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_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
RP11-146E13.4	0	broad.mit.edu	37	14	19857036	19857036	+	RNA	SNP	A	A	G			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr14:19857036A>G	ENST00000548109.1	+	0	72																											CTGGATAATAAAGTTCATCTC	0.373000													6	199					0	0	0.021553	0	0
MMS22L	253714	broad.mit.edu	37	6	97702537	97702537	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr6:97702537T>C	ENST00000275053.4	-	10	1280	c.1015A>G	c.(1015-1017)Atg>Gtg	p.M339V	MMS22L_ENST00000369251.2_Missense_Mutation_p.M339V	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	339					double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding			breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						ATTACAGGCATAGAGGATCTT	0.368000													7	152					0	0	0.038147	0	0
AGAP2	116986	broad.mit.edu	37	12	58129157	58129157	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr12:58129157G>A	ENST00000257897.3	-	2	299	c.214C>T	c.(214-216)Cgc>Tgc	p.R72C	AGAP2_ENST00000547588.1_Missense_Mutation_p.R408C	NM_014770.3	NP_055585.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	408					axon guidance|negative regulation of neuron apoptosis|negative regulation of protein catabolic process|protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	mitochondrion|nucleolus	ARF GTPase activator activity|GTP binding|zinc ion binding	p.R72S(1)|p.R408S(1)		breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						CCTACCAGGCGCAGTTCAGGA	0.567000													3	38					0	0	0.009096	0	0
FDXACB1	91893	broad.mit.edu	37	11	111745983	111745983	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr11:111745983C>T	ENST00000260257.4	-	5	1585	c.1538G>A	c.(1537-1539)cGt>cAt	p.R513H	ALG9_ENST00000527377.1_Intron|FDXACB1_ENST00000542429.1_Missense_Mutation_p.R364H|ALG9_ENST00000524880.1_Intron	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	513					phenylalanyl-tRNA aminoacylation|tRNA processing		ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						TTTCAGGAAACGGTTATCAAA	0.383000													4	89					0	0	0.009096	0	0
CIC	23152	broad.mit.edu	37	19	42791718	42791718	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr19:42791718C>T	ENST00000572681.2	+	6	3399	c.3331C>T	c.(3331-3333)Cgg>Tgg	p.R1111W	CIC_ENST00000160740.3_Missense_Mutation_p.R202W|CIC_ENST00000575354.2_Missense_Mutation_p.R202W			Q96RK0	CIC_HUMAN	capicua transcriptional repressor	202	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding	p.R202W(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CCACATCCGGCGGCCCATGAA	0.622000			"""Mis, F, S"""		oligodendroglioma								51	28					0	0	0.139131	0	0
USP6	9098	broad.mit.edu	37	17	5074028	5074028	+	Missense_Mutation	SNP	A	A	T			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr17:5074028A>T	ENST00000574788.1	+	36	6002	c.3772A>T	c.(3772-3774)Act>Tct	p.T1258S	USP6_ENST00000304328.5_Missense_Mutation_p.T941S|USP6_ENST00000250066.6_Missense_Mutation_p.T1258S|USP6_ENST00000332776.4_3'UTR			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6 (Tre-2 oncogene)	1258					protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						AGAGCTGGTCACTCCTCAGGA	0.572000			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								5	141					0	0	0.021553	0	0
RAB20	55647	broad.mit.edu	37	13	111176298	111176298	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr13:111176298C>T	ENST00000267328.3	-	2	632	c.419G>A	c.(418-420)cGt>cAt	p.R140H		NM_017817.1	NP_060287.1	Q9NX57	RAB20_HUMAN	RAB20, member RAS oncogene family	140					protein transport|small GTPase mediated signal transduction	Golgi apparatus	GTP binding			endometrium(2)|large_intestine(2)|lung(3)	7	all_cancers(4;1.54e-11)|all_epithelial(4;1.22e-06)|all_lung(23;1e-05)|Lung NSC(43;0.000453)|Colorectal(4;0.00323)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.197)			TGGGGAGACACGGTCCCCAGC	0.577000													4	150					0	0	0.009096	0	0
