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	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
WASH7P	653635	broad.mit.edu	37	1	15029	15029	+	RNA	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr1:15029G>A	uc009vis.2	-	3		c.316C>T			WASH7P_uc009vit.2_RNA|WASH7P_uc001aae.3_RNA|WASH7P_uc009viu.2_RNA|WASH7P_uc001aab.3_RNA|WASH7P_uc001aah.3_RNA|WASH7P_uc009vir.2_RNA|WASH7P_uc009viq.2_Intron|WASH7P_uc001aac.3_RNA|WASH7P_uc009viv.2_RNA|WASH7P_uc009viw.2_RNA					Homo sapiens cDNA FLJ31670 fis, clone NT2RI2004984.												0						ACCTTGGCTCGTGGCTCTCAC	0.632000													3	14					0	0	0.001168	0	0
RPS6KA1	6195	broad.mit.edu	37	1	26898350	26898350	+	Missense_Mutation	SNP	G	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr1:26898350G>T	uc001bmr.1	+	19	1926	c.1763G>T	c.(1762-1764)CGC>CTC	p.R588L	RPS6KA1_uc010ofe.1_Missense_Mutation_p.R496L|RPS6KA1_uc010off.1_Missense_Mutation_p.R572L|RPS6KA1_uc001bms.1_Missense_Mutation_p.R597L|RPS6KA1_uc009vsl.1_Missense_Mutation_p.R431L	NM_002953	NP_002944	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	588	Protein kinase 2.				axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|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	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		GTGCTGAAGCGCCAGGGCTAC	0.627000													27	35					3.00307e-07	3.40733e-07	0.008361	1	0
GBP3	2635	broad.mit.edu	37	1	89486247	89486247	+	Missense_Mutation	SNP	T	C	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr1:89486247T>C	uc001dmt.2	-	2	363	c.158A>G	c.(157-159)TAC>TGC	p.Y53C	GBP3_uc010oss.1_5'UTR|GBP3_uc001dmu.2_5'UTR|GBP3_uc001dmv.2_RNA	NM_018284	NP_060754	Q9H0R5	GBP3_HUMAN	guanylate binding protein 3	53						integral to membrane	GTP binding|GTPase activity			ovary(1)|pancreas(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		GTTCATCAGGTAGGATTTTCC	0.517000													30	159					0	0	0.006320	0	0
ABCB10	23456	broad.mit.edu	37	1	229685030	229685030	+	Silent	SNP	C	G	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr1:229685030C>G	uc001htp.3	-	2	712	c.669G>C	c.(667-669)CTG>CTC	p.L223L		NM_012089	NP_036221	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B, member 10	223	Mitochondrial intermembrane (Potential).|Helical; (Potential).|ABC transmembrane type-1.					integral to mitochondrial membrane|mitochondrial inner membrane	ATP binding|oligopeptide-transporting ATPase activity			breast(2)	2	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				CAGCACCACACAGAAACACGG	0.522000													15	68					0	0	0.012319	0	0
NEBL	10529	broad.mit.edu	37	10	21097515	21097515	+	Silent	SNP	G	A	A	rs140245727	byFrequency	TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr10:21097515G>A	uc001iqi.2	-	26	3082	c.2685C>T	c.(2683-2685)GAC>GAT	p.D895D	NEBL_uc001iqj.2_RNA|NEBL_uc001iqk.2_Intron	NM_006393	NP_006384	O76041	NEBL_HUMAN	nebulette sarcomeric isoform	895	Linker.				regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2						CTGACCTGTCGTCTCCGAGAC	0.458000													7	331					0	0	0.003080	0	0
CHAT	1103	broad.mit.edu	37	10	50901834	50901834	+	Nonstop_Mutation	SNP	G	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr10:50901834G>T	uc010qgs.1	+	15	1878	c.1638G>T	c.(1636-1638)TAG>TAT	p.*546Y	C10orf53_uc001jib.2_Missense_Mutation_p.D38Y|C10orf53_uc001jic.1_Missense_Mutation_p.D38Y|C10orf53_uc001jid.1_Missense_Mutation_p.D38Y	NM_020986	NP_066266	P28329	CLAT_HUMAN	choline acetyltransferase isoform 1	546					neurotransmitter biosynthetic process|neurotransmitter secretion	cytosol|nucleus	choline O-acetyltransferase activity			central_nervous_system(3)	3		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)	GTTGGCCATAGATGGACATGA	0.463000													12	127					2.27111e-07	2.62736e-07	0.013537	1	0
