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	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
NBPF1	55672	broad.mit.edu	37	1	16918734	16918734	+	5'UTR	SNP	G	C	C	rs3928093	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918734G>C	uc009vos.1	-	6					NBPF1_uc010oce.1_5'UTR	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CCTGAACTCAGAGCTGAAAGC	0.453													4	9	---	---	---	---	PASS
B4GALT2	8704	broad.mit.edu	37	1	44450654	44450654	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44450654G>T	uc001clg.2	+	4	1037	c.667G>T	c.(667-669)GAT>TAT	p.D223Y	B4GALT2_uc001clh.2_Missense_Mutation_p.D157Y|B4GALT2_uc010okl.1_Missense_Mutation_p.D252Y|B4GALT2_uc001cli.2_Missense_Mutation_p.D223Y	NM_003780	NP_003771	O60909	B4GT2_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	223	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			N-Acetyl-D-glucosamine(DB00141)	GGTCCCCATGGATGACCGCAA	0.597													15	30	---	---	---	---	PASS
KIAA0494	9813	broad.mit.edu	37	1	47149017	47149017	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47149017C>T	uc001cqk.3	-	10	2244	c.1267G>A	c.(1267-1269)GCC>ACC	p.A423T	KIAA0494_uc010omh.1_Missense_Mutation_p.A359T|KIAA0494_uc010omj.1_Missense_Mutation_p.A215T	NM_014774	NP_055589	O75071	K0494_HUMAN	hypothetical protein LOC9813	423							calcium ion binding				0	Acute lymphoblastic leukemia(166;0.155)					CTTAGTTGGGCAGCTTTCTCA	0.388													33	60	---	---	---	---	PASS
LPPR5	163404	broad.mit.edu	37	1	99422183	99422183	+	Nonsense_Mutation	SNP	G	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99422183G>A	uc001dsb.2	-	2	574	c.352C>T	c.(352-354)CGA>TGA	p.R118*	LPPR5_uc001dsc.2_Nonsense_Mutation_p.R118*	NM_001037317	NP_001032394	Q32ZL2	LPPR5_HUMAN	phosphatidic acid phosphatase type 2d isoform 1	118						integral to membrane	hydrolase activity				0						CGGACAGTTCGGCGCACCAGC	0.358													25	28	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142803312	142803312	+	Intron	SNP	G	C	C	rs2039402		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142803312G>C	uc001eiw.1	+						uc001ejb.2_RNA|uc001ejc.2_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																		caaACAGGATGTAAAGCATAC	0.189													4	6	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142803543	142803543	+	Intron	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142803543C>T	uc001eiw.1	+						uc001ejb.2_RNA|uc001ejc.2_RNA					Homo sapiens PNAS-130 mRNA, complete cds.																		TGTTGGAATTCCTGATGAATC	0.179													6	190	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144828704	144828704	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144828704T>G	uc009wig.1	+	23	2825	c.2749T>G	c.(2749-2751)TAC>GAC	p.Y917D	NBPF9_uc010oxn.1_Missense_Mutation_p.Y815D|NBPF9_uc010oxo.1_Missense_Mutation_p.Y842D|NBPF9_uc010oxr.1_Missense_Mutation_p.Y944D|NBPF9_uc010oxt.1_Missense_Mutation_p.Y732D|NBPF9_uc001ekg.1_Missense_Mutation_p.Y244D|NBPF9_uc001ekk.1_Missense_Mutation_p.Y488D|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Missense_Mutation_p.Y244D|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Missense_Mutation_p.Y577D|uc001elr.3_5'Flank	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	917	NBPF 7.					cytoplasm					0						CTTCGCCCTTTACGTGGACAA	0.438													6	288	---	---	---	---	PASS
NOTCH2NL	388677	broad.mit.edu	37	1	145209366	145209366	+	Translation_Start_Site	SNP	A	G	G	rs856450	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145209366A>G	uc001emn.3	+	1	256	c.-114A>G	c.(-116--112)ATACC>ATGCC		NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Translation_Start_Site|NOTCH2NL_uc001emm.3_Translation_Start_Site|NOTCH2NL_uc001emo.2_Translation_Start_Site|NOTCH2NL_uc010oyh.1_RNA	NM_203458	NP_982283	Q7Z3S9	NT2NL_HUMAN	Notch homolog 2 N-terminal like protein						cell differentiation|multicellular organismal development|Notch signaling pathway	cytoplasm|extracellular region	calcium ion binding			ovary(1)	1						CCGAGAAGATACCCGCCCTGC	0.592													4	6	---	---	---	---	PASS
VANGL2	57216	broad.mit.edu	37	1	160395211	160395211	+	3'UTR	SNP	A	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160395211A>G	uc001fwb.1	+	9					VANGL2_uc001fwc.1_3'UTR	NM_020335	NP_065068	Q9ULK5	VANG2_HUMAN	vang-like 2						apical protein localization|heart looping|nonmotile primary cilium assembly	apical plasma membrane|integral to membrane				ovary(1)	1	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGGGGTCCTGAGGGGGTGGGA	0.542													5	14	---	---	---	---	PASS
C1orf192	257177	broad.mit.edu	37	1	161334829	161334829	+	Missense_Mutation	SNP	A	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161334829A>G	uc001gal.2	-	5	466	c.460T>C	c.(460-462)TCC>CCC	p.S154P		NM_001013625	NP_001013647	Q5VTH2	CA192_HUMAN	hypothetical protein LOC257177	154											0	all_cancers(52;4.64e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TCATCTGGGGAATTGAGGTTG	0.498													35	70	---	---	---	---	PASS
HSPA6	3310	broad.mit.edu	37	1	161494903	161494903	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161494903T>G	uc001gap.2	+	2	1115	c.455T>G	c.(454-456)TTC>TGC	p.F152C	HSPA6_uc001gaq.2_Missense_Mutation_p.F152C	NM_002155	NP_002146	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	152					response to unfolded protein		ATP binding			skin(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			CCCGCCTATTTCAATGACTCG	0.632													17	44	---	---	---	---	PASS
PLXNA2	5362	broad.mit.edu	37	1	208200500	208200500	+	3'UTR	SNP	T	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208200500T>C	uc001hgz.2	-	32					PLXNA2_uc001hgy.2_3'UTR	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CTCTGGGGCCTGATCCCCATC	0.597													3	33	---	---	---	---	PASS
NID1	4811	broad.mit.edu	37	1	236156998	236156998	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236156998C>T	uc001hxo.2	-	13	2804	c.2702G>A	c.(2701-2703)CGC>CAC	p.R901H	NID1_uc009xgd.2_Missense_Mutation_p.R768H|NID1_uc009xgc.2_5'UTR	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	901	Thyroglobulin type-1.				cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	GCGGCCGTCGCGATCCACGCA	0.697													5	12	---	---	---	---	PASS
PPP3R1	5534	broad.mit.edu	37	2	68408039	68408039	+	3'UTR	SNP	G	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68408039G>C	uc002sei.1	-	6						NM_000945	NP_000936	P63098	CANB1_HUMAN	protein phosphatase 3, regulatory subunit B,						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	calcineurin complex|cytosol	calcium ion binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding				0					Pimecrolimus(DB00337)	GTCTTGAGCAGATCTTCAGAG	0.423													5	11	---	---	---	---	PASS
TGOLN2	10618	broad.mit.edu	37	2	85553644	85553644	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85553644T>C	uc010fgd.1	-	2	1500	c.1211A>G	c.(1210-1212)CAC>CGC	p.H404R	TGOLN2_uc002soz.2_Missense_Mutation_p.H404R|TGOLN2_uc002spa.2_RNA|TGOLN2_uc002spb.2_Missense_Mutation_p.H346R|TGOLN2_uc002spc.1_Missense_Mutation_p.H404R	NM_006464	NP_006455	O43493	TGON2_HUMAN	trans-golgi network protein 2	404	Cytoplasmic (Potential).					integral to membrane|nucleus|plasma membrane|trans-Golgi network|transport vesicle	protein binding				0						CCGCTTGTTGTGATGAGCGAT	0.562													26	41	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89475970	89475970	+	RNA	SNP	G	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89475970G>C	uc010ytr.1	-	28		c.3511C>G			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		AGTCTTGGAGGCTGGCCTGGC	0.522													6	213	---	---	---	---	PASS
ANKRD36	375248	broad.mit.edu	37	2	97869931	97869931	+	Missense_Mutation	SNP	A	T	T	rs76309140		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97869931A>T	uc010yva.1	+	50	3236	c.2992A>T	c.(2992-2994)ACA>TCA	p.T998S	ANKRD36_uc002sxp.3_RNA	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	998											0						CATTCAGGCTACAAGTGATGA	0.289													3	13	---	---	---	---	PASS
POTEF	728378	broad.mit.edu	37	2	130832762	130832762	+	Silent	SNP	T	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130832762T>C	uc010fmh.2	-	17	2683	c.2283A>G	c.(2281-2283)AAA>AAG	p.K761K		NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on	761	Actin-like.					cell cortex	ATP binding			skin(3)|ovary(2)	5						GGATGCCTCTTTTGCTCTGGG	0.582													4	157	---	---	---	---	PASS
SCN3A	6328	broad.mit.edu	37	2	166020180	166020180	+	Silent	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166020180C>T	uc002ucx.2	-	7	1134	c.642G>A	c.(640-642)GCG>GCA	p.A214A	SCN3A_uc002ucy.2_Silent_p.A214A|SCN3A_uc002ucz.2_Intron|SCN3A_uc002uda.1_Silent_p.A83A|SCN3A_uc002udb.1_Intron	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	214	Helical; Voltage-sensor; Name=S4 of repeat I; (Potential).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)	ATGTTCTCAACGCTGAGACAT	0.408													26	32	---	---	---	---	PASS