SRSF12	135295	broad.mit.edu	37	6	89816964	89816964	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr6:89816964G>A	ENST00000452027.2	-	2	272	c.79C>T	c.(79-81)Cgc>Tgc	p.R27C		NM_080743.4	NP_542781.3	Q8WXF0	SRS12_HUMAN	serine/arginine-rich splicing factor 12	27	RRM.				assembly of spliceosomal tri-snRNP|cytoplasmic transport|negative regulation of nuclear mRNA splicing, via spliceosome|nuclear mRNA 5'-splice site recognition|regulation of alternative nuclear mRNA splicing, via spliceosome	nucleoplasm	nucleotide binding|RNA binding|RS domain binding|unfolded protein binding	p.R27C(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)	8						AACTCACGGCGCAAGTCCTCA	0.398000													4	111					0	0	0.009096	0	0
NOTCH1	4851	broad.mit.edu	37	9	139412204	139412204	+	Splice_Site	SNP	C	C	G			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr9:139412204C>G	ENST00000277541.6	-	8	1516	c.1441_splice	c.e8+1	p.G481_splice		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	481	EGF-like 12; calcium-binding (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity	p.G481S(2)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GCCGACGCACCGGGCATGCAG	0.667000			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			43	74					0	0	0.117977	0	0
RYR3	6263	broad.mit.edu	37	15	34157386	34157386	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr15:34157386G>A	ENST00000389232.4	+	104	14642	c.14572G>A	c.(14572-14574)Ggt>Agt	p.G4858S	RYR3_ENST00000415757.3_Missense_Mutation_p.G4853S	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4858					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CTTCCCAGCCGGTGACTGCTT	0.393000													3	90					0	0	0.115264	0	0
PSG4	5672	broad.mit.edu	37	19	43702179	43702179	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr19:43702179G>A	ENST00000405312.3	-	3	916	c.679C>T	c.(679-681)Cgc>Tgc	p.R227C	PSG4_ENST00000244295.9_Missense_Mutation_p.R227C|PSG4_ENST00000433626.2_Intron	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	227	Ig-like C2-type 1.				defense response|female pregnancy	extracellular region				central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				GGGTCACTGCGGCTGGCACTC	0.522000													9	260					0	0	0.093190	0	0
PRDM10	56980	broad.mit.edu	37	11	129795084	129795084	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr11:129795084C>T	ENST00000358825.5	-	13	1814	c.1583G>A	c.(1582-1584)cGg>cAg	p.R528Q	PRDM10_ENST00000526082.1_Missense_Mutation_p.R442Q|PRDM10_ENST00000304538.6_Missense_Mutation_p.R438Q|PRDM10_ENST00000528746.1_Missense_Mutation_p.R498Q|PRDM10_ENST00000423662.2_Missense_Mutation_p.R442Q|PRDM10_ENST00000360871.3_Missense_Mutation_p.R524Q	NM_020228.2	NP_064613.2	Q9NQV6	PRD10_HUMAN	PR domain containing 10	528					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TTTAAAAGGCCGGAAGGACTT	0.483000													6	248					0	0	0.038147	0	0
TCFL5	10732	broad.mit.edu	37	20	61488943	61488943	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr20:61488943G>A	ENST00000335351.3	-	4	1134	c.1042C>T	c.(1042-1044)Cgt>Tgt	p.R348C	TCFL5_ENST00000217162.5_Missense_Mutation_p.R300C	NM_006602.2	NP_006593.2	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 (basic helix-loop-helix)	348	R3 epitope (recognized by Chagas's antibodies).				cell differentiation|multicellular organismal development|regulation of cell differentiation|regulation of cell proliferation|spermatogenesis|transcription from RNA polymerase II promoter		DNA binding|sequence-specific DNA binding transcription factor activity	p.R348C(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(1)|urinary_tract(1)	9	Breast(26;5.68e-08)					TCCAACTGACGCATTCTACTC	0.463000													84	134					0	0	0.139131	0	0