LGI1	9211	broad.mit.edu	37	10	95557106	95557106	+	Missense_Mutation	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr10:95557106G>A	uc001kjc.3	+	8	1556	c.1220G>A	c.(1219-1221)CGT>CAT	p.R407H	LGI1_uc010qnv.1_Missense_Mutation_p.R359H|LGI1_uc001kjd.3_Intron|LGI1_uc009xui.2_RNA|LGI1_uc001kje.2_Intron	NM_005097	NP_005088	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1 precursor	407	EAR 4.				axon guidance|cell proliferation|positive regulation of cell growth|positive regulation of synaptic transmission	cell junction|extracellular space|synapse	receptor binding			ovary(2)|central_nervous_system(1)|skin(1)	4		Colorectal(252;0.124)				AGTTCCCAGCGTCCTGTAATT	0.433000													113	82					0	0	0.014410	0	0
PAX6	5080	broad.mit.edu	37	11	31815341	31815341	+	Missense_Mutation	SNP	A	G	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr11:31815341A>G	uc001mtd.3	-	9	1665	c.775T>C	c.(775-777)TCT>CCT	p.S259P	PAX6_uc001mte.3_Missense_Mutation_p.S259P|PAX6_uc001mtg.3_Missense_Mutation_p.S273P|PAX6_uc001mtf.3_Missense_Mutation_p.S259P|PAX6_uc001mth.3_Missense_Mutation_p.S259P|PAX6_uc009yjr.2_Missense_Mutation_p.S259P	NM_001127612	NP_001121084	P26367	PAX6_HUMAN	paired box gene 6 isoform a	259	Homeobox.				blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	9	Lung SC(675;0.225)					CTTCGATTAGAAAACCATACC	0.522000									Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				78	5					0	0	0.014410	0	0
ACCS	84680	broad.mit.edu	37	11	44089197	44089197	+	Missense_Mutation	SNP	A	G	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr11:44089197A>G	uc009yks.1	+	2	164	c.20A>G	c.(19-21)AAG>AGG	p.K7R	ACCS_uc010rfm.1_5'UTR|ACCS_uc010rfn.1_Missense_Mutation_p.K7R|ACCS_uc001mxx.2_Missense_Mutation_p.K7R	NM_001127219	NP_001120691	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase	7							1-aminocyclopropane-1-carboxylate synthase activity|protein homodimerization activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			breast(2)|ovary(1)|lung(1)	4						CTTCCTCAAAAGGACTTCAGG	0.537000													3	139					0	0	0.004672	0	0
AHNAK	79026	broad.mit.edu	37	11	62287998	62287998	+	Missense_Mutation	SNP	C	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr11:62287998C>A	uc001ntl.2	-	5	14191	c.13891G>T	c.(13891-13893)GAC>TAC	p.D4631Y	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	4631				RD -> KG (in Ref. 2; AAA69898).	nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				ACTTTGGGGTCCCTGATGTCA	0.522000													100	338					2.6645e-62	3.41751e-62	0.014410	1	0
DPAGT1	1798	broad.mit.edu	37	11	118971495	118971495	+	Missense_Mutation	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr11:118971495G>A	uc001pvi.2	-	3	761	c.341C>T	c.(340-342)GCG>GTG	p.A114V	DPAGT1_uc001pvj.2_Missense_Mutation_p.A7V|DPAGT1_uc009zaq.2_RNA|DPAGT1_uc001pvk.2_Intron|DPAGT1_uc010ryz.1_Missense_Mutation_p.A114V|DPAGT1_uc001pvm.1_Missense_Mutation_p.A7V|DPAGT1_uc010rza.1_Missense_Mutation_p.A7V	NM_001382	NP_001373	Q9H3H5	GPT_HUMAN	UDP-N-acetylglucosamine-dolichyl-phosphate	114	Helical; (Potential).				dolichol biosynthetic process|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|protein oligomerization	integral to endoplasmic reticulum membrane|microsome	phospho-N-acetylmuramoyl-pentapeptide-transferase activity|transferase activity, transferring glycosyl groups|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity			breast(2)|ovary(1)	3	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		TACATCATCCGCAAAGCCCAG	0.567000											OREG0021396	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	115					0	0	0.009096	0	0
