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
CAMTA1	23261	broad.mit.edu	37	1	7725006	7725006	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr1:7725006G>A	uc001aoi.2	+	9	2606	c.2399G>A	c.(2398-2400)AGC>AAC	p.S800N		NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	800					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)		TCGGGGGACAGCACGGCGCTC	0.647000												
KIRREL	55243	broad.mit.edu	37	1	158045982	158045982	+	Silent	SNP	G	G	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr1:158045982G>A	uc001frn.3	+	2	536	c.132G>A	c.(130-132)CTG>CTA	p.L44L	KIRREL_uc010pib.1_Intron|KIRREL_uc009wsq.2_5'UTR	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor	44	Extracellular (Potential).|Ig-like C2-type 1.					integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)					CCTGTGTGCTGCTCAACTACT	0.632000												
PLXNA2	5362	broad.mit.edu	37	1	208216499	208216499	+	Missense_Mutation	SNP	G	G	C			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr1:208216499G>C	uc001hgz.2	-	21	4682	c.3924C>G	c.(3922-3924)GAC>GAG	p.D1308E		NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	1308	Potential.|Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TTCCTGAGCGGTCCAGGTCAC	0.582000												
ITIH5	80760	broad.mit.edu	37	10	7608308	7608308	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr10:7608308G>A	uc001ijq.2	-	13	2291	c.2212C>T	c.(2212-2214)CGC>TGC	p.R738C	ITIH5_uc001ijp.2_Missense_Mutation_p.R524C	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	738					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4						AAGTAAGTGCGCTGTTTCTTG	0.502000												
C10orf54	64115	broad.mit.edu	37	10	73521610	73521610	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr10:73521610G>A	uc001jsd.2	-	2	397	c.256C>T	c.(256-258)CGC>TGC	p.R86C	CDH23_uc001jrx.3_Intron|C10orf54_uc001jse.2_5'UTR|C10orf54_uc009xqm.2_Intron|C10orf54_uc001jsf.1_Missense_Mutation_p.R86C	NM_022153	NP_071436	Q9H7M9	GI24_HUMAN	platelet receptor Gi24 precursor	86	Ig-like.|Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)|central_nervous_system(1)	3						ATGGGCCGGCGCTCTGAGCAG	0.652000												
RNLS	55328	broad.mit.edu	37	10	90341418	90341418	+	Silent	SNP	C	C	T	rs148977593		TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr10:90341418C>T	uc001kfe.2	-	3	408	c.273G>A	c.(271-273)TCG>TCA	p.S91S	RNLS_uc010qms.1_Intron|RNLS_uc001kfd.2_Silent_p.S91S	NM_001031709	NP_001026879	Q5VYX0	RNLS_HUMAN	renalase isoform 1	91						extracellular region	oxidoreductase activity			ovary(1)	1						CTTCAATAGGCGAGCTTAGAG	0.348000												
CWF19L1	55280	broad.mit.edu	37	10	102006563	102006563	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr10:102006563G>A	uc001kqq.1	-	8	925	c.838C>T	c.(838-840)CTT>TTT	p.L280F	CWF19L1_uc001kqs.1_Missense_Mutation_p.L32F|CWF19L1_uc001kqr.1_Missense_Mutation_p.L280F|CWF19L1_uc001kqt.1_5'UTR|CWF19L1_uc010qpn.1_Missense_Mutation_p.L143F	NM_018294	NP_060764	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control	280							catalytic activity				0		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		ACAGGGGCAAGAATTTGCTTT	0.398000												
PHLDA2	7262	broad.mit.edu	37	11	2950367	2950367	+	Missense_Mutation	SNP	G	G	T			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr11:2950367G>T	uc001lxa.1	-	1	284	c.228C>A	c.(226-228)GAC>GAA	p.D76E		NM_003311	NP_003302	Q53GA4	PHLA2_HUMAN	pleckstrin homology-like domain family A member	76	PH.				apoptosis	cytoplasm|membrane					0		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTCCTTGTGGTCGGTGGTGA	0.662000												
PAMR1	25891	broad.mit.edu	37	11	35513643	35513643	+	Missense_Mutation	SNP	C	C	G			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr11:35513643C>G	uc001mwg.2	-	3	372	c.329G>C	c.(328-330)GGG>GCG	p.G110A	PAMR1_uc001mwf.2_Missense_Mutation_p.G110A|PAMR1_uc010rew.1_Missense_Mutation_p.G110A|PAMR1_uc010rex.1_Missense_Mutation_p.G70A	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform	110					proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2						ACAGTAGAACCCCTTCACATA	0.502000												