TUBGCP6	85378	broad.mit.edu	37	22	50658942	50658942	+	Silent	SNP	G	G	C	rs151156085	byFrequency	TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr22:50658942G>C	ENST00000439308.2	-	16	4338	c.3846C>G	c.(3844-3846)ctC>ctG	p.L1282L	TUBGCP6_ENST00000248846.5_Silent_p.L1282L|TUBGCP6_ENST00000491449.1_5'UTR	NM_020461.3	NP_065194.2	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1282					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		CTTCTGGTGAGAGAGCCCCCA	0.657000													3	46					0	0	0.115264	0	0
PKD1	5310	broad.mit.edu	37	16	2155892	2155892	+	Silent	SNP	A	A	G	rs149467954	by1000genomes	TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr16:2155892A>G	ENST00000262304.4	-	20	8045	c.7837T>C	c.(7837-7839)Ttg>Ctg	p.L2613L	PKD1_ENST00000423118.1_Silent_p.L2613L|PKD1_ENST00000561991.1_5'UTR	NM_001009944.2	NP_001009944.2	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2613	REJ.		Missing (in ADPKD1; could be a polymorphism).		calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding	p.L2613L(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ACCAGGGCCAACGAGTACTCG	0.657000													4	76					0	0	0.009096	0	0
SSH2	85464	broad.mit.edu	37	17	27994187	27994187	+	Silent	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr17:27994187G>A	ENST00000269033.3	-	9	934	c.783C>T	c.(781-783)atC>atT	p.I261I	RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Silent_p.I288I	NM_033389.2	NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	261					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCTGCATCATGATCTCCCTTA	0.383000													51	100					0	0	0.139131	0	0
SMC4	10051	broad.mit.edu	37	3	160141575	160141575	+	Missense_Mutation	SNP	G	G	C			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr3:160141575G>C	ENST00000357388.3	+	15	2723	c.2272G>C	c.(2272-2274)Gta>Cta	p.V758L	SMC4_ENST00000462787.1_Missense_Mutation_p.V758L|SMC4_ENST00000469762.1_Missense_Mutation_p.V733L|SMC4_ENST00000344722.5_Missense_Mutation_p.V758L|SMC4_ENST00000360111.2_Missense_Mutation_p.V758L|RP11-432B6.3_ENST00000483754.1_Intron	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	758	Flexible hinge.				cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TGGAAGCAAAGTAATGAAAGG	0.383000													30	133					0	0	0.074837	0	0
FBP2	8789	broad.mit.edu	37	9	97333814	97333814	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr9:97333814G>A	ENST00000375337.3	-	4	563	c.497C>T	c.(496-498)gCg>gTg	p.A166V		NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	166					fructose metabolic process|gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|metal ion binding			endometrium(1)|large_intestine(3)|lung(5)	9		Acute lymphoblastic leukemia(62;0.136)				ACCGTACAGCGCATAACCTGC	0.547000													5	166					0	0	0.014758	0	0
ANKRD11	29123	broad.mit.edu	37	16	89350191	89350191	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr16:89350191C>T	ENST00000301030.4	-	9	3219	c.2759G>A	c.(2758-2760)aGg>aAg	p.R920K	ANKRD11_ENST00000378330.2_Missense_Mutation_p.R920K	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	920	Lys-rich.					nucleus				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CTGCTCTTTCCTCTTCTCAGA	0.547000													104	204					0	0	0.139131	0	0
DNM1P46	0	broad.mit.edu	37	15	100332827	100332827	+	RNA	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr15:100332827G>A	ENST00000341853.1	-	0	1364					NR_003260.1																						TGACTACAACGAGGGACACAG	0.612000													27	22					0	0	0.125774	0	0
