1684-1686)GTG>ATG	p.V562M	HEPH_uc004dwn.2_Missense_Mutation_p.V562M|HEPH_uc004dwo.2_Missense_Mutation_p.V292M|HEPH_uc010nkr.2_Intron|HEPH_uc011mpa.1_Missense_Mutation_p.V562M	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	559	Extracellular (Potential).|Plastocyanin-like 3.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9						CCCGCTGCTGGTGTGCAGGGC	0.567													6	4	---	---	---	---	PASS
KIF4A	24137	broad.mit.edu	37	X	69561758	69561758	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:69561758C>T	uc004dyg.2	+	11	1370	c.1243C>T	c.(1243-1245)CAG>TAG	p.Q415*	KIF4A_uc010nkw.2_Nonsense_Mutation_p.Q415*|KIF4A_uc004dyf.1_Nonsense_Mutation_p.Q415*	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	415	Potential.				anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4						TCAGACAGCCCAGATGTTGGA	0.418													5	56	---	---	---	---	PASS
ZCCHC13	389874	broad.mit.edu	37	X	73524496	73524496	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:73524496G>A	uc004ebs.3	+	1	472	c.395G>A	c.(394-396)CGA>CAA	p.R132Q		NM_203303	NP_976048	Q8WW36	ZCH13_HUMAN	zinc finger, CCHC domain containing 13	132	CCHC-type 6.						nucleic acid binding|zinc ion binding				0						AAGTGTTACCGATGCGGCGAG	0.552													13	16	---	---	---	---	PASS
TBX22	50945	broad.mit.edu	37	X	79286003	79286003	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:79286003G>A	uc010nmg.1	+	9	1090	c.956G>A	c.(955-957)AGC>AAC	p.S319N	TBX22_uc004edi.1_Missense_Mutation_p.S199N|TBX22_uc004edj.1_Missense_Mutation_p.S319N	NM_001109878	NP_001103348	Q9Y458	TBX22_HUMAN	T-box 22 isoform 1	319					multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(7)|large_intestine(3)|central_nervous_system(2)|breast(1)|skin(1)|ovary(1)	15						ACAGGTGGAAGCAGTGGCTCA	0.423													9	22	---	---	---	---	PASS
OCRL	4952	broad.mit.edu	37	X	128709224	128709224	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:128709224G>A	uc004euq.2	+	16	1875	c.1710G>A	c.(1708-1710)AGG>AGA	p.R570R	OCRL_uc004eur.2_Silent_p.R570R	NM_000276	NP_000267	Q01968	OCRL_HUMAN	phosphatidylinositol polyphosphate 5-phosphatase	570					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	clathrin-coated vesicle|cytosol|early endosome|Golgi stack|Golgi-associated vesicle	GTPase activator activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			lung(2)|ovary(1)|kidney(1)	4						TCAGCAGGAGGGAGGTGAGCA	0.403													12	11	---	---	---	---	PASS
ELF4	2000	broad.mit.edu	37	X	129203604	129203604	+	Silent	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:129203604C>A	uc004evd.3	-	8	1243	c.858G>T	c.(856-858)CTG>CTT	p.L286L	ELF4_uc004eve.3_Silent_p.L286L	NM_001421	NP_001412	Q99607	ELF4_HUMAN	E74-like factor 4	286	ETS.				natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter	PML body	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						ACTGGTACACCAGCCTCTGCC	0.577			T	ERG	AML								4	31	---	---	---	---	PASS
ENOX2	10495	broad.mit.edu	37	X	129790626	129790626	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:129790626C>A	uc004evw.2	-	11	1563	c.1145G>T	c.(1144-1146)CGA>CTA	p.R382L	ENOX2_uc004evx.2_Missense_Mutation_p.R353L|ENOX2_uc004evy.2_Missense_Mutation_p.R353L|ENOX2_uc004evv.2_Missense_Mutation_p.R209L	NM_182314	NP_872114	Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2 isoform b	382	Potential.				cell growth|electron transport chain|regulation of growth|transport|ultradian rhythm	cytosol|external side of plasma membrane|extracellular space	nucleic acid binding|nucleotide binding|protein disulfide oxidoreductase activity			ovary(1)	1						TTCTTCTTCTCGCCTGATTCC	0.313													3	40	---	---	---	---	PASS
MAGEC1	9947	broad.mit.edu	37	X	140996085	140996085	+	Silent	SNP	G	A	A			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:140996085G>A	uc004fbt.2	+	4	3181	c.2895G>A	c.(2893-2895)CTG>CTA	p.L965L	MAGEC1_uc010nsl.1_Silent_p.L32L	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	965	MAGE.						protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					GCATTTCCCTGAGAGAAGTGG	0.498										HNSCC(15;0.026)			7	81	---	---	---	---	PASS
FOSL2	2355	broad.mit.edu	37	2	28634924	28634928	+	Frame_Shift_Del	DEL	AGCGC	-	-	rs145499484	by1000genomes	TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr2:28634924_28634928delAGCGC	uc002rma.2	+	4	1399_1403	c.590_594delAGCGC	c.(589-594)GAGCGCfs	p.E197fs	FOSL2_uc010ymi.1_Frame_Shift_Del_p.E158fs	NM_005253	NP_005244	P15408	FOSL2_HUMAN	FOS-like antigen 2	197_198					cell death|regulation of transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(172;0.155)					AGCCCCGAGGAGCGCCGATCGCCCC	0.639													33	16	---	---	---	---	
NIPBL	25836	broad.mit.edu	37	5	37036542	37036542	+	Frame_Shift_Del	DEL	T	-	-			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr5:37036542delT	uc003jkl.3	+	33	6423	c.5924delT	c.(5923-5925)GTTfs	p.V1975fs	NIPBL_uc003jkk.3_Frame_Shift_Del_p.V1975fs	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1975	HEAT 3.				brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			ACTCAACTTGTTGATAACCTA	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	43283606	43283606	+	RNA	DEL	A	-	-			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chr11:43283606delA	uc001mxe.1	-	2		c.1330delT								Homo sapiens cDNA FLJ44864 fis, clone BRALZ2013621, moderately similar to Heterogeneous nuclear ribonucleoprotein K.																		AAGCAAATGTAAAAAAAAAAA	0.388													4	2	---	---	---	---	
DCAF12L1	139170	broad.mit.edu	37	X	125685932	125685932	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2771-01A-01D-0983-08	TCGA-66-2771-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	58c73372-223f-400a-a2df-073a78c58b62	1c33d8c0-dd62-474a-8047-4cd4410deafe	g.chrX:125685932delC	uc004eul.2	-	1	911	c.660delG	c.(658-660)TGGfs	p.W220fs		NM_178470	NP_848565	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	220	WD 2.									skin(3)|ovary(1)	4						GGTCCATCCGCCACAGCGCCA	0.652													12	8	---	---	---	---