TMEM126B	55863	broad.mit.edu	37	11	85347202	85347202	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr11:85347202G>A	uc001pao.2	+	6	784	c.532G>A	c.(532-534)GGA>AGA	p.G178R	TMEM126B_uc001pap.2_Missense_Mutation_p.G178R|TMEM126B_uc001paq.1_3'UTR	NM_018480	NP_060950	Q8IUX1	T126B_HUMAN	transmembrane protein 126B	208	Helical; (Potential).					integral to membrane					0		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GATTATGTTTGGAATATTAAA	0.348000												
ZBTB39	9880	broad.mit.edu	37	12	57397688	57397688	+	Silent	SNP	C	C	T			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr12:57397688C>T	uc001sml.1	-	2	1100	c.1014G>A	c.(1012-1014)CGG>CGA	p.R338R	RDH16_uc010sqx.1_5'Flank	NM_014830	NP_055645	O15060	ZBT39_HUMAN	zinc finger and BTB domain containing 39	338					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1						CCTTATTCTCCCGATTGTCAT	0.517000												
BTBD11	121551	broad.mit.edu	37	12	108004034	108004034	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr12:108004034G>A	uc001tmk.1	+	5	2232	c.1711G>A	c.(1711-1713)GAC>AAC	p.D571N	BTBD11_uc009zut.1_Missense_Mutation_p.D571N|BTBD11_uc001tmj.2_Missense_Mutation_p.D571N|BTBD11_uc001tml.1_Missense_Mutation_p.D108N	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a	571						integral to membrane	DNA binding			skin(2)|ovary(1)	3						GTTTAAGCAGGACCTGGGTTT	0.562000											OREG0022090	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
SPRED1	161742	broad.mit.edu	37	15	38643405	38643405	+	Missense_Mutation	SNP	A	A	T			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr15:38643405A>T	uc001zka.3	+	7	1210	c.875A>T	c.(874-876)TAT>TTT	p.Y292F		NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain	292					inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		AAATCAGACTATCTGTACTCT	0.383000									Legius_syndrome			
FSIP1	161835	broad.mit.edu	37	15	40018838	40018838	+	Silent	SNP	G	G	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr15:40018838G>A	uc001zki.2	-	9	1220	c.1002C>T	c.(1000-1002)TCC>TCT	p.S334S		NM_152597	NP_689810	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	334										ovary(2)|skin(1)	3		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		AAATTGTAGGGGAGGCTGCAG	0.423000												
USP7	7874	broad.mit.edu	37	16	9009114	9009114	+	Missense_Mutation	SNP	T	T	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr16:9009114T>A	uc002czl.2	-	10	1274	c.1075A>T	c.(1075-1077)AAT>TAT	p.N359Y	USP7_uc010uyk.1_Missense_Mutation_p.N260Y|USP7_uc010uyj.1_Missense_Mutation_p.N260Y|USP7_uc002czk.2_Missense_Mutation_p.N343Y|USP7_uc010uyl.1_RNA	NM_003470	NP_003461	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7	359					interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3						CACTTACTATTTTTCTTTCCT	0.294000												
STX4	6810	broad.mit.edu	37	16	31051116	31051116	+	Missense_Mutation	SNP	G	G	T			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr16:31051116G>T	uc002eal.2	+	10	1110	c.886G>T	c.(886-888)GTT>TTT	p.V296F	STX4_uc002eak.2_Missense_Mutation_p.V294F|STX4_uc002eam.2_Missense_Mutation_p.V218F|uc002ean.1_5'Flank	NM_004604	NP_004595	Q12846	STX4_HUMAN	syntaxin 4	296	Helical; Anchor for type IV membrane protein; (Potential).|Interaction with CENPF (By similarity).				intracellular protein transport|platelet activation|post-Golgi vesicle-mediated transport	basolateral plasma membrane|cell surface|cytosol|integral to membrane|plasma membrane enriched fraction|specific granule|vacuole	SNAP receptor activity				0						CGTCACAGTGGTTGGATAATG	0.587000												
FTO	79068	broad.mit.edu	37	16	53913791	53913791	+	Silent	SNP	C	C	T			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr16:53913791C>T	uc002ehr.2	+	6	1233	c.1011C>T	c.(1009-1011)CGC>CGT	p.R337R	FTO_uc010vha.1_Silent_p.R41R	NM_001080432	NP_001073901	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	337					DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						TTTTACAACGCTGTCAGTTGG	0.408000												