CPS1	1373	broad.mit.edu	37	2	211541794	211541794	+	Silent	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211541794C>T	uc002vee.3	+	37	4470	c.4338C>T	c.(4336-4338)GTC>GTT	p.V1446V	CPS1_uc010fur.2_Silent_p.V1452V|CPS1_uc010fus.2_Silent_p.V995V	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	1446					carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		CTAAATTTGTCCATGATAATT	0.378													48	89	---	---	---	---	PASS
SPAG16	79582	broad.mit.edu	37	2	214794778	214794778	+	Missense_Mutation	SNP	C	T	T	rs142357329	byFrequency	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214794778C>T	uc002veq.2	+	12	1401	c.1309C>T	c.(1309-1311)CGC>TGC	p.R437C	SPAG16_uc010fuz.1_Missense_Mutation_p.R288C|SPAG16_uc002ver.2_Missense_Mutation_p.R383C|SPAG16_uc010zjk.1_Missense_Mutation_p.R343C	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1	437	WD 3.				cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		AGGACACAGCCGCGCAGTGTG	0.438													49	50	---	---	---	---	PASS
RPUSD3	285367	broad.mit.edu	37	3	9882343	9882343	+	Intron	SNP	A	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9882343A>C	uc011atk.1	-						ARPC4_uc003btc.1_Intron|RPUSD3_uc011atl.1_Intron|RPUSD3_uc011atm.1_Intron|RPUSD3_uc003btn.2_3'UTR	NM_173659	NP_775930	Q6P087	RUSD3_HUMAN	RNA pseudouridylate synthase domain containing 3						pseudouridine synthesis		pseudouridine synthase activity|RNA binding			central_nervous_system(1)	1	Medulloblastoma(99;0.227)					GCTTGCTGGGACCTCCCCACC	0.602													9	41	---	---	---	---	PASS
FBLN2	2199	broad.mit.edu	37	3	13663379	13663379	+	Intron	SNP	G	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13663379G>T	uc011avb.1	+						FBLN2_uc011auz.1_Intron|FBLN2_uc011ava.1_Missense_Mutation_p.D754Y|FBLN2_uc011avc.1_Missense_Mutation_p.D754Y	NM_001998	NP_001989	P98095	FBLN2_HUMAN	fibulin 2 isoform b precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			GCTCTGTGCCGATGGCTATAT	0.612													11	27	---	---	---	---	PASS
PRSS50	29122	broad.mit.edu	37	3	46759103	46759103	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46759103G>A	uc003cqe.1	-	2	190	c.131C>T	c.(130-132)CCG>CTG	p.P44L	PRSS50_uc003cqf.1_Intron	NM_013270	NP_037402	Q9UI38	TSP50_HUMAN	testes-specific protease 50 precursor	44					proteolysis	endoplasmic reticulum	serine-type endopeptidase activity|threonine-type endopeptidase activity				0						CAGCGCCCCCGGGGCTTCCCC	0.706													12	17	---	---	---	---	PASS
MYH15	22989	broad.mit.edu	37	3	108189627	108189627	+	Missense_Mutation	SNP	C	T	T	rs4299484	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108189627C>T	uc003dxa.1	-	14	1418	c.1361G>A	c.(1360-1362)CGG>CAG	p.R454Q		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	454	Myosin head-like.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						CCTGTTGATCCGTGCCACTAG	0.458													3	46	---	---	---	---	PASS
MYLK	4638	broad.mit.edu	37	3	123451902	123451902	+	Missense_Mutation	SNP	G	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123451902G>C	uc003ego.2	-	11	1639	c.1357C>G	c.(1357-1359)CCC>GCC	p.P453A	MYLK_uc011bjw.1_Missense_Mutation_p.P453A|MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Missense_Mutation_p.P453A|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Missense_Mutation_p.P277A	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	453	Ig-like C2-type 3.				aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CTCCTCACGGGGGTGCCTTCC	0.572													6	26	---	---	---	---	PASS
IFT122	55764	broad.mit.edu	37	3	129188218	129188218	+	Missense_Mutation	SNP	C	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129188218C>G	uc003emm.2	+	9	980	c.774C>G	c.(772-774)GAC>GAG	p.D258E	IFT122_uc003eml.2_Missense_Mutation_p.D309E|IFT122_uc003emn.2_Missense_Mutation_p.D199E|IFT122_uc003emo.2_Missense_Mutation_p.D147E|IFT122_uc003emp.2_Missense_Mutation_p.D108E|IFT122_uc010htc.2_Missense_Mutation_p.D250E|IFT122_uc011bky.1_Missense_Mutation_p.D49E|IFT122_uc003emq.2_Missense_Mutation_p.D98E|IFT122_uc003emr.2_Missense_Mutation_p.D49E|IFT122_uc011bla.1_Missense_Mutation_p.D49E|IFT122_uc011bkx.1_Missense_Mutation_p.D98E|IFT122_uc011bkz.1_RNA	NM_052989	NP_443715	Q9HBG6	IF122_HUMAN	WD repeat domain 10 isoform 2	258					camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2						CTGTGGCTGACTGGGGACAGA	0.443													63	79	---	---	---	---	PASS
ACPP	55	broad.mit.edu	37	3	132075554	132075554	+	Silent	SNP	T	C	C	rs3181784	byFrequency	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132075554T>C	uc010htp.2	+	10	1083	c.993T>C	c.(991-993)TAT>TAC	p.Y331Y	ACPP_uc003eon.3_Silent_p.Y298Y|ACPP_uc003eop.3_Silent_p.Y331Y	NM_001099	NP_001090	P15309	PPAP_HUMAN	acid phosphatase, prostate short isoform	331						extracellular region|lysosomal membrane	5'-nucleotidase activity|acid phosphatase activity			ovary(1)	1						AGATGTACTATCGGAATGAGA	0.537													4	134	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164764719	164764719	+	Silent	SNP	C	A	A	rs9838509	byFrequency	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164764719C>A	uc003fei.2	-	16	1859	c.1797G>T	c.(1795-1797)GCG>GCT	p.A599A		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	599	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	CTAACCAATGCGCAGCATGTC	0.383										HNSCC(35;0.089)			4	86	---	---	---	---	PASS
TNK2	10188	broad.mit.edu	37	3	195591016	195591016	+	3'UTR	SNP	T	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195591016T>A	uc003fvu.1	-	15					TNK2_uc003fvq.1_3'UTR|TNK2_uc003fvr.1_3'UTR|TNK2_uc003fvs.1_3'UTR|TNK2_uc003fvt.1_3'UTR	NM_005781	NP_005772	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2 isoform 1						positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction	adherens junction|cytoplasmic vesicle membrane|endosome|nucleus	ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1)	10	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	CTCAGGTGATTCCTTCAGGCA	0.607													25	50	---	---	---	---	PASS
DGKQ	1609	broad.mit.edu	37	4	956320	956320	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:956320T>C	uc003gbw.2	-	18	2191	c.2117A>G	c.(2116-2118)GAG>GGG	p.E706G	DGKQ_uc010ibn.2_Missense_Mutation_p.E693G	NM_001347	NP_001338	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta	706	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|platelet activation|protein kinase C signaling cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to ATP|thrombin receptor signaling pathway	cytoskeleton|cytosol|nuclear speck|plasma membrane	activating transcription factor binding|ATP binding|diacylglycerol kinase activity|kinase binding|metal ion binding|phospholipase binding			kidney(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCGTCGGCCTCGTCCACAGA	0.657													8	22	---	---	---	---	PASS
DRD5	1816	broad.mit.edu	37	4	9783982	9783982	+	Missense_Mutation	SNP	G	A	A	rs2227849	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9783982G>A	uc003gmb.3	+	1	725	c.329G>A	c.(328-330)GGA>GAA	p.G110E		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	110	Extracellular (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)	TGGCCCTTTGGAGCGTTCTGC	0.612													3	51	---	---	---	---	PASS
PTPN13	5783	broad.mit.edu	37	4	87691273	87691273	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87691273G>T	uc003hpz.2	+	30	5204	c.4724G>T	c.(4723-4725)AGG>ATG	p.R1575M	PTPN13_uc003hpy.2_Missense_Mutation_p.R1580M|PTPN13_uc003hqa.2_Missense_Mutation_p.R1556M|PTPN13_uc003hqb.2_Missense_Mutation_p.R1384M|PTPN13_uc003hqc.1_Translation_Start_Site	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	1575	PDZ 3.					cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TCTGCTCTCAGGGGAACTGCT	0.443													3	29	---	---	---	---	PASS
ADH1B	125	broad.mit.edu	37	4	100237249	100237249	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100237249G>T	uc003hus.3	-	5	457	c.373C>A	c.(373-375)CAG>AAG	p.Q125K	ADH1A_uc011ceg.1_Intron|ADH1B_uc003hut.3_Missense_Mutation_p.Q85K|ADH1B_uc011ceh.1_Intron|ADH1B_uc011cei.1_Missense_Mutation_p.Q85K	NM_000668	NP_000659	P00325	ADH1B_HUMAN	class I alcohol dehydrogenase, beta subunit	125					ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|zinc ion binding			ovary(1)|breast(1)	2				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Fomepizole(DB01213)|NADH(DB00157)	GTGCCATCCTGCAGGGTCCCC	0.547													20	33	---	---	---	---	PASS