Unknown	0	broad.mit.edu	37	12	92081	92081	+	Nonsense_Mutation	SNP	C	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr12:92081C>A	uc010sdi.1	-	2	257	c.229G>T	c.(229-231)GGA>TGA	p.G77*	uc010sdj.1_RNA					SubName: Full=DEAD/H box polypeptide 11 like 11;																		ACACCGTCTCCAGCGGGCAGA	0.597000													7	29					5.18039e-06	5.76685e-06	0.003080	1	0
SLC6A13	6540	broad.mit.edu	37	12	346407	346407	+	Missense_Mutation	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr12:346407G>A	uc001qic.1	-	6	666	c.613C>T	c.(613-615)CGC>TGC	p.R205C	SLC6A13_uc009zdj.1_Missense_Mutation_p.R205C|SLC6A13_uc010sdl.1_Missense_Mutation_p.R113C|SLC6A13_uc010sdm.1_Missense_Mutation_p.R86C	NM_016615	NP_057699	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter	205	Extracellular (Potential).				neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			AGCTCCCAGCGCAGGGCCCCC	0.602000													5	269					0	0	0.000602	0	0
MMP19	4327	broad.mit.edu	37	12	56233333	56233333	+	Missense_Mutation	SNP	C	T	T	rs138516871		TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr12:56233333C>T	uc001sib.2	-	5	834	c.713G>A	c.(712-714)CGG>CAG	p.R238Q	MMP19_uc001sia.2_5'UTR|MMP19_uc001sid.2_RNA|MMP19_uc010spw.1_Intron	NM_002429	NP_002420	Q99542	MMP19_HUMAN	matrix metalloproteinase 19 isoform rasi-1	238					angiogenesis|cell differentiation|collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)	1						AAAGTGGGGCCGGTAGCCCTC	0.617000													18	63					0	0	0.007413	0	0
CMA1	1215	broad.mit.edu	37	14	24976583	24976583	+	Missense_Mutation	SNP	G	A	A	rs13306251	by1000genomes	TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr14:24976583G>A	uc001wpp.1	-	2	218	c.188C>T	c.(187-189)ACG>ATG	p.T63M	CMA1_uc010alx.1_Intron	NM_001836	NP_001827	P23946	CMA1_HUMAN	chymase 1, mast cell preproprotein	63	Peptidase S1.				interleukin-1 beta biosynthetic process|proteolysis	extracellular region	serine-type endopeptidase activity				0				GBM - Glioblastoma multiforme(265;0.0271)		ATGAGCAGCCGTCAGCACAAA	0.488000													83	163					0	0	0.014410	0	0
EIF2AK4	440275	broad.mit.edu	37	15	40258023	40258023	+	Silent	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr15:40258023G>A	uc001zkm.1	+	8	1046	c.996G>A	c.(994-996)AAG>AAA	p.K332K	EIF2AK4_uc001zkl.2_Silent_p.K332K|EIF2AK4_uc010bbj.1_Silent_p.K61K	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha	332	Protein kinase 1.				translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		AAAAAGAGAAGATTGATAAGT	0.443000													37	115					0	0	0.004289	0	0
MAN2A2	4122	broad.mit.edu	37	15	91450665	91450665	+	Missense_Mutation	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr15:91450665G>A	uc010bnz.2	+	8	1251	c.1136G>A	c.(1135-1137)CGC>CAC	p.R379H	MAN2A2_uc010boa.2_Missense_Mutation_p.R421H|MAN2A2_uc002bqc.2_Missense_Mutation_p.R379H|MAN2A2_uc010uql.1_Missense_Mutation_p.R83H|MAN2A2_uc010uqm.1_Missense_Mutation_p.A26T	NM_006122	NP_006113	P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	379	Lumenal (Potential).				mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			large_intestine(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			CCTGGTGGGCGCATCAACTGC	0.567000													5	184					0	0	0.000602	0	0
OSGIN1	29948	broad.mit.edu	37	16	83994303	83994303	+	Missense_Mutation	SNP	C	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr16:83994303C>T	uc002fha.2	+	5	966	c.583C>T	c.(583-585)CGG>TGG	p.R195W	OSGIN1_uc002fhb.2_Missense_Mutation_p.R112W|OSGIN1_uc002fhc.2_Missense_Mutation_p.R112W	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	195					cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						CTGGAAGCACCGGAAGGAGCA	0.657000													21	101					0	0	0.014323	0	0