ST8SIA1	6489	broad.mit.edu	37	12	22408291	22408291	+	Silent	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr12:22408291G>A	ENST00000396037.4	-	3	895	c.414C>T	c.(412-414)tgC>tgT	p.C138C	ST8SIA1_ENST00000539510.1_Intron	NM_003034.3	NP_003025.1	Q92185	SIA8A_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	138					glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity	p.C138F(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	25						CCACCACCGCGCATTTCTTCA	0.483000													5	285					0	0	0.014758	0	0
PLCB1	23236	broad.mit.edu	37	20	8862304	8862304	+	Missense_Mutation	SNP	A	A	C			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr20:8862304A>C	ENST00000338037.6	+	32	3486	c.3459A>C	c.(3457-3459)aaA>aaC	p.K1153N	PLCB1_ENST00000378641.3_3'UTR	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	1153					activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						ACCAAGACAAATTCAAAAGAC	0.468000													159	228					0	0	0.139131	0	0
KCNU1	157855	broad.mit.edu	37	8	36766859	36766859	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr8:36766859C>T	ENST00000399881.3	+	21	2174	c.2137C>T	c.(2137-2139)Cgg>Tgg	p.R713W		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	713	Segment S9.					voltage-gated potassium channel complex	binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity	p.R713W(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		GTATAAGTTTCGGAACCATAT	0.468000													238	352					0	0	0.139131	0	0
SBF1	6305	broad.mit.edu	37	22	50898523	50898523	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr22:50898523T>C	ENST00000380817.2	-	26	3532	c.3349A>G	c.(3349-3351)Acc>Gcc	p.T1117A	SBF1_ENST00000390679.3_Missense_Mutation_p.T1117A|SBF1_ENST00000348911.6_Missense_Mutation_p.T1118A	NM_002972.2	NP_002963.2	O95248	MTMR5_HUMAN	SET binding factor 1	1117					protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		CTGCTCATGGTCATGCGGTCG	0.677000													3	91					0	0	0.115264	0	0
RIOK1	83732	broad.mit.edu	37	6	7398936	7398936	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr6:7398936G>A	ENST00000379834.2	+	5	950	c.443G>A	c.(442-444)cGc>cAc	p.R148H		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	148							ATP binding|protein serine/threonine kinase activity			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					GTTAGGTATCGCATCAAAGAT	0.313000													4	145					0	0	0.014758	0	0
KIAA1324L	222223	broad.mit.edu	37	7	86526826	86526826	+	Missense_Mutation	SNP	A	A	C			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr7:86526826A>C	ENST00000450689.2	-	19	2866	c.2681T>G	c.(2680-2682)tTt>tGt	p.F894C	KIAA1324L_ENST00000444627.1_Missense_Mutation_p.F823C|KIAA1324L_ENST00000297222.6_Missense_Mutation_p.F654C|KIAA1324L_ENST00000416314.1_Missense_Mutation_p.F727C	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	894						integral to membrane				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					CCTTACCTGAAATCCTCTCTT	0.468000													69	129					0	0	0.139131	0	0
HEATR5B	54497	broad.mit.edu	37	2	37265041	37265041	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr2:37265041G>A	ENST00000233099.5	-	21	3268	c.3173C>T	c.(3172-3174)gCa>gTa	p.A1058V	HEATR5B_ENST00000354531.2_Missense_Mutation_p.A1058V	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1058							binding			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				ATGTCGTGGTGCAAACATGTG	0.383000													43	71					0	0	0.139131	0	0
PPFIA1	8500	broad.mit.edu	37	11	70208264	70208264	+	Silent	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr11:70208264G>A	ENST00000253925.7	+	20	2861	c.2646G>A	c.(2644-2646)acG>acA	p.T882T	PPFIA1_ENST00000389547.3_Silent_p.T882T|AP000487.6_ENST00000528607.1_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	882	SAM 1.				cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			ACGGGCCAACGGTTGTGGTCT	0.448000													59	94					0	0	0.139131	0	0