SLC9A3	6550	broad.mit.edu	37	5	476353	476353	+	Silent	SNP	C	T	T	rs2230437	byFrequency	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:476353C>T	uc003jbe.2	-	13	2143	c.2031G>A	c.(2029-2031)GCG>GCA	p.A677A	SLC9A3_uc011clx.1_Silent_p.A668A|uc011cly.1_5'Flank	NM_004174	NP_004165	P48764	SL9A3_HUMAN	solute carrier family 9 (sodium/hydrogen	677	Cytoplasmic (Potential).					cell surface|integral to membrane	sodium:hydrogen antiporter activity				0			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			ACAGCTTGGCCGCCTTCTTGT	0.642													3	48	---	---	---	---	PASS
LPCAT1	79888	broad.mit.edu	37	5	1466919	1466919	+	Silent	SNP	G	A	A	rs2277006	byFrequency	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1466919G>A	uc003jcm.2	-	13	1482	c.1365C>T	c.(1363-1365)ACC>ACT	p.T455T	LPCAT1_uc003jcl.2_Silent_p.T29T	NM_024830	NP_079106	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	455	Lumenal (Potential).|EF-hand 2.				phospholipid biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		GGTCGGTCACGGTGAGCTCTG	0.632													5	98	---	---	---	---	PASS
TAS2R1	50834	broad.mit.edu	37	5	9629200	9629200	+	3'UTR	SNP	T	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9629200T>G	uc003jem.1	-	1						NM_019599	NP_062545	Q9NYW7	TA2R1_HUMAN	taste receptor T2R1						chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity			ovary(3)	3						CAGGCATGGGTAAATCATTGA	0.433													5	53	---	---	---	---	PASS
LMBRD2	92255	broad.mit.edu	37	5	36142648	36142648	+	Silent	SNP	A	G	G	rs12658867	byFrequency	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36142648A>G	uc003jkb.1	-	3	643	c.228T>C	c.(226-228)AAT>AAC	p.N76N		NM_001007527	NP_001007528	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	76	Extracellular (Potential).					integral to membrane					0	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TAATGTTGCTATTCTCAGGAG	0.358													4	144	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45262807	45262807	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45262807C>A	uc003jok.2	-	8	1914	c.1889G>T	c.(1888-1890)AGG>ATG	p.R630M		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	630	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						CACCATCTCCCTGTCATGTTT	0.448													4	83	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70806649	70806649	+	Missense_Mutation	SNP	T	A	A	rs1961760	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70806649T>A	uc003kbp.1	+	17	3993	c.3730T>A	c.(3730-3732)TTC>ATC	p.F1244I	BDP1_uc003kbn.1_Missense_Mutation_p.F1244I|BDP1_uc003kbo.2_Missense_Mutation_p.F1244I	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	1244	Potential.|9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.|8; approximate.				regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		GCTAGCAGAGTTCAGTGCTAT	0.403													7	184	---	---	---	---	PASS
MEGF10	84466	broad.mit.edu	37	5	126771182	126771182	+	Splice_Site	SNP	G	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126771182G>C	uc003kuh.3	+	17	2466	c.2104_splice	c.e17+1	p.P702_splice	MEGF10_uc003kui.3_Splice_Site_p.P702_splice	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor						cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		TGCTCTCAACGTAAGTCTTGT	0.373													15	17	---	---	---	---	PASS
TRIM31	11074	broad.mit.edu	37	6	30075864	30075864	+	Silent	SNP	A	G	G	rs113157818		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30075864A>G	uc003npg.1	-	6	959	c.849T>C	c.(847-849)CAT>CAC	p.H283H	TRIM31_uc003npi.3_RNA	NM_007028	NP_008959	Q9BZY9	TRI31_HUMAN	tripartite motif protein 31	283	Potential.					mitochondrion	ligase activity|zinc ion binding			lung(1)	1						TGATGGAGTCATGTCTTGATT	0.438													3	53	---	---	---	---	PASS
FOXO3	2309	broad.mit.edu	37	6	108985053	108985053	+	Silent	SNP	T	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108985053T>C	uc003psk.2	+	3	1333	c.1017T>C	c.(1015-1017)GAT>GAC	p.D339D	FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Silent_p.D339D|FOXO3_uc011ean.1_Silent_p.D119D|FOXO3_uc010kdj.1_Silent_p.D119D	NM_201559	NP_963853	O43524	FOXO3_HUMAN	forkhead box O3A	339					antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding			central_nervous_system(4)|lung(2)	6		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		TCCAGGACGATGATGCGCCTC	0.587													3	32	---	---	---	---	PASS
LAMA4	3910	broad.mit.edu	37	6	112441551	112441551	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112441551T>G	uc003pvu.2	-	33	4909	c.4600A>C	c.(4600-4602)AAT>CAT	p.N1534H	LAMA4_uc003pvv.2_Missense_Mutation_p.N1527H|LAMA4_uc003pvt.2_Missense_Mutation_p.N1527H	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	1534	Laminin G-like 4.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TGACCAACATTAAACATGTAA	0.418													20	16	---	---	---	---	PASS
TSPYL1	7259	broad.mit.edu	37	6	116599606	116599606	+	3'UTR	SNP	T	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116599606T>A	uc003pwp.3	-	1					DSE_uc011ebf.1_Intron|DSE_uc003pwq.1_5'Flank|DSE_uc003pwr.2_5'Flank|DSE_uc003pws.2_5'Flank	NM_003309	NP_003300	Q9H0U9	TSYL1_HUMAN	TSPY-like 1						nucleosome assembly	nucleolus					0		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)		GGCATACTCATTGCTGATGCC	0.483													24	4	---	---	---	---	PASS
C6orf170	221322	broad.mit.edu	37	6	121577370	121577370	+	Missense_Mutation	SNP	T	C	C	rs7745023	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121577370T>C	uc003pyo.1	-	16	1863	c.1795A>G	c.(1795-1797)ATA>GTA	p.I599V	C6orf170_uc003pyq.1_RNA|C6orf170_uc003pyp.1_Missense_Mutation_p.I118V	NM_152730	NP_689943	Q96NH3	BROMI_HUMAN	hypothetical protein LOC221322	599					multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)		CCAGAAAATATAGAAATATCT	0.353													3	45	---	---	---	---	PASS
SRCRB4D	136853	broad.mit.edu	37	7	76029805	76029805	+	Silent	SNP	G	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76029805G>A	uc003ufb.2	-	4	621	c.273C>T	c.(271-273)GAC>GAT	p.D91D	ZP3_uc003ufc.3_Intron	NM_080744	NP_542782	Q8WTU2	SRB4D_HUMAN	scavenger receptor cysteine rich domain	91	SRCR 1.					extracellular region|membrane	scavenger receptor activity			pancreas(1)	1						CTACGTTGGCGTCCACCACGT	0.701													6	7	---	---	---	---	PASS
ABCB1	5243	broad.mit.edu	37	7	87138593	87138593	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87138593T>C	uc003uiz.1	-	27	3905	c.3487A>G	c.(3487-3489)AAT>GAT	p.N1163D	ABCB1_uc011khc.1_Missense_Mutation_p.N1099D	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	1163	Cytoplasmic (Potential).|ABC transporter 2.				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	AGACTTACATTAGGCAGTGAC	0.493													23	178	---	---	---	---	PASS
SERPINE1	5054	broad.mit.edu	37	7	100780229	100780229	+	Intron	SNP	T	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100780229T>G	uc003uxt.2	+						SERPINE1_uc011kkj.1_Intron|SERPINE1_uc003uxu.1_3'UTR	NM_000602	NP_000593	P05121	PAI1_HUMAN	plasminogen activator inhibitor-1 isoform 1						angiogenesis|cellular response to chemical stimulus|cellular response to lipopolysaccharide|chronological cell aging|defense response to Gram-negative bacterium|fibrinolysis|negative regulation of apoptosis|negative regulation of cell adhesion mediated by integrin|negative regulation of fibrinolysis|negative regulation of plasminogen activation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell-matrix adhesion|negative regulation of vascular wound healing|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of interleukin-8 production|positive regulation of leukotriene production involved in inflammatory response|positive regulation of monocyte chemotaxis|positive regulation of receptor-mediated endocytosis|regulation of receptor activity	extracellular matrix|extracellular space|plasma membrane|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)				Atorvastatin(DB01076)|Dimethyl sulfoxide(DB01093)|Drotrecogin alfa(DB00055)|Simvastatin(DB00641)|Tenecteplase(DB00031)|Troglitazone(DB00197)|Urokinase(DB00013)	GGGGTGGGGGTGGTGCCAGTG	0.348													9	34	---	---	---	---	PASS
CUX1	1523	broad.mit.edu	37	7	101845118	101845118	+	Silent	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101845118C>T	uc003uyx.3	+	18	2579	c.2541C>T	c.(2539-2541)GGC>GGT	p.G847G	CUX1_uc003uys.3_Silent_p.G858G|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a	847					negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						AAGAAACGGGCGGCGGGAAAG	0.687													5	75	---	---	---	---	PASS
CTTNBP2	83992	broad.mit.edu	37	7	117386131	117386131	+	Missense_Mutation	SNP	A	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117386131A>T	uc003vjf.2	-	13	3463	c.3371T>A	c.(3370-3372)ATT>AAT	p.I1124N		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1124										ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		GCCGTGGAAAATGACATTATG	0.398											OREG0003442	type=REGULATORY REGION|Gene=CTTNBP2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	24	47	---	---	---	---	PASS