TP53	7157	broad.mit.edu	37	17	7578550	7578550	+	Missense_Mutation	SNP	G	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr17:7578550G>T	uc002gim.2	-	5	574	c.380C>A	c.(379-381)TCC>TAC	p.S127Y	TP53_uc002gig.1_Missense_Mutation_p.S127Y|TP53_uc002gih.2_Missense_Mutation_p.S127Y|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'UTR|TP53_uc010cng.1_5'UTR|TP53_uc002gii.1_5'UTR|TP53_uc010cnh.1_Missense_Mutation_p.S127Y|TP53_uc010cni.1_Missense_Mutation_p.S127Y|TP53_uc002gij.2_Missense_Mutation_p.S127Y|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.S34Y|TP53_uc002gio.2_5'UTR|TP53_uc010vug.1_Missense_Mutation_p.S88Y	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	127	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		S -> C (in a sporadic cancer; somatic mutation).|S -> F (in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).|S -> P (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.S127F(18)|p.S127Y(8)|p.0?(7)|p.Y126_K132delYSPALNK(6)|p.Y126_N131delYSPALN(3)|p.S127P(3)|p.S127T(2)|p.P128fs*42(2)|p.V73fs*9(1)|p.S127fs*36(1)|p.P128fs*18(1)|p.Y126fs*11(1)|p.S127S(1)|p.S127C(1)|p.S127_Q136del10(1)|p.P13fs*18(1)|p.?(1)|p.S127fs*43(1)|p.S127fs*42(1)|p.Y126fs*18(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GAGGGCAGGGGAGTACTGTAG	0.552000		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			44	0					1.00001e-27	1.20409e-27	0.009718	1	0
ALKBH6	84964	broad.mit.edu	37	19	36501795	36501795	+	Splice_Site	SNP	C	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr19:36501795C>T	uc002oct.2	-	5	436	c.336_splice	c.e5+1	p.M112_splice	C19orf46_uc002ocr.1_5'Flank|C19orf46_uc002ocs.1_5'Flank|C19orf46_uc002ocq.1_5'Flank|C19orf46_uc010een.1_5'Flank|ALKBH6_uc002ocv.1_Splice_Site_p.M140_splice|ALKBH6_uc002ocx.1_Splice_Site_p.M43_splice|ALKBH6_uc002ocw.1_Splice_Site_p.M140_splice|ALKBH6_uc010eeo.1_Splice_Site_p.M112_splice|ALKBH6_uc010eep.1_Missense_Mutation_p.V141I	NM_032878	NP_116267	Q3KRA9	ALKB6_HUMAN	alkB, alkylation repair homolog 6 isoform 2							cytoplasm|nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0	all_lung(56;1.35e-06)|Lung NSC(56;2.15e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TGTGTGGTTACCATGATGCCC	0.592000													35	88					0	0	0.003271	0	0
ETAA1	54465	broad.mit.edu	37	2	67631847	67631847	+	Missense_Mutation	SNP	A	G	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:67631847A>G	uc002sdz.1	+	5	2172	c.2033A>G	c.(2032-2034)AAC>AGC	p.N678S		NM_019002	NP_061875	Q9NY74	ETAA1_HUMAN	ETAA16 protein	678						cytoplasm|nucleus				ovary(3)|large_intestine(1)	4						GGAGCCAAAAACATGTTTGCT	0.363000													90	110					0	0	0.014410	0	0
ALMS1	7840	broad.mit.edu	37	2	73718168	73718168	+	Missense_Mutation	SNP	T	G	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:73718168T>G	uc002sje.1	+	12	9196	c.9085T>G	c.(9085-9087)TGT>GGT	p.C3029G	ALMS1_uc002sjf.1_Missense_Mutation_p.C2985G|ALMS1_uc002sjg.2_Missense_Mutation_p.C2415G|ALMS1_uc002sjh.1_Missense_Mutation_p.C2415G	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3027					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9						CCCAAATCACTGTACATTAGC	0.378000													64	195					0	0	0.014410	0	0
NAT8	9027	broad.mit.edu	37	2	73868641	73868641	+	Missense_Mutation	SNP	G	C	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:73868641G>C	uc002sji.1	-	2	282	c.115C>G	c.(115-117)CTG>GTG	p.L39V		NM_003960	NP_003951	Q9UHE5	NAT8_HUMAN	N-acetyltransferase 8	39					gastrulation with mouth forming second|response to drug	integral to membrane	N-acetyltransferase activity			ovary(1)	1						GTTCGAGGCAGCTTCAGCAAT	0.622000													63	209					0	0	0.014410	0	0
ANKRD36	375248	broad.mit.edu	37	2	97875420	97875420	+	Missense_Mutation	SNP	T	G	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:97875420T>G	uc010yva.1	+	55	3512	c.3268T>G	c.(3268-3270)TCT>GCT	p.S1090A		NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	1090											0						CTTTTCAGTGTCTTCTCGGAA	0.358000													14	95					0	0	0.007413	0	0