LRRC46	90506	broad.mit.edu	37	17	45913414	45913414	+	Missense_Mutation	SNP	G	G	C			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr17:45913414G>C	uc002ima.2	+	6	654	c.398G>C	c.(397-399)AGC>ACC	p.S133T	LRRC46_uc002imb.2_Missense_Mutation_p.S86T	NM_033413	NP_219481	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	133										ovary(1)	1						TTCCCCCAGAGCCTTCTCATC	0.448000												
MED13	9969	broad.mit.edu	37	17	60140634	60140634	+	Missense_Mutation	SNP	T	T	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr17:60140634T>A	uc002izo.2	-	2	172	c.95A>T	c.(94-96)AAA>ATA	p.K32I		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	32					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						CCATACATATTTTTTCCACTT	0.393000												
MUC16	94025	broad.mit.edu	37	19	9085666	9085666	+	Missense_Mutation	SNP	G	G	T	rs34029599		TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr19:9085666G>T	uc002mkp.2	-	1	6353	c.6149C>A	c.(6148-6150)TCC>TAC	p.S2050Y		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	2050	Ser-rich.|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						CCATAGCCAGGAAGTGATTGC	0.483000												
NCAN	1463	broad.mit.edu	37	19	19338422	19338422	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr19:19338422G>A	uc002nlz.2	+	8	2092	c.1993G>A	c.(1993-1995)GCC>ACC	p.A665T	NCAN_uc010ecc.1_Missense_Mutation_p.A229T	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	665					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			TGAGGCCACCGCCACGGCTCC	0.607000												
ZNF534	147658	broad.mit.edu	37	19	52941686	52941686	+	Missense_Mutation	SNP	C	C	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr19:52941686C>A	uc002pzk.2	+	4	1073	c.1012C>A	c.(1012-1014)CCT>ACT	p.P338T	ZNF534_uc002pzj.1_Intron|ZNF534_uc010epo.1_Intron|ZNF534_uc002pzl.2_Missense_Mutation_p.P325T	NM_001143939	NP_001137411	Q76KX8	ZN534_HUMAN	zinc finger protein 534 isoform 2	338					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGGAGAGAAACCTTATGATTG	0.408000												
ST3GAL5	8869	broad.mit.edu	37	2	86075089	86075089	+	Missense_Mutation	SNP	T	T	C			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr2:86075089T>C	uc002sqq.1	-	4	686	c.557A>G	c.(556-558)CAC>CGC	p.H186R	ST3GAL5_uc010fgq.1_Missense_Mutation_p.H58R|ST3GAL5_uc002sqp.1_Missense_Mutation_p.H163R	NM_003896	NP_003887	Q9UNP4	SIAT9_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase	186	Lumenal (Potential).				ganglioside biosynthetic process|protein glycosylation	integral to Golgi membrane|integral to plasma membrane	lactosylceramide alpha-2,3-sialyltransferase activity|neolactotetraosylceramide alpha-2,3-sialyltransferase activity				0						GGCTTTCAAGTGTTCAGGGAG	0.527000												
BUB1	699	broad.mit.edu	37	2	111419292	111419292	+	Missense_Mutation	SNP	C	C	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr2:111419292C>A	uc002tgc.2	-	10	1196	c.1084G>T	c.(1084-1086)GTT>TTT	p.V362F	BUB1_uc010yxh.1_Missense_Mutation_p.V342F|BUB1_uc010fkb.2_Missense_Mutation_p.V362F|BUB1_uc002tgd.2_Missense_Mutation_p.V362F	NM_004336	NP_004327	O43683	BUB1_HUMAN	budding uninhibited by benzimidazoles 1	362					apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)|breast(2)|stomach(1)|ovary(1)|kidney(1)	7		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		AAAGGAGGAACAACAGGAGGT	0.517000												
NINL	22981	broad.mit.edu	37	20	25470531	25470531	+	Missense_Mutation	SNP	C	C	G			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr20:25470531C>G	uc002wux.1	-	12	1650	c.1576G>C	c.(1576-1578)GAG>CAG	p.E526Q	NINL_uc010gdn.1_Missense_Mutation_p.E526Q|NINL_uc010gdo.1_Missense_Mutation_p.E309Q	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like	526	Potential.				G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						AGCACAAACTCCAGGTCCTTC	0.597000												
LMOD3	56203	broad.mit.edu	37	3	69168779	69168779	+	Missense_Mutation	SNP	C	C	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr3:69168779C>A	uc003dns.2	-	2	936	c.727G>T	c.(727-729)GGG>TGG	p.G243W	LMOD3_uc003dnt.2_Missense_Mutation_p.G243W	NM_198271	NP_938012	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	243						cytoplasm|cytoskeleton	tropomyosin binding			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		CTCAAGCTCCCATCCAGGTCT	0.398000												