TRYX3	136541	broad.mit.edu	37	7	141952406	141952406	+	Silent	SNP	A	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141952406A>C	uc003vxb.2	-	4	782	c.462T>G	c.(460-462)ACT>ACG	p.T154T	TRYX3_uc003vxc.3_Silent_p.T154T	NM_001001317	NP_001001317	Q8IYP2	PRS58_HUMAN	trypsin X3 precursor	154	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity				0	Melanoma(164;0.0272)					AGATGTTCACAGTTTGCAGTG	0.383													9	229	---	---	---	---	PASS
FUT10	84750	broad.mit.edu	37	8	33246419	33246419	+	Intron	SNP	G	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33246419G>A	uc003xje.2	-						FUT10_uc003xjc.2_Intron|FUT10_uc003xjd.2_Intron|FUT10_uc011lbi.1_Intron|FUT10_uc003xjf.2_3'UTR|FUT10_uc003xjg.2_3'UTR|FUT10_uc003xjh.2_3'UTR	NM_032664	NP_116053	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10						embryo development|fertilization|hemopoiesis|L-fucose catabolic process|nervous system development|protein folding|protein glycosylation|protein targeting|wound healing	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)|pancreas(1)	2				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		GGAAATGCAGGAGAGCAGAGA	0.468													14	18	---	---	---	---	PASS
TRIM55	84675	broad.mit.edu	37	8	67064654	67064654	+	Missense_Mutation	SNP	A	G	G	rs7843605	byFrequency	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67064654A>G	uc003xvv.2	+	8	1254	c.1028A>G	c.(1027-1029)AAA>AGA	p.K343R	TRIM55_uc003xvu.2_Missense_Mutation_p.K343R|TRIM55_uc003xvw.2_Missense_Mutation_p.K343R|TRIM55_uc003xvx.2_Intron	NM_184085	NP_908973	Q9BYV6	TRI55_HUMAN	tripartite motif-containing 55 isoform 1	343						cytoplasm|microtubule|nucleus	signal transducer activity|zinc ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			gaaggagaaaaagaaggagaa	0.199													3	49	---	---	---	---	PASS
SLC45A4	57210	broad.mit.edu	37	8	142222492	142222492	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142222492C>T	uc003ywd.1	-	7	2260	c.1952G>A	c.(1951-1953)GGC>GAC	p.G651D	SLC45A4_uc003ywc.1_Missense_Mutation_p.G651D|SLC45A4_uc010meq.1_Missense_Mutation_p.G649D	NM_001080431	NP_001073900	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4	702	Helical; (Potential).				transport	integral to membrane				ovary(2)	2	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			CAGGAAAGAGCCCACAGAGGC	0.627													18	37	---	---	---	---	PASS
BAI1	575	broad.mit.edu	37	8	143603449	143603449	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143603449C>T	uc003ywm.2	+	20	3331	c.3148C>T	c.(3148-3150)CGC>TGC	p.R1050C		NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1050	Cytoplasmic (Potential).				axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1)	8	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCGCCTCATCCGCAAGCGCTT	0.652													10	30	---	---	---	---	PASS
PIGO	84720	broad.mit.edu	37	9	35090094	35090094	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35090094C>A	uc003zwd.2	-	9	3434	c.3038G>T	c.(3037-3039)GGC>GTC	p.G1013V	PIGO_uc003zwc.1_3'UTR|PIGO_uc003zwe.2_Missense_Mutation_p.G596V|PIGO_uc003zwf.2_Missense_Mutation_p.G596V|PIGO_uc003zwg.1_3'UTR	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	1013					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GTACTTGAGGCCCAGCTGCAG	0.537													5	79	---	---	---	---	PASS
NTRK2	4915	broad.mit.edu	37	9	87285613	87285613	+	5'UTR	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87285613C>T	uc004aoa.1	+	4					NTRK2_uc004anv.1_5'UTR|NTRK2_uc004any.1_5'UTR|NTRK2_uc004anz.1_5'UTR|NTRK2_uc011lsz.1_5'UTR|NTRK2_uc011lta.1_5'UTR|NTRK2_uc004aob.1_5'UTR|NTRK2_uc011ltb.1_5'Flank	NM_001018064	NP_001018074	Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16						TGGGGGAAAGCGGCCGGTGCA	0.682										TSP Lung(25;0.17)			8	91	---	---	---	---	PASS
RC3H2	54542	broad.mit.edu	37	9	125642493	125642493	+	Intron	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125642493C>T	uc010mwc.1	-						RC3H2_uc004bnc.2_Intron|RC3H2_uc004bnd.1_Intron|RC3H2_uc004bne.3_Intron|RC3H2_uc011lzf.1_Intron|RC3H2_uc011lzg.1_Intron|SNORD90_uc004bnf.1_RNA	NM_001100588	NP_001094058	Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type zinc finger domains 2							cell surface|endomembrane system|membrane|membrane fraction|perinuclear region of cytoplasm	DNA binding|zinc ion binding			ovary(2)|lung(2)	4						ATATTTAATACGTTTTCAAGT	0.313													34	40	---	---	---	---	PASS
SLC27A4	10999	broad.mit.edu	37	9	131107632	131107632	+	Silent	SNP	C	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131107632C>G	uc004but.2	+	3	644	c.360C>G	c.(358-360)GCC>GCG	p.A120A	SLC27A4_uc004buu.2_Intron	NM_005094	NP_005085	Q6P1M0	S27A4_HUMAN	solute carrier family 27 (fatty acid	120					long-chain fatty acid transport|transmembrane transport	integral to membrane	fatty acid transporter activity|nucleotide binding|protein binding				0						TCCTGCAGGCCCGGGGCCTGG	0.622													16	29	---	---	---	---	PASS
HSD17B7P2	158160	broad.mit.edu	37	10	38645343	38645343	+	5'UTR	SNP	C	T	T	rs75687299	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38645343C>T	uc010qex.1	+	1					HSD17B7P2_uc001izq.2_RNA|HSD17B7P2_uc010qew.1_5'UTR|HSD17B7P2_uc001izo.1_RNA|HSD17B7P2_uc001izp.1_5'UTR					SubName: Full=cDNA FLJ60462, highly similar to 3-keto-steroid reductase (EC 1.1.1.270);												0						AAAGCAGCGGCGGCGTTTGCT	0.597													9	7	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	51818992	51818992	+	RNA	SNP	G	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51818992G>T	uc001jiz.1	-	3		c.1439C>A								Homo sapiens cDNA FLJ31813 fis, clone NT2RI2009517.																		AGGCTTCTGTGGCTCCTTCAT	0.473													3	31	---	---	---	---	PASS
TET1	80312	broad.mit.edu	37	10	70446226	70446226	+	Silent	SNP	G	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70446226G>A	uc001jok.3	+	11	5671	c.5166G>A	c.(5164-5166)AAG>AAA	p.K1722K		NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6	1722					DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9						TTGGCTCCAAGGAAGGAATGG	0.498													51	75	---	---	---	---	PASS
ADAMTS14	140766	broad.mit.edu	37	10	72493828	72493828	+	Intron	SNP	A	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72493828A>C	uc001jrh.2	+						ADAMTS14_uc001jrg.2_Intron|ADAMTS14_uc001jri.1_5'UTR	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6						GGAGCATGCGACCTGCCACTC	0.627													6	13	---	---	---	---	PASS
MKI67	4288	broad.mit.edu	37	10	129901213	129901213	+	Missense_Mutation	SNP	C	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129901213C>G	uc001lke.2	-	13	9086	c.8891G>C	c.(8890-8892)CGG>CCG	p.R2964P	MKI67_uc001lkf.2_Missense_Mutation_p.R2604P|MKI67_uc009yav.1_Missense_Mutation_p.R2539P|MKI67_uc009yaw.1_Missense_Mutation_p.R2114P	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	2964					cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTTAGGGGCCCGAAGAACTCT	0.493													58	133	---	---	---	---	PASS
JAKMIP3	282973	broad.mit.edu	37	10	133955427	133955427	+	Missense_Mutation	SNP	A	G	G	rs11592585	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133955427A>G	uc001lkx.3	+	10	1477	c.1477A>G	c.(1477-1479)ATG>GTG	p.M493V		NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TCTCCAGGGCATGGCCAAGGA	0.642													5	7	---	---	---	---	PASS
NDUFV1	4723	broad.mit.edu	37	11	67378012	67378012	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67378012G>T	uc001omj.2	+	5	824	c.671G>T	c.(670-672)CGC>CTC	p.R224L	NDUFV1_uc010rpv.1_Missense_Mutation_p.R123L|NDUFV1_uc001oml.2_Missense_Mutation_p.R217L|NDUFV1_uc001omk.3_Missense_Mutation_p.R215L|NDUFV1_uc009yrz.1_Missense_Mutation_p.R123L|NDUFV1_uc010rpw.1_5'Flank	NM_007103	NP_009034	P49821	NDUV1_HUMAN	NADH dehydrogenase ubiquinone flavoprotein 1	224	FMN (By similarity).				mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|FMN binding|metal ion binding|NAD binding|NADH dehydrogenase (ubiquinone) activity			skin(1)	1					NADH(DB00157)	GGCAAGCCCCGCCTGAAGCCC	0.617													8	49	---	---	---	---	PASS
FAM181B	220382	broad.mit.edu	37	11	82443417	82443417	+	3'UTR	SNP	C	T	T	rs3780	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82443417C>T	uc001ozp.2	-	1						NM_175885	NP_787081	A6NEQ2	F181B_HUMAN	hypothetical protein LOC220382											large_intestine(1)	1						CATCGTTCTTCAGATTTAGGA	0.493													8	3	---	---	---	---	PASS
A2M	2	broad.mit.edu	37	12	9268473	9268473	+	5'UTR	SNP	A	C	C	rs226380	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9268473A>C	uc001qvk.1	-	1					A2M_uc009zgk.1_5'UTR	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor						blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	CTGGAGGAGAACAGACTGTAT	0.502													4	66	---	---	---	---	PASS