HECW2	57520	broad.mit.edu	37	2	197298053	197298053	+	Missense_Mutation	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:197298053G>A	uc002utm.1	-	2	278	c.95C>T	c.(94-96)GCC>GTC	p.A32V		NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin	32					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						GCTCTGGGCGGCAAGGCTCTG	0.602000													5	231					0	0	0.000602	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	T	T	rs121913500		TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:209113112C>T	uc002vcs.2	-	4	641	c.395G>A	c.(394-396)CGT>CAT	p.R132H	IDH1_uc002vct.2_Missense_Mutation_p.R132H|IDH1_uc002vcu.2_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|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).|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 -> 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).		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(2023)|p.R132C(344)|p.R132?(210)|p.R132G(117)|p.R132S(79)|p.R132L(58)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393000			Mis		gliobastoma 								107	83					0	0	0.014410	0	0
KCNJ13	3769	broad.mit.edu	37	2	233633140	233633140	+	Missense_Mutation	SNP	A	G	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:233633140A>G	uc002vto.2	-	2	887	c.844T>C	c.(844-846)TGC>CGC	p.C282R	GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vti.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron|KCNJ13_uc002vtn.2_3'UTR|KCNJ13_uc002vtp.2_Missense_Mutation_p.C282R	NM_002242	NP_002233	O60928	IRK13_HUMAN	potassium inwardly-rectifying channel J13	282	Cytoplasmic (By similarity).					voltage-gated potassium channel complex	inward rectifier potassium channel activity				0		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)		CTCCTTTGGCATATTTCTCCA	0.433000													131	120					0	0	0.014410	0	0
PRDM15	63977	broad.mit.edu	37	21	43281674	43281674	+	Missense_Mutation	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr21:43281674G>A	uc002yzq.1	-	7	1000	c.889C>T	c.(889-891)CCG>TCG	p.P297S	PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1	297					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GTGCGCACCGGCATGTCCTTC	0.463000													4	146					0	0	0.001168	0	0
Unknown	0	broad.mit.edu	37	22	20294162	20294162	+	RNA	SNP	C	G	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr22:20294162C>G	uc002zrw.1	+	1		c.2602C>G								Homo sapiens mRNA for KIAA1653 protein, partial cds.																		CTCACTTGAGCAATAGTTGCT	0.647000													2	14					0	0	0.004672	0	0
FYCO1	79443	broad.mit.edu	37	3	46014621	46014621	+	Silent	SNP	C	T	T	rs149291592	byFrequency	TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr3:46014621C>T	uc003cpb.3	-	6	704	c.498G>A	c.(496-498)TCG>TCA	p.S166S	FYCO1_uc011bal.1_Silent_p.S166S	NM_024513	NP_078789	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	166	RUN.				transport	integral to membrane	metal ion binding|protein binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CAAAGCCCCTCGACGCCAGGT	0.483000													26	74					0	0	0.003954	0	0
EPHA3	2042	broad.mit.edu	37	3	89448615	89448615	+	Nonsense_Mutation	SNP	G	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr3:89448615G>T	uc003dqy.2	+	7	1804	c.1579G>T	c.(1579-1581)GAA>TAA	p.E527*	EPHA3_uc003dqx.1_Nonsense_Mutation_p.E527*|EPHA3_uc010hon.1_RNA	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor	527	Extracellular (Potential).|Fibronectin type-III 2.					extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		GTTTGAGTTTGAAACTAGTCC	0.448000										TSP Lung(6;0.00050)			30	92					1.57351e-24	1.85675e-24	0.003755	1	0