LMOD3	56203	broad.mit.edu	37	3	69168781	69168781	+	Missense_Mutation	SNP	T	T	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr3:69168781T>A	uc003dns.2	-	2	934	c.725A>T	c.(724-726)GAT>GTT	p.D242V	LMOD3_uc003dnt.2_Missense_Mutation_p.D242V	NM_198271	NP_938012	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	242						cytoplasm|cytoskeleton	tropomyosin binding			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		CAAGCTCCCATCCAGGTCTGT	0.403000												
BAI3	577	broad.mit.edu	37	6	70064152	70064152	+	Silent	SNP	A	A	C			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr6:70064152A>C	uc003pev.3	+	27	3935	c.3487A>C	c.(3487-3489)AGA>CGA	p.R1163R	BAI3_uc010kak.2_Silent_p.R1163R|BAI3_uc011dxx.1_Silent_p.R369R	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1163	Cytoplasmic (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				ATGCCGATTGAGAAACTGTCA	0.398000												
NCOA2	10499	broad.mit.edu	37	8	71071839	71071839	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr8:71071839G>A	uc003xyn.1	-	10	1187	c.1025C>T	c.(1024-1026)TCT>TTT	p.S342F		NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	342					cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			AGTGCCATCAGACAAGGAAAA	0.413000			T	RUNXBP2	AML							
KIAA2026	158358	broad.mit.edu	37	9	5922218	5922218	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr9:5922218C>T	uc003zjq.3	-	8	3994	c.3778G>A	c.(3778-3780)GCT>ACT	p.A1260T	KIAA2026_uc010mht.2_Missense_Mutation_p.A435T	NM_001017969	NP_001017969	Q5HYC2	K2026_HUMAN	hypothetical protein LOC158358	1260										ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		GAAGAATCAGCAGTCTGTTGT	0.438000												
TAF1L	138474	broad.mit.edu	37	9	32631710	32631710	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr9:32631710C>T	uc003zrg.1	-	1	3958	c.3868G>A	c.(3868-3870)GGA>AGA	p.G1290R	uc003zrh.1_5'Flank	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1290					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CTCATATGTCCAATGGCACCA	0.473000												
MED12	9968	broad.mit.edu	37	X	70349258	70349258	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chrX:70349258C>T	uc004dyy.2	+	26	3869	c.3670C>T	c.(3670-3672)CTC>TTC	p.L1224F	MED12_uc011mpq.1_Missense_Mutation_p.L1224F|MED12_uc004dyz.2_Missense_Mutation_p.L1224F|MED12_uc004dza.2_Missense_Mutation_p.L1071F|MED12_uc010nla.2_5'Flank	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1224					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)					GTTTGCTGTTCTCAAGGCTGT	0.562000											OREG0019857	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
ALS2CR8	79800	broad.mit.edu	37	2	203848308	203848309	+	Frame_Shift_Ins	INS	-	-	A			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr2:203848307_203848308C>CA	uc002uzo.2	+	15	2418_2419	c.2138_2139C>CA	c.(2137-2139)gcafs	p.A713fs	ALS2CR8_uc010zia.1_Frame_Shift_Ins_p.A637fs|ALS2CR8_uc010zib.1_Frame_Shift_Ins_p.A637fs|ALS2CR8_uc010zic.1_Frame_Shift_Ins_p.A625fs|ALS2CR8_uc002uzp.2_Frame_Shift_Ins_p.A713fs	NM_001104586	NP_079020	Q8N187	AL2S8_HUMAN	Homo sapiens amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8 (ALS2CR8), mRNA.	713										breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	20						TCTATGGAAGCAAAAAAAACTG	0.327												
SPHKAP	80309	broad.mit.edu	37	2	228886571	228886572	+	Frame_Shift_Ins	INS	-	-	CCAG			TCGA-BR-4294-01A-01D-1126-08	TCGA-BR-4294-11A-01D-1126-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cb82319e-a676-4d80-b3e6-95f29d9266b3	5afac6e7-55d3-49a2-89e4-6509ed424a83	g.chr2:228886570_228886571A>ACCAG	uc002vpq.2	-	5	600_601	c.553_554T>CTGGT	c.(553-555)gtgfs	p.V185fs	SPHKAP_uc002vpp.2_Frame_Shift_Ins_p.V185fs|SPHKAP_uc010zlx.1_Frame_Shift_Ins_p.V185fs	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	Homo sapiens SPHK1 interactor, AKAP domain containing (SPHKAP), transcript variant 1, mRNA.	185						cytoplasm	protein binding			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCGCTCCTGCACCAGTTCCAGA	0.455