KLRD1	3824	broad.mit.edu	37	12	10467533	10467533	+	3'UTR	SNP	T	A	A	rs2537752	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10467533T>A	uc001qxw.3	+	7					KLRD1_uc001qxx.3_3'UTR|KLRD1_uc001qxy.3_3'UTR|KLRD1_uc009zhh.2_3'UTR|KLRD1_uc009zhi.2_3'UTR|KLRD1_uc001qxz.3_3'UTR	NM_001114396	NP_001107868	Q13241	KLRD1_HUMAN	killer cell lectin-like receptor subfamily D,						cell surface receptor linked signaling pathway|regulation of immune response	integral to membrane|plasma membrane	sugar binding|transmembrane receptor activity				0						AATTGTCATGTATGTGAAACA	0.209													5	3	---	---	---	---	PASS
RPL13AP20	387841	broad.mit.edu	37	12	13028751	13028751	+	Missense_Mutation	SNP	G	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13028751G>C	uc010sho.1	+	1	341	c.319G>C	c.(319-321)GGC>CGC	p.G107R		NR_003932				SubName: Full=Ribosomal protein L13a variant; Flags: Fragment;												0						GGTGTTTGACGGCATCCCACC	0.612													3	11	---	---	---	---	PASS
TWF1	5756	broad.mit.edu	37	12	44189532	44189532	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44189532C>A	uc001rob.2	-	10	1060	c.1032G>T	c.(1030-1032)TTG>TTT	p.L344F	TWF1_uc001rnz.2_Missense_Mutation_p.L205F|TWF1_uc001roa.2_Missense_Mutation_p.L337F|TWF1_uc001roc.2_Missense_Mutation_p.L205F	NM_002822	NP_002813	Q12792	TWF1_HUMAN	twinfilin 1	303	ADF-H 2.					actin cytoskeleton|cytoplasm	actin binding|protein tyrosine kinase activity			stomach(1)	1	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		AGTCTGCAGTCAACTCATCCC	0.383													38	59	---	---	---	---	PASS
KRT6A	3853	broad.mit.edu	37	12	52886490	52886490	+	Silent	SNP	A	G	G	rs711317	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52886490A>G	uc001sam.2	-	1	692	c.483T>C	c.(481-483)GCT>GCC	p.A161A		NM_005554	NP_005545	P02538	K2C6A_HUMAN	keratin 6A	161	Head.				cell differentiation|ectoderm development|positive regulation of cell proliferation	keratin filament	protein binding|structural constituent of cytoskeleton			ovary(4)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.189)		CACGCTCCTCAGCCCGCACCC	0.597													4	152	---	---	---	---	PASS
NACA	4666	broad.mit.edu	37	12	57108203	57108203	+	Silent	SNP	A	G	G	rs4902	byFrequency	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57108203A>G	uc001slz.2	-	4	526	c.177T>C	c.(175-177)ATT>ATC	p.I59I	NACA_uc001sly.2_Silent_p.I59I|NACA_uc009zoy.1_Silent_p.I1922I|NACA_uc001smc.2_Silent_p.I59I|NACA_uc001sma.2_Silent_p.I769I|NACA_uc001smb.2_Silent_p.I59I|NACA_uc010squ.1_RNA	NM_001113201	NP_001106672	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha	59					interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1						GTTCTTCATCAATTTCAGCTG	0.398			T	BCL6	NHL								3	61	---	---	---	---	PASS
RFX4	5992	broad.mit.edu	37	12	107075878	107075878	+	Intron	SNP	G	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107075878G>T	uc001tlr.2	+						RFX4_uc010swv.1_Intron|RFX4_uc001tls.2_Intron|RFX4_uc001tlt.2_Intron|RFX4_uc001tlv.2_5'Flank|uc001tlu.3_RNA	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c						transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1						ACATCTATGGGCCTCGAGACA	0.562													9	53	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19415742	19415742	+	RNA	SNP	T	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19415742T>C	uc010tcj.1	-	1		c.30368A>G				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						GCTGTTTTCCTAATCTTTCTT	0.313													4	60	---	---	---	---	PASS
TPTE2	93492	broad.mit.edu	37	13	20049751	20049751	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20049751C>A	uc001umd.2	-	6	403	c.192G>T	c.(190-192)AAG>AAT	p.K64N	TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_RNA	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	64						endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		GCACAATTTTCTTAATCTTGC	0.244													20	33	---	---	---	---	PASS
DLK1	8788	broad.mit.edu	37	14	101200645	101200645	+	Silent	SNP	T	C	C	rs1802710	byFrequency	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101200645T>C	uc001yhs.3	+	5	717	c.564T>C	c.(562-564)ATT>ATC	p.I188I	DLK1_uc001yhu.3_Silent_p.I188I	NM_003836	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog precursor	188	EGF-like 5.|Extracellular (Potential).				multicellular organismal development	extracellular space|integral to membrane|soluble fraction				ovary(2)|breast(1)|skin(1)	4		Melanoma(154;0.155)				GCACTGACATTGGGGGCGACT	0.667													3	82	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106208715	106208715	+	RNA	SNP	T	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106208715T>G	uc010tyt.1	-	3626		c.58617A>C			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_5'UTR|uc001ysf.2_5'UTR					Parts of antibodies, mostly variable regions.												0						TGTCACAAGATTTGGGCTCTG	0.582													91	130	---	---	---	---	PASS
MIR1826	100302162	broad.mit.edu	37	16	33965582	33965582	+	RNA	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33965582C>T	hsa-mir-1826|MI0008194	+			c.75C>T																				0						GCGTCGCTTGCCGATCAGTAG	0.632													4	27	---	---	---	---	PASS
MIR1826	100302162	broad.mit.edu	37	16	33965589	33965589	+	RNA	SNP	G	A	A	rs62030476	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33965589G>A	hsa-mir-1826|MI0008194	+			c.82G>A																				0						TTGCCGATCAGTAGTCCCCGG	0.647													6	26	---	---	---	---	PASS
CCDC113	29070	broad.mit.edu	37	16	58313805	58313805	+	3'UTR	SNP	G	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58313805G>A	uc002ene.2	+	9					CCDC113_uc010vid.1_3'UTR	NM_014157	NP_054876	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113 isoform 1							protein complex					0						CACCCAGGCTGCGTATCATCT	0.542													10	2	---	---	---	---	PASS
ZZEF1	23140	broad.mit.edu	37	17	3980274	3980274	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3980274T>G	uc002fxe.2	-	20	3063	c.2999A>C	c.(2998-3000)CAG>CCG	p.Q1000P	ZZEF1_uc002fxk.1_Missense_Mutation_p.Q1001P	NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1	1000							calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TGCCAGAAACTGGCCCACATC	0.363													18	40	---	---	---	---	PASS
ALOX15	246	broad.mit.edu	37	17	4542894	4542894	+	Silent	SNP	A	G	G	rs145728418	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4542894A>G	uc002fyh.2	-	2	182	c.168T>C	c.(166-168)TAT>TAC	p.Y56Y	ALOX15_uc010vsd.1_Intron|ALOX15_uc010vse.1_Silent_p.Y78Y	NM_001140	NP_001131	P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	56	PLAT.				inflammatory response|leukotriene biosynthetic process	nucleus	arachidonate 15-lipoxygenase activity|iron ion binding|lipoxygenase activity			skin(3)|ovary(1)|lung(1)	5				READ - Rectum adenocarcinoma(115;0.0327)	Ciclopirox(DB01188)|Masoprocol(DB00179)|Zileuton(DB00744)	GCGGCCCCAGATACTCCGGTA	0.657													5	25	---	---	---	---	PASS
ACAP1	9744	broad.mit.edu	37	17	7250419	7250419	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7250419C>T	uc002ggd.2	+	14	1407	c.1201C>T	c.(1201-1203)CCT>TCT	p.P401S		NM_014716	NP_055531	Q15027	ACAP1_HUMAN	centaurin beta1	401					intracellular signal transduction|lipid metabolic process|protein transport|regulation of ARF GTPase activity		ARF GTPase activator activity|phospholipase C activity|protein binding|zinc ion binding			breast(2)|large_intestine(1)	3						GGGAAGGGAGCCTGGGGGAGT	0.677													7	40	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9061392	9061392	+	Missense_Mutation	SNP	G	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9061392G>C	uc002mkp.2	-	3	26258	c.26054C>G	c.(26053-26055)ACA>AGA	p.T8685R		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8687	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GGAAACACTTGTATTCCCCAG	0.458													35	45	---	---	---	---	PASS
CILP2	148113	broad.mit.edu	37	19	19654189	19654189	+	Silent	SNP	G	A	A	rs45556231	byFrequency	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19654189G>A	uc002nmv.3	+	7	1195	c.1110G>A	c.(1108-1110)TCG>TCA	p.S370S	CILP2_uc002nmw.3_Silent_p.S376S	NM_153221	NP_694953	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	370	Ig-like C2-type.					proteinaceous extracellular matrix	carbohydrate binding|carboxypeptidase activity			ovary(1)	1						CCGTGCGCTCGGGCACTGCCC	0.647													3	64	---	---	---	---	PASS
MAP3K10	4294	broad.mit.edu	37	19	40698519	40698519	+	Missense_Mutation	SNP	A	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40698519A>G	uc002ona.2	+	1	869	c.581A>G	c.(580-582)CAC>CGC	p.H194R		NM_002446	NP_002437	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase	194	Protein kinase.				activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway	cytoplasm	ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity			ovary(2)|lung(2)|skin(1)|pancreas(1)	6						GTGCCACCTCACGTGCTGGTC	0.642													10	17	---	---	---	---	PASS