KIAA1407	57577	broad.mit.edu	37	3	113761686	113761686	+	Silent	SNP	C	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr3:113761686C>T	uc003eax.2	-	4	426	c.279G>A	c.(277-279)GAG>GAA	p.E93E	KIAA1407_uc011bin.1_RNA|KIAA1407_uc011bio.1_Silent_p.E71E|KIAA1407_uc011bip.1_Silent_p.E80E	NM_020817	NP_065868	Q8NCU4	K1407_HUMAN	hypothetical protein LOC57577	93										ovary(2)	2						CATTGACCAGCTCCTGAGCTA	0.313000													48	137					0	0	0.014410	0	0
MUC4	4585	broad.mit.edu	37	3	195475779	195475779	+	Missense_Mutation	SNP	C	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr3:195475779C>T	uc011bto.1	-	25	16104	c.15644G>A	c.(15643-15645)CGC>CAC	p.R5215H	MUC4_uc010hzq.2_Missense_Mutation_p.R200H|MUC4_uc003fuz.2_Missense_Mutation_p.R941H|MUC4_uc003fva.2_Missense_Mutation_p.R823H|MUC4_uc003fvb.2_Missense_Mutation_p.R859H|MUC4_uc003fvc.2_RNA|MUC4_uc003fvd.2_RNA|MUC4_uc003fve.2_Missense_Mutation_p.R859H|MUC4_uc010hzr.2_RNA|MUC4_uc011btf.1_Missense_Mutation_p.R823H|MUC4_uc011btg.1_RNA|MUC4_uc011bth.1_Missense_Mutation_p.R907H|MUC4_uc011bti.1_Missense_Mutation_p.R907H|MUC4_uc011btj.1_Missense_Mutation_p.R1084H|MUC4_uc011btk.1_Missense_Mutation_p.R823H|MUC4_uc011btl.1_Missense_Mutation_p.R852H|MUC4_uc011btm.1_Missense_Mutation_p.R1032H|MUC4_uc011btn.1_Missense_Mutation_p.R823H|MUC4_uc003fvo.2_Missense_Mutation_p.R1107H|MUC4_uc003fvp.2_Missense_Mutation_p.R1056H	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	2100	EGF-like 2.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCACCTGCAGCGGGGCCCACT	0.647000													24	234					0	0	0.003954	0	0
CNGA1	1259	broad.mit.edu	37	4	47938995	47938995	+	Missense_Mutation	SNP	T	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr4:47938995T>A	uc003gxt.3	-	11	1782	c.1516A>T	c.(1516-1518)ATT>TTT	p.I506F	uc003gxr.1_Intron|CNGA1_uc003gxu.2_Missense_Mutation_p.I575F	NM_000087	NP_000078	P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1 isoform	506	cGMP (Potential).|Cytoplasmic (Potential).				response to stimulus|visual perception	integral to plasma membrane	cGMP binding|ion channel activity			ovary(2)	2						TTCTTGCAAATATAATCTCCA	0.438000													16	283					0	0	0.004990	0	0
COL25A1	84570	broad.mit.edu	37	4	109765700	109765700	+	Missense_Mutation	SNP	C	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr4:109765700C>T	uc003hze.1	-	29	2135	c.1604G>A	c.(1603-1605)GGT>GAT	p.G535D	COL25A1_uc003hzg.2_Missense_Mutation_p.G535D|COL25A1_uc003hzd.2_RNA|COL25A1_uc003hzf.2_Missense_Mutation_p.G293D	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1	535	Extracellular (Potential).					collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		gccatggggacctggtgggcc	0.274000													48	100					0	0	0.014410	0	0
PKHD1	5314	broad.mit.edu	37	6	51513908	51513908	+	Missense_Mutation	SNP	G	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr6:51513908G>T	uc003pah.1	-	62	11561	c.11285C>A	c.(11284-11286)CCA>CAA	p.P3762Q		NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3762	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					TACCAATTGTGGCTGCACTGG	0.413000													82	132					1.55521e-42	1.91161e-42	0.014410	1	0
PHF3	23469	broad.mit.edu	37	6	64356551	64356551	+	Missense_Mutation	SNP	A	G	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr6:64356551A>G	uc003pep.1	+	1	121	c.95A>G	c.(94-96)GAG>GGG	p.E32G	PHF3_uc010kaf.1_Missense_Mutation_p.E32G|PHF3_uc003pem.2_5'UTR|PHF3_uc010kag.1_Intron|PHF3_uc010kah.1_Intron|PHF3_uc003pen.2_5'UTR|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_Missense_Mutation_p.E32G	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	32					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GAAGTCTGTGAGGATTTTAGT	0.393000													49	143					0	0	0.014410	0	0
