Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
B4GALT2	8704	broad.mit.edu	37	1	44450654	44450654	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
NBPF9	400818	broad.mit.edu	37	1	144828704	144828704	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
C1orf192	257177	broad.mit.edu	37	1	161334829	161334829	+	Missense_Mutation	SNP	A	G	G			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
NID1	4811	broad.mit.edu	37	1	236156998	236156998	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
TGOLN2	10618	broad.mit.edu	37	2	85553644	85553644	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
PRSS50	29122	broad.mit.edu	37	3	46759103	46759103	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
DGKQ	1609	broad.mit.edu	37	4	956320	956320	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
LMBRD2	92255	broad.mit.edu	37	5	36142648	36142648	+	Silent	SNP	A	G	G	rs12658867	byFrequency	TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
C6orf170	221322	broad.mit.edu	37	6	121577370	121577370	+	Missense_Mutation	SNP	T	C	C	rs7745023	by1000genomes	TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
CUX1	1523	broad.mit.edu	37	7	101845118	101845118	+	Silent	SNP	C	T	T			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
TRIM55	84675	broad.mit.edu	37	8	67064654	67064654	+	Missense_Mutation	SNP	A	G	G	rs7843605	byFrequency	TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
SLC27A4	10999	broad.mit.edu	37	9	131107632	131107632	+	Silent	SNP	C	G	G			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
Unknown	0	broad.mit.edu	37	10	51818992	51818992	+	RNA	SNP	G	T	T			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
MKI67	4288	broad.mit.edu	37	10	129901213	129901213	+	Missense_Mutation	SNP	C	G	G			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
RPL13AP20	387841	broad.mit.edu	37	12	13028751	13028751	+	Missense_Mutation	SNP	G	C	C			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
LOC284232	284232	broad.mit.edu	37	13	19415742	19415742	+	RNA	SNP	T	C	C			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	g.chr16:33965589G>A	hsa-mir-1826|MI0008194	+			c.82G>A																				0						TTGCCGATCAGTAGTCCCCGG	0.647													6	26	---	---	---	---	PASS
ZZEF1	23140	broad.mit.edu	37	17	3980274	3980274	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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
NOX3	50508	broad.mit.edu	37	6	155761273	155761274	+	Splice_Site	INS	-	A	A			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33312723	33312723	+	Frame_Shift_Del	DEL	T	-	-			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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	---	---	---	---	
OR51D1	390038	broad.mit.edu	37	11	4661689	4661690	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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	---	---	---	---	
PPP1R13B	23368	broad.mit.edu	37	14	104205266	104205268	+	In_Frame_Del	DEL	GAC	-	-			TCGA-G9-6496-01A-11D-1786-08	TCGA-G9-6496-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	259386a0-60a4-4990-a3c3-36b9bab40927	ecd9e666-76cf-4984-a6b7-01764f387579	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	---	---	---	---	