C19orf47	126526	broad.mit.edu	37	19	40832339	40832339	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40832339C>T	uc002oni.3	-	7	606	c.605G>A	c.(604-606)CGG>CAG	p.R202Q	C19orf47_uc002ong.2_Missense_Mutation_p.R61Q|C19orf47_uc002onh.2_Missense_Mutation_p.R135Q	NM_178830	NP_849152	Q8N9M1	CS047_HUMAN	hypothetical protein LOC126526	202										ovary(1)|skin(1)	2			Lung(22;0.000636)			AGCAGTGACCCGGCGCCGCTT	0.627													11	26	---	---	---	---	PASS
SIRPB1	10326	broad.mit.edu	37	20	1600530	1600530	+	Silent	SNP	G	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1600530G>A	uc010gai.2	-	1	160	c.61C>T	c.(61-63)CTG>TTG	p.L21L	SIRPB1_uc002wfk.3_Silent_p.L21L|SIRPB1_uc002wfl.3_Silent_p.L21L	NM_006065	NP_006056	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1 isoform 1	21					cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding			ovary(1)	1						AGTCTCCCCAGCAGTAGCGTC	0.562													28	41	---	---	---	---	PASS
C20orf191	149934	broad.mit.edu	37	20	26084111	26084111	+	Missense_Mutation	SNP	A	G	G	rs75722320	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26084111A>G	uc002wvj.3	-	2	360	c.305T>C	c.(304-306)GTC>GCC	p.V102A		NR_003678				SubName: Full=Putative uncharacterized protein ENSP00000323172;												0						AATATATTAGACGAAGACTTT	0.194													2	18	---	---	---	---	PASS
SULF2	55959	broad.mit.edu	37	20	46301111	46301111	+	Silent	SNP	C	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46301111C>A	uc002xto.2	-	11	1737	c.1407G>T	c.(1405-1407)ACG>ACT	p.T469T	SULF2_uc002xtr.2_Silent_p.T469T|SULF2_uc002xtq.2_Silent_p.T469T	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	469					bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6						TCAGCTTCCCCGTGGCGTCCT	0.652													3	29	---	---	---	---	PASS
XIST	7503	broad.mit.edu	37	X	73066388	73066388	+	RNA	SNP	G	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73066388G>T	uc004ebm.1	-	1		c.6201C>A				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0						AATGAGCAGTGTGCGATTACG	0.463													63	15	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76891438	76891438	+	Missense_Mutation	SNP	A	G	G			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76891438A>G	uc004ecp.3	-	16	4899	c.4667T>C	c.(4666-4668)ATG>ACG	p.M1556T	ATRX_uc004ecq.3_Missense_Mutation_p.M1518T|ATRX_uc004eco.3_Missense_Mutation_p.M1341T	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	1556					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)	TTTGATAACCATATTTCTATG	0.338			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						18	5	---	---	---	---	PASS
RBMX	27316	broad.mit.edu	37	X	135960230	135960230	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135960230C>T	uc004fae.1	-	4	442	c.232G>A	c.(232-234)GCC>ACC	p.A78T	RBMX_uc011mwf.1_Intron|RBMX_uc004fad.1_Missense_Mutation_p.A78T|RBMX_uc011mwg.1_Missense_Mutation_p.A39T|RBMX_uc004faf.1_Intron|RBMX_uc010nsf.1_Missense_Mutation_p.A39T|RBMX_uc004fag.1_5'UTR	NM_002139	NP_002130	P38159	HNRPG_HUMAN	RNA binding motif protein, X-linked isoform 1	78	RRM.					catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					ACCTTGATGGCTTTTCCATCT	0.398													9	20	---	---	---	---	PASS
CAPZA1	829	broad.mit.edu	37	1	113202204	113202208	+	Intron	DEL	CTCTC	-	-	rs60025142	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113202204_113202208delCTCTC	uc001ecj.1	+							NM_006135	NP_006126	P52907	CAZA1_HUMAN	F-actin capping protein alpha-1 subunit						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex|WASH complex	actin binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTTCTCTCTCTCTCTTTTTTTTTT	0.395													5	3	---	---	---	---	
MAGI3	260425	broad.mit.edu	37	1	114186352	114186352	+	Intron	DEL	T	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114186352delT	uc001edk.2	+						MAGI3_uc001edh.3_Intron|MAGI3_uc001edi.3_Intron|MAGI3_uc010owm.1_Intron|MAGI3_uc001edj.2_Intron	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3						apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTTTGGTTCATTTTTTTTTTA	0.378													47	8	---	---	---	---	
RGPD4	285190	broad.mit.edu	37	2	108479623	108479623	+	Intron	DEL	T	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108479623delT	uc010ywk.1	+						RGPD4_uc002tdu.2_Intron|RGPD4_uc010ywl.1_Intron	NM_182588	NP_872394	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4						intracellular transport		binding			skin(2)	2						CATTTTGGTCttttttttttt	0.234													14	7	---	---	---	---	
UGGT1	56886	broad.mit.edu	37	2	128908420	128908421	+	Intron	INS	-	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128908420_128908421insT	uc002tps.2	+						UGGT1_uc010fme.1_Intron|UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1						'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						TTGTTGCCAGAtttttttttct	0.218													4	2	---	---	---	---	
TTC21B	79809	broad.mit.edu	37	2	166802307	166802310	+	Intron	DEL	CTGT	-	-	rs5836067		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166802307_166802310delCTGT	uc002udk.2	-						TTC21B_uc002udl.2_Intron|uc002udm.1_Intron	NM_024753	NP_079029	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B							cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5						TATAGTGgtactgtctaatagaaa	0.123													6	5	---	---	---	---	
COL4A3	1285	broad.mit.edu	37	2	228118135	228118135	+	Intron	DEL	C	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228118135delC	uc002vom.1	+						COL4A3_uc002von.1_Intron|COL4A3_uc002voo.1_Intron|COL4A3_uc002vop.1_Intron|uc002voq.1_Intron|uc002vor.1_Intron	NM_000091	NP_000082	Q01955	CO4A3_HUMAN	alpha 3 type IV collagen isoform 1 precursor						activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		TACTTACGGGCCAAGCTGAAA	0.388													97	15	---	---	---	---	
USP4	7375	broad.mit.edu	37	3	49339623	49339624	+	Intron	DEL	AA	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49339623_49339624delAA	uc003cwq.2	-						USP4_uc003cwo.2_Intron|USP4_uc003cwp.2_Intron|USP4_uc003cwr.2_Intron	NM_003363	NP_003354	Q13107	UBP4_HUMAN	ubiquitin specific protease 4 isoform a						negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)|lung(1)	4		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		gtctctatttaaaaaaaaaaaa	0.208													3	3	---	---	---	---	
SEC24B	10427	broad.mit.edu	37	4	110442148	110442149	+	Intron	INS	-	A	A	rs149123491	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110442148_110442149insA	uc003hzk.2	+						SEC24B_uc003hzl.2_Intron|SEC24B_uc011cfp.1_Intron|SEC24B_uc011cfq.1_Intron|SEC24B_uc011cfr.1_Intron	NM_006323	NP_006314	O95487	SC24B_HUMAN	SEC24 (S. cerevisiae) homolog B isoform a						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		aactccatctcaaaaaaataaa	0.094													3	4	---	---	---	---	
METTL14	57721	broad.mit.edu	37	4	119613381	119613382	+	Intron	INS	-	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119613381_119613382insT	uc003icf.2	+						METTL14_uc003icg.2_Intron	NM_020961	NP_066012	Q9HCE5	MTL14_HUMAN	methyltransferase like 14							nucleus	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity				0						cttttcttttcttttttttttt	0.139													3	3	---	---	---	---	
WWC2	80014	broad.mit.edu	37	4	184192200	184192200	+	Intron	DEL	T	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184192200delT	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron|WWC2_uc003ivn.3_Intron|WWC2_uc010irz.2_Intron	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		CTCTTCCTTATTTTTTTTTCT	0.299													3	9	---	---	---	---	
SLC9A3	6550	broad.mit.edu	37	5	482152	482152	+	Intron	DEL	C	-	-	rs56916156		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:482152delC	uc003jbe.2	-						SLC9A3_uc011clx.1_Intron	NM_004174	NP_004165	P48764	SL9A3_HUMAN	solute carrier family 9 (sodium/hydrogen							cell surface|integral to membrane	sodium:hydrogen antiporter activity				0			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			ACACGCAGTGCCCCCCCCCCG	0.706													3	4	---	---	---	---	
C6	729	broad.mit.edu	37	5	41149200	41149200	+	Intron	DEL	C	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41149200delC	uc003jmk.2	-						C6_uc003jml.1_Intron	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor						complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				attttcctttctgtttaaatc	0.075													22	15	---	---	---	---	