MAP3K5	4217	broad.mit.edu	37	6	136932510	136932510	+	Missense_Mutation	SNP	T	C	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr6:136932510T>C	uc003qhc.2	-	18	2792	c.2431A>G	c.(2431-2433)ATT>GTT	p.I811V	MAP3K5_uc011edj.1_Missense_Mutation_p.I58V|MAP3K5_uc011edk.1_Missense_Mutation_p.I656V	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase	811	Protein kinase.				activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		TAGGTATTAATCAACACATTG	0.368000													7	123					0	0	0.001984	0	0
RINT1	60561	broad.mit.edu	37	7	105189063	105189063	+	Missense_Mutation	SNP	C	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr7:105189063C>A	uc003vda.1	+	7	1133	c.902C>A	c.(901-903)TCT>TAT	p.S301Y	RINT1_uc010ljj.1_Intron	NM_021930	NP_068749	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	301	RINT1/TIP20.				cell cycle|G2/M transition DNA damage checkpoint|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane	protein binding			ovary(3)|central_nervous_system(1)	4						GCCTCCCCTTCTGTCATCCTG	0.443000													98	347					9.15355e-43	1.14906e-42	0.014410	1	0
STK3	6788	broad.mit.edu	37	8	99779474	99779474	+	Missense_Mutation	SNP	T	C	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr8:99779474T>C	uc003yip.2	-	3	374	c.233A>G	c.(232-234)GAC>GGC	p.D78G	STK3_uc003yio.2_Missense_Mutation_p.D106G|STK3_uc010mbm.1_Missense_Mutation_p.D78G	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3	78	Protein kinase.				apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		TTCATACCTGTCACATTGCTG	0.308000													54	60					0	0	0.014410	0	0
CSMD3	114788	broad.mit.edu	37	8	113988170	113988170	+	Missense_Mutation	SNP	T	C	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr8:113988170T>C	uc003ynu.2	-	7	1397	c.1238A>G	c.(1237-1239)GAC>GGC	p.D413G	CSMD3_uc003ynt.2_Missense_Mutation_p.D373G|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	413	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						AGAGAGCCCGTCCTTGGACGT	0.478000										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			73	265					0	0	0.014410	0	0
PLEC	5339	broad.mit.edu	37	8	145007212	145007212	+	Missense_Mutation	SNP	C	T	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr8:145007212C>T	uc003zaf.1	-	14	2067	c.1897G>A	c.(1897-1899)GTG>ATG	p.V633M	PLEC_uc003zab.1_Missense_Mutation_p.V496M|PLEC_uc003zac.1_Missense_Mutation_p.V500M|PLEC_uc003zad.2_Missense_Mutation_p.V496M|PLEC_uc003zae.1_Missense_Mutation_p.V464M|PLEC_uc003zag.1_Missense_Mutation_p.V474M|PLEC_uc003zah.2_Missense_Mutation_p.V482M|PLEC_uc003zaj.2_Missense_Mutation_p.V523M	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	633	Globular 1.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9						GGGGCCGCCACGCCTGCCTTC	0.662000													3	4					0	0	0.008291	0	0
SPATC1	375686	broad.mit.edu	37	8	145101698	145101698	+	Silent	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr8:145101698G>A	uc011lkw.1	+	5	1719	c.1617G>A	c.(1615-1617)CCG>CCA	p.P539P	SPATC1_uc011lkx.1_3'UTR	NM_198572	NP_940974	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	539										ovary(1)|central_nervous_system(1)	2	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-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;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GAGAGCGCCCGGAGCTGGCGG	0.687000													4	132					0	0	0.001168	0	0
Unknown	0	broad.mit.edu	37	9	78965754	78965754	+	Silent	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr9:78965754G>A	uc004akc.1	+	8	1372	c.1152G>A	c.(1150-1152)GCG>GCA	p.A384A						Homo sapiens cDNA FLJ16215 fis, clone CTONG2025610, moderately similar to PC6B.																		GAAAAGGAGCGTTGAATTGTT	0.448000													129	128					0	0	0.014410	0	0