FRAS1	80144	broad.mit.edu	37	4	79420950	79420950	+	Missense_Mutation	SNP	A	A	G			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr4:79420950A>G	ENST00000264895.6	+	61	9631	c.9191A>G	c.(9190-9192)aAc>aGc	p.N3064S		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	3059	Calx-beta 5.				cell communication	integral to membrane|plasma membrane	metal ion binding			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GCGATTCTGAACATCAAGGTG	0.532000													106	142					0	0	0.139131	0	0
IL15	3600	broad.mit.edu	37	4	142651106	142651106	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr4:142651106T>C	ENST00000477265.1	+	6	5274	c.266T>C	c.(265-267)aTc>aCc	p.I89T	IL15_ENST00000514653.1_Missense_Mutation_p.I89T|IL15_ENST00000529613.1_Missense_Mutation_p.I116T|IL15_ENST00000296545.7_Missense_Mutation_p.I116T|IL15_ENST00000320650.4_Missense_Mutation_p.I116T|IL15_ENST00000394159.1_Missense_Mutation_p.I89T			P40933	IL15_HUMAN	interleukin 15	116					cell-cell signaling|immune response|positive regulation of interleukin-17 production	endosome|extracellular space|Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	cytokine activity|cytokine receptor binding|signal transducer activity			kidney(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_hematologic(180;0.158)					AATCTGATCATCCTAGCAAAC	0.388000													62	166					0	0	0.139131	0	0
PIWIL4	143689	broad.mit.edu	37	11	94328554	94328554	+	Silent	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr11:94328554G>A	ENST00000299001.6	+	10	1441	c.1230G>A	c.(1228-1230)cgG>cgA	p.R410R	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	410					cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|meiosis|multicellular organismal development|piRNA metabolic process|regulation of translation|spermatogenesis	nucleus|piP-body	piRNA binding			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CTTCAGGCCGGCAGCAGCGCC	0.512000													5	228					0	0	0.014758	0	0
KCNJ13	3769	broad.mit.edu	37	2	233635999	233635999	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr2:233635999C>T	ENST00000233826.3	-	2	213	c.74G>A	c.(73-75)gGc>gAc	p.G25D	GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000452341.2_Intron|GIGYF2_ENST00000409451.3_Intron|GIGYF2_ENST00000373563.4_Intron|KCNJ13_ENST00000410029.1_Missense_Mutation_p.G25D|GIGYF2_ENST00000409547.1_Intron|GIGYF2_ENST00000373566.3_Intron|KCNJ13_ENST00000409779.1_Missense_Mutation_p.G25D	NM_002242.4	NP_002233.2	O60928	IRK13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	25						voltage-gated potassium channel complex	inward rectifier potassium channel activity			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		TGTGCTGTGGCCATCCTTGGT	0.468000													4	117					0	0	0.014758	0	0
UBAC2	337867	broad.mit.edu	37	13	99853778	99853778	+	Missense_Mutation	SNP	G	G	T			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr13:99853778G>T	ENST00000376440.2	+	1	616	c.113G>T	c.(112-114)tGc>tTc	p.C38F	UBAC2_ENST00000403766.3_Intron	NM_177967.3	NP_808882.1	Q8NBM4	UBAC2_HUMAN	UBA domain containing 2	0						integral to membrane		p.C38F(1)		breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)	10	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CAGCTGTGCTGCTGGATGTTG	0.507000											OREG0022482	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	108					0.0293803	0.0349766	0.029380	1	0
BCL9	607	broad.mit.edu	37	1	147092354	147092354	+	Missense_Mutation	SNP	G	G	T			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr1:147092354G>T	ENST00000234739.3	+	8	3133	c.2393G>T	c.(2392-2394)cGg>cTg	p.R798L		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	798	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					AGTGGCTTGCGGAATCTCAGA	0.587000			T	"""IGH@, IGL@"""	B-ALL								4	52					5.18039e-06	6.47549e-06	0.038147	1	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H			O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393000			Mis		gliobastoma								68	89					0	0	0.139131	0	0