SNCAIP	9627	broad.mit.edu	37	5	121787399	121787400	+	Intron	INS	-	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121787399_121787400insA	uc003ksw.1	+						SNCAIP_uc011cwl.1_Intron|SNCAIP_uc003ksx.1_Intron|SNCAIP_uc003ksy.1_Intron|SNCAIP_uc003ksz.1_Intron|SNCAIP_uc010jcu.2_Intron|uc003ktb.1_Intron|SNCAIP_uc003ktc.1_Intron	NM_005460	NP_005451	Q9Y6H5	SNCAP_HUMAN	synuclein alpha interacting protein						cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		GAATCCCCAGGAAAAAAAAAAA	0.376													6	3	---	---	---	---	
SLC35B3	51000	broad.mit.edu	37	6	8417377	8417377	+	Intron	DEL	A	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8417377delA	uc010joe.2	-						SLC35B3_uc003mya.2_Intron|SLC35B3_uc003myc.2_Intron|SLC35B3_uc003myb.2_Intron|SLC35B3_uc011did.1_Intron|SLC35B3_uc003myd.2_Intron	NM_001142541	NP_001136013	Q9H1N7	S35B3_HUMAN	solute carrier family 35, member B3						transmembrane transport	Golgi membrane|integral to membrane					0	Ovarian(93;0.0569)					TGATTTAATGAAAAAAAAATG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	12514213	12514236	+	IGR	DEL	CACACACACACACACACACACGCG	-	-	rs145031469	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12514213_12514236delCACACACACACACACACACACGCG								EDN1 (216787 upstream) : PHACTR1 (202652 downstream)																							cacacacacacacacacacacacacacacacgcgcacacacaca	0.308													4	3	---	---	---	---	
NOX3	50508	broad.mit.edu	37	6	155761273	155761274	+	Splice_Site	INS	-	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155761273_155761274insA	uc003qqm.2	-	6	590	c.487_splice	c.e6-1	p.N163_splice		NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3								electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		GGTTGTGTTCTaaaaaaaacaa	0.322													33	28	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	33075635	33075635	+	Intron	DEL	A	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33075635delA	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						AGCAAAAGAGAAAAAAAAAAG	0.328													206	8	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33312723	33312723	+	Frame_Shift_Del	DEL	T	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33312723delT	uc003tdn.1	+	8	1315	c.802delT	c.(802-804)TTTfs	p.F268fs	BBS9_uc003tdo.1_Frame_Shift_Del_p.F268fs|BBS9_uc003tdp.1_Frame_Shift_Del_p.F268fs|BBS9_uc003tdq.1_Frame_Shift_Del_p.F268fs|BBS9_uc010kwn.1_RNA|BBS9_uc011kan.1_Frame_Shift_Del_p.F268fs|BBS9_uc011kao.1_Frame_Shift_Del_p.F146fs	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	268					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			TGAGAGAAACTTTTTTTGCCT	0.393									Bardet-Biedl_syndrome				512	7	---	---	---	---	
NUP205	23165	broad.mit.edu	37	7	135287859	135287860	+	Intron	DEL	AC	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135287859_135287860delAC	uc003vsw.2	+							NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						GCCTCAttttactttttttttt	0.153													6	4	---	---	---	---	
AGK	55750	broad.mit.edu	37	7	141321435	141321436	+	Intron	DEL	TG	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141321435_141321436delTG	uc003vwi.2	+						AGK_uc011krg.1_Intron	NM_018238	NP_060708	Q53H12	AGK_HUMAN	acylglycerol kinase precursor						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway	mitochondrial membrane	acylglycerol kinase activity|ATP binding|diacylglycerol kinase activity|NAD+ kinase activity			ovary(1)|breast(1)	2	Melanoma(164;0.0171)					agagagaAtatgtgtgtgtgtg	0.188													24	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142139683	142139684	+	Intron	INS	-	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142139683_142139684insA	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc011krv.1_5'Flank|uc003vyt.3_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		cctacacacaGAAAAAAAAATG	0.332													245	8	---	---	---	---	
AQP7P1	375719	broad.mit.edu	37	9	67272725	67272725	+	Intron	DEL	G	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67272725delG	uc004aem.1	-						AQP7P1_uc004aen.1_Intron|AQP7P1_uc004aeo.1_RNA|AQP7P1_uc004aep.1_RNA					Homo sapiens aquaporin 7 pseudogene 1, mRNA (cDNA clone IMAGE:6191443).												0						GTGAAGATGCGGGGGGGGGGG	0.577													4	4	---	---	---	---	
TLE4	7091	broad.mit.edu	37	9	82269146	82269146	+	Intron	DEL	T	-	-	rs35639126		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82269146delT	uc004ald.2	+						TLE4_uc004alc.2_Intron|TLE4_uc010mpr.2_Intron|TLE4_uc004ale.2_Intron|TLE4_uc011lsq.1_Intron|TLE4_uc010mps.2_Intron|TLE4_uc004alf.2_Intron	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4											lung(2)|ovary(1)|breast(1)|skin(1)	5						GTGTGGTTGattttttttttt	0.303													9	4	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	52912754	52912754	+	Intron	DEL	G	-	-	rs75959880		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52912754delG	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTTTTTTTTTGTTTTGCTGCC	0.333													5	10	---	---	---	---	
ENTPD1	953	broad.mit.edu	37	10	97516047	97516048	+	Intron	INS	-	A	A	rs76946264		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97516047_97516048insA	uc001klh.3	+						ENTPD1_uc001kle.1_Intron|ENTPD1_uc001kli.3_Intron|uc001klg.1_RNA|ENTPD1_uc010qoj.1_Intron|ENTPD1_uc010qok.1_Intron|ENTPD1_uc010qol.1_Intron|ENTPD1_uc010qom.1_Intron|ENTPD1_uc010qon.1_Intron|ENTPD1_uc009xva.2_Intron|ENTPD1_uc009xuz.2_Intron	NM_001776	NP_001767	P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1						cell adhesion	integral to plasma membrane	ATP binding			ovary(3)	3		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		GAATCCTTAAGAAAAAAAAAAT	0.406													5	4	---	---	---	---	
OR51D1	390038	broad.mit.edu	37	11	4661689	4661690	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4661689_4661690delCT	uc010qyk.1	+	1	669_670	c.669_670delCT	c.(667-672)GACTCTfs	p.D223fs		NM_001004751	NP_001004751	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D,	223_224	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGGTGTGGACTCTCTCTTCAT	0.495													76	40	---	---	---	---	
ABCC8	6833	broad.mit.edu	37	11	17452094	17452095	+	Intron	INS	-	T	T	rs72866869	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17452094_17452095insT	uc001mnc.2	-							NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8						carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	ctcaacaCTGGTTTTTTTTTTT	0.243													2	4	---	---	---	---	
SLC38A2	54407	broad.mit.edu	37	12	46758407	46758407	+	Intron	DEL	A	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46758407delA	uc001rpg.2	-						SLC38A2_uc010sli.1_Intron|SLC38A2_uc001rph.2_Intron	NM_018976	NP_061849	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2						cellular nitrogen compound metabolic process|glutamate secretion|neurotransmitter secretion|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			urinary_tract(1)|skin(1)	2	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		aattttttctaaaaaaaaaat	0.353													80	7	---	---	---	---	
LETMD1	25875	broad.mit.edu	37	12	51449474	51449476	+	Intron	DEL	CTG	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51449474_51449476delCTG	uc001rxm.2	+						LETMD1_uc010smz.1_Intron|LETMD1_uc010sna.1_Intron|LETMD1_uc001rxl.2_Intron|LETMD1_uc009zlv.2_Intron|LETMD1_uc001rxs.2_Intron|LETMD1_uc009zlw.2_Intron|LETMD1_uc001rxn.2_Intron|LETMD1_uc001rxo.2_Intron|LETMD1_uc001rxp.2_Intron|LETMD1_uc001rxq.2_Intron|LETMD1_uc001rxr.2_Intron|LETMD1_uc001rxt.2_Intron	NM_015416	NP_056231	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1 isoform 1							integral to membrane|mitochondrial outer membrane	protein binding			central_nervous_system(2)	2						aaaaaaaaaaCTGAAAAAGAAAA	0.197													4	2	---	---	---	---	
KLF5	688	broad.mit.edu	37	13	73650108	73650109	+	3'UTR	INS	-	A	A	rs148760123	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73650108_73650109insA	uc001vje.2	+	4					KLF5_uc001vjd.2_3'UTR	NM_001730	NP_001721	Q13887	KLF5_HUMAN	Kruppel-like factor 5						transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|pancreas(1)	3		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		ACAACAAAAACAAACAAAAGCA	0.396													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95193579	95193580	+	IGR	INS	-	A	A			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95193579_95193580insA								SERPINA13 (80249 upstream) : GSC (40981 downstream)																							ATCAGTTTCTTAAaaaaaaaaa	0.361													5	3	---	---	---	---	