AKNA	80709	broad.mit.edu	37	9	117139492	117139492	+	Missense_Mutation	SNP	T	C	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr9:117139492T>C	uc004biq.3	-	2	730	c.595A>G	c.(595-597)AGG>GGG	p.R199G	AKNA_uc004bio.3_5'Flank|AKNA_uc004bip.3_Missense_Mutation_p.R118G|AKNA_uc004bir.3_Missense_Mutation_p.R199G|AKNA_uc004bis.3_Missense_Mutation_p.R199G|AKNA_uc010mve.2_Missense_Mutation_p.R80G|AKNA_uc004biu.1_Intron|AKNA_uc004biv.1_Missense_Mutation_p.R199G|AKNA_uc004biw.1_Missense_Mutation_p.R199G	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	199					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6						CTCCAGGACCTTGCCGGGCTG	0.612000													87	61					0	0	0.014410	0	0
ATRX	546	broad.mit.edu	37	X	76814313	76814313	+	Nonsense_Mutation	SNP	G	A	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chrX:76814313G>A	uc004ecp.3	-	29	6563	c.6331C>T	c.(6331-6333)CGA>TGA	p.R2111*	ATRX_uc004ecq.3_Nonsense_Mutation_p.R2073*|ATRX_uc004eco.3_Nonsense_Mutation_p.R1896*	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	2111	Helicase C-terminal.				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	ATAAATAATCGTCCTCTGAAA	0.274000			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						69	1					0	0	0.014410	0	0
MST1P2	11209	broad.mit.edu	37	1	16974141	16974141	+	RNA	DEL	G	-	-			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr1:16974141delG	uc009vow.2	+	5		c.951delG			CROCCL1_uc001azg.1_5'Flank|CROCCL1_uc001azi.1_5'Flank|MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_Intron|MST1P2_uc001azm.3_Intron					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						TGGCTTGGCCGGGGAGGTCAG	0.667													4	8	---	---	---	---					
DYNLL1	8655	broad.mit.edu	37	12	120935907	120935908	+	Frame_Shift_Ins	INS	-	TT	TT	rs142458935	by1000genomes	TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr12:120935907_120935908insTT	uc001tyj.2	+	3	418_419	c.164_165insTT	c.(163-165)CATfs	p.H55fs	uc001tyk.1_5'Flank|DYNLL1_uc001tyl.2_Frame_Shift_Ins_p.H55fs|DYNLL1_uc001tym.2_Frame_Shift_Ins_p.H55fs	NM_001037494	NP_001032583	P63167	DYL1_HUMAN	dynein light chain 1	55					actin cytoskeleton organization|activation of pro-apoptotic gene products|anatomical structure morphogenesis|female gamete generation|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|microtubule-based process|negative regulation of phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transport	centrosome|cytoplasmic dynein complex|cytosol|microtubule|mitochondrion|nucleus|plasma membrane	motor activity|protein binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCCACCTGGCATTGCATCGTGG	0.426													35	58	---	---	---	---					
KIAA0182	23199	broad.mit.edu	37	16	85682289	85682290	+	Frame_Shift_Ins	INS	-	C	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr16:85682289_85682290insC	uc002fix.2	+	3	432_433	c.358_359insC	c.(358-360)ACCfs	p.T120fs	KIAA0182_uc002fiw.2_Frame_Shift_Ins_p.T16fs|KIAA0182_uc002fiy.2_Frame_Shift_Ins_p.T47fs	NM_014615	NP_055430	Q14687	GSE1_HUMAN	genetic suppressor element 1 isoform 1	120							protein binding			large_intestine(3)|ovary(1)|skin(1)	5						CGTGCCCAGCACCCCCCCCGTG	0.688													8	197	---	---	---	---					
Unknown	0	broad.mit.edu	37	X	2583202	2583205	+	RNA	DEL	CCTT	-	-			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chrX:2583202_2583205delCCTT	uc004cql.2	+	1		c.858_861delCCTT								Homo sapiens cDNA FLJ39679 fis, clone SMINT2010068.																		CAATGGCCGGccttccttccttcc	0.230													5	7	---	---	---	---					
IRS4	8471	broad.mit.edu	37	X	107977802	107977803	+	Frame_Shift_Ins	INS	-	C	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chrX:107977802_107977803insC	uc004eoc.2	-	1	1805_1806	c.1772_1773insG	c.(1771-1773)GGCfs	p.G591fs		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	591						plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	10						CTGAGCCTTTGCCCCCCCCAGA	0.545													8	421	---	---	---	---					