ECM1	1893	broad.mit.edu	37	1	150482440	150482440	+	Missense_Mutation	SNP	A	A	G			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr1:150482440A>G	ENST00000369047.4	+	4	391	c.266A>G	c.(265-267)gAa>gGa	p.E89G	ECM1_ENST00000346569.6_Missense_Mutation_p.E89G|ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Missense_Mutation_p.E116G	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	89					angiogenesis|biomineral tissue development|negative regulation of bone mineralization|negative regulation of peptidase activity|ossification|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of I-kappaB kinase/NF-kappaB cascade	proteinaceous extracellular matrix	laminin binding|protease binding|protein C-terminus binding|signal transducer activity			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CTCCAACAGGAAAAGCTGCTA	0.597000													9	188					0	0	0.058154	0	0
PCDHGA3	0	broad.mit.edu	37	5	140724038	140724038	+	Silent	SNP	G	G	A			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr5:140724038G>A	ENST00000253812.6	+	1	438	c.438G>A	c.(436-438)acG>acA	p.T146T	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1												p.T146T(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGAACTAACGGTTCCTGGAA	0.353000													78	68					0	0	0.139131	0	0
RP11-343N15.1	0	broad.mit.edu	37	1	121137836	121137836	+	RNA	DEL	A	A	-	rs57034034		TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr1:121137836delA	ENST00000437515.1	-	0	329																											GCCGCGGCTTATTCCCCCCAC	0.687													5	11	---	---	---	---					
AC018359.1	0	broad.mit.edu	37	3	34320590	34320591	+	RNA	INS	-	-	TTCT			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr3:34320590_34320591insTTCT	ENST00000424786.1	+	0	159																											tccttccttccttccttccttc	0.391													5	8	---	---	---	---					
CTD-2269F5.1	0	broad.mit.edu	37	5	83687394	83687395	+	RNA	DEL	TG	TG	-	rs72518535		TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr5:83687394_83687395delTG	ENST00000502253.1	+	0	599				CTD-2269F5.1_ENST00000514696.1_RNA|CTD-2269F5.1_ENST00000515688.1_RNA|CTD-2269F5.1_ENST00000509406.1_RNA																							AGGCTATCTTtgtgtgtgtgtg	0.282													4	2	---	---	---	---					
SEPT7P2	0	broad.mit.edu	37	7	45764989	45764990	+	RNA	DEL	AG	AG	-	rs78521790		TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr7:45764989_45764990delAG	ENST00000429741.1	-	0	1730_1731																											agaaaagaaaagggaaggaagg	0.406													2	4	---	---	---	---					
KRT223P	0	broad.mit.edu	37	17	38875133	38875134	+	RNA	INS	-	-	T	rs144586963	by1000genomes	TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr17:38875133_38875134insT	ENST00000422957.1	-	0	106																											ATGGAAAGTTGTTTTTTTTTTC	0.277													2	4	---	---	---	---					
PSMD8	5714	broad.mit.edu	37	19	38865398	38865398	+	Frame_Shift_Del	DEL	A	A	-			TCGA-E1-5311-01A-01D-1468-08	TCGA-E1-5311-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4b97717e-c288-4833-8161-03ae0b529aaf	3342b28b-0c68-47fb-9593-786c32c2cbe7	g.chr19:38865398delA	ENST00000215071.4	+	1	223	c.157delA	c.(157-159)aafs	p.K53fs	PSMD8_ENST00000602911.1_Intron	NM_002812.4	NP_002803.2	P48556	PSMD8_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	53					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome regulatory particle	protein binding			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(1)	6	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GCGCTGCCGTAAATCAGGCGG	0.736													2	4	---	---	---	---