PPP1R13B	23368	broad.mit.edu	37	14	104205266	104205268	+	In_Frame_Del	DEL	GAC	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104205266_104205268delGAC	uc001yof.1	-	13	2968_2970	c.2685_2687delGTC	c.(2683-2688)GCGTCT>GCT	p.S896del	PPP1R13B_uc010awv.1_RNA	NM_015316	NP_056131	Q96KQ4	ASPP1_HUMAN	apoptosis-stimulating protein of p53, 1	896					apoptosis|induction of apoptosis|negative regulation of cell cycle	cytoplasm|nucleus|plasma membrane	protein binding			ovary(1)	1		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				TCCTTCCAGAGACGCGTCTAGGA	0.626													88	40	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23098652	23098655	+	Intron	DEL	TTCT	-	-	rs3057778		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23098652_23098655delTTCT	uc001yvf.2	-											Homo sapiens cDNA clone IMAGE:5275816.																		tgagtcctacttctctctccatct	0.211													11	5	---	---	---	---	
FRMD5	84978	broad.mit.edu	37	15	44168002	44168003	+	Intron	INS	-	T	T	rs34063043		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44168002_44168003insT	uc001ztl.2	-						FRMD5_uc001ztj.1_Intron|FRMD5_uc001ztk.1_Intron|FRMD5_uc010uef.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		CCTGGGCCTAGttttttttttt	0.218													5	4	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	48058484	48058484	+	Intron	DEL	G	-	-	rs528882	by1000genomes	TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48058484delG	uc010bek.2	+						SEMA6D_uc001zvw.2_Intron|SEMA6D_uc001zvy.2_Intron|SEMA6D_uc001zvz.2_Intron|SEMA6D_uc001zwa.2_Intron|SEMA6D_uc001zwb.2_Intron|SEMA6D_uc001zwc.2_Intron	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CTTTTTTTTTGTTGTTATGGG	0.358													4	2	---	---	---	---	
CLPX	10845	broad.mit.edu	37	15	65477364	65477365	+	Intron	INS	-	C	C			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65477364_65477365insC	uc002aom.2	-						CLPX_uc010uiu.1_Intron|CLPX_uc010bhg.1_Intron	NM_006660	NP_006651	O76031	CLPX_HUMAN	ClpX caseinolytic protease X homolog precursor						protein folding|proteolysis involved in cellular protein catabolic process	mitochondrial endopeptidase Clp complex|mitochondrial inner membrane|mitochondrial nucleoid	ATP binding|ATPase activity|metal ion binding|peptidase activator activity|unfolded protein binding				0						TGGCCAGTCCACCCCCCCCCCG	0.708													4	2	---	---	---	---	
DNAH3	55567	broad.mit.edu	37	16	21071848	21071848	+	Intron	DEL	T	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21071848delT	uc010vbe.1	-							NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		tttttttttcttttttttttt	0.209													8	5	---	---	---	---	
CPNE2	221184	broad.mit.edu	37	16	57168642	57168642	+	Intron	DEL	T	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57168642delT	uc002eks.1	+						CPNE2_uc010cct.1_Intron|CPNE2_uc010ccu.1_Intron|CPNE2_uc002ekt.1_Intron	NM_152727	NP_689940	Q96FN4	CPNE2_HUMAN	copine II											central_nervous_system(1)|skin(1)	2		all_neural(199;0.224)				TGGGTCTGGGTTTGGGGGCGG	0.612													23	25	---	---	---	---	
USP10	9100	broad.mit.edu	37	16	84797632	84797632	+	Intron	DEL	T	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84797632delT	uc002fii.2	+						USP10_uc010voe.1_Intron|USP10_uc010vof.1_Intron|USP10_uc002fij.2_Intron	NM_005153	NP_005144	Q14694	UBP10_HUMAN	ubiquitin specific protease 10						DNA damage response, signal transduction by p53 class mediator|DNA repair|protein deubiquitination|ubiquitin-dependent protein catabolic process	early endosome|intermediate filament cytoskeleton|nucleus	cystic fibrosis transmembrane conductance regulator binding|p53 binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0						GATCTGTGCCTTTTTTTTTTT	0.433													4	2	---	---	---	---	
TSR1	55720	broad.mit.edu	37	17	2232241	2232242	+	Intron	DEL	AC	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2232241_2232242delAC	uc002fuj.2	-							NM_018128	NP_060598	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation						ribosome assembly	nucleolus	protein binding			ovary(1)	1						aaaaaaaaaaaCAGAAACAAAA	0.119													4	2	---	---	---	---	
NCOR1	9611	broad.mit.edu	37	17	15943900	15943902	+	Intron	DEL	TTT	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15943900_15943902delTTT	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpl.2_Intron|NCOR1_uc002gpm.2_Intron|NCOR1_uc010vwb.1_Intron|NCOR1_uc010coy.2_Intron	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		AAAATTAATCTTTTTATTTTTCA	0.207													2	5	---	---	---	---	
STAT5B	6777	broad.mit.edu	37	17	40368184	40368184	+	Intron	DEL	T	-	-	rs67502138		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40368184delT	uc002hzh.2	-							NM_012448	NP_036580	P51692	STA5B_HUMAN	signal transducer and activator of transcription						2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|skin(1)	6		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)	TCCTTCTCTCTTTTTTTTTTT	0.418													4	3	---	---	---	---	
RPL27	6155	broad.mit.edu	37	17	41154524	41154524	+	Intron	DEL	A	-	-	rs76067241		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41154524delA	uc002icj.2	+						RPL27_uc002ick.2_Intron	NM_000988	NP_000979	P61353	RL27_HUMAN	ribosomal protein L27						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	structural constituent of ribosome				0		Breast(137;0.000717)|Ovarian(249;0.0776)		BRCA - Breast invasive adenocarcinoma(366;0.157)		actccgtctcaaaaaaaaaaa	0.204													4	2	---	---	---	---	
EFCAB3	146779	broad.mit.edu	37	17	60475386	60475387	+	Intron	INS	-	A	A	rs146811952		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60475386_60475387insA	uc002izu.1	+						EFCAB3_uc010wpc.1_Intron	NM_173503	NP_775774	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3 isoform b								calcium ion binding			skin(1)	1			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			gactccatctcaaaaaaaaaaa	0.183													5	4	---	---	---	---	
SCN1B	6324	broad.mit.edu	37	19	35524267	35524267	+	Intron	DEL	T	-	-	rs72550271		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35524267delT	uc002nxp.2	+						SCN1B_uc002nxo.1_Intron|SCN1B_uc010xsg.1_Intron	NM_001037	NP_001028	Q07699	SCN1B_HUMAN	sodium channel, voltage-gated, type I, beta						axon guidance|synaptic transmission	integral to membrane	voltage-gated sodium channel activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GTGCCCTCCCTGCCTGAGGTC	0.597													3	4	---	---	---	---	
ZNF816A	125893	broad.mit.edu	37	19	53452836	53452836	+	3'UTR	DEL	G	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53452836delG	uc002qal.1	-	5					ZNF321_uc010eqj.2_Intron|ZNF321_uc002qak.1_Intron|ZNF816A_uc002qam.1_3'UTR	NM_001031665	NP_001026835	Q0VGE8	ZN816_HUMAN	zinc finger protein 816A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0313)		ACACTTGTGAGGTTTCTCTCC	0.393													4	2	---	---	---	---	
KIR3DX1	90011	broad.mit.edu	37	19	55049050	55049050	+	Intron	DEL	A	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55049050delA	uc010erm.2	+						KIR3DX1_uc010yfa.1_Intron|KIR3DX1_uc010yfb.1_Intron|KIR3DX1_uc010yfc.1_Intron|KIR3DX1_uc010yfd.1_Intron					Homo sapiens killer cell immunoglobulin-like receptor, three domains, X1, mRNA (cDNA clone IMAGE:4849085).											ovary(1)	1				GBM - Glioblastoma multiforme(193;0.099)		actccatctcaaaaaaaaaaa	0.075													6	5	---	---	---	---	
MCM8	84515	broad.mit.edu	37	20	5958754	5958754	+	Intron	DEL	A	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5958754delA	uc002wmi.2	+						MCM8_uc002wmj.2_Intron|MCM8_uc002wmk.2_Intron|MCM8_uc002wml.2_Intron|MCM8_uc010gbp.2_Intron|MCM8_uc002wmm.2_Intron	NM_032485	NP_115874	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8						cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1						TGTTTAAGAGAAACATTTAGA	0.338													12	8	---	---	---	---	
CECR2	27443	broad.mit.edu	37	22	18003413	18003413	+	Intron	DEL	C	-	-	rs695465		TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18003413delC	uc010gqw.1	+						CECR2_uc010gqv.1_Intron|CECR2_uc002zml.2_Intron	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		CCGGCAATTTCtttttttttt	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	24447606	24447607	+	IGR	INS	-	T	T			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24447606_24447607insT								FAM48B1 (64066 upstream) : PDK3 (35737 downstream)																							aattaaacctcttttttttTTT	0.163													3	3	---	---	---	---	
DKC1	1736	broad.mit.edu	37	X	153994771	153994771	+	Intron	DEL	A	-	-			TCGA-G9-6496-01	TCGA-G9-6496-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153994771delA	uc004fmm.2	+						DKC1_uc010nvf.2_Intron|SNORA36A_uc004fmn.2_5'Flank	NM_001363	NP_001354	O60832	DKC1_HUMAN	dyskerin isoform 1						cell proliferation|pseudouridine synthesis|rRNA processing|telomere maintenance via telomerase	Cajal body|nucleolus|telomerase holoenzyme complex	protein binding|pseudouridine synthase activity|RNA binding|telomerase activity				0	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CTTCATTAAGAAAAAAAAAAA	0.418									Congenital_Dyskeratosis				4	2	---	---	---	---	
