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
PABPC4	8761	broad.mit.edu	37	1	40027846	40027846	+	Missense_Mutation	SNP	T	C	C	rs141368472		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40027846T>C	uc010oiv.1	-	14	2642	c.1744A>G	c.(1744-1746)ATG>GTG	p.M582V	PPIEL_uc001cdk.2_5'Flank|PABPC4_uc001cdl.2_Missense_Mutation_p.M598V|PABPC4_uc001cdm.2_Missense_Mutation_p.M569V	NM_003819	NP_003810	Q13310	PABP4_HUMAN	poly A binding protein, cytoplasmic 4 isoform 2	582	PABC.				blood coagulation|RNA catabolic process|RNA processing|translation	cytoplasm|ribonucleoprotein complex	nucleotide binding|poly(A) RNA binding|poly(U) RNA binding|protein binding				0	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TTTGAATGCATTGTTTGGATG	0.473													5	141	---	---	---	---	PASS
KIAA0467	23334	broad.mit.edu	37	1	43897409	43897409	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43897409A>G	uc001cjk.1	+	21	2876	c.2414A>G	c.(2413-2415)GAG>GGG	p.E805G		NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334	1704						peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTGGAAGATGAGATGGTGGGG	0.567													3	162	---	---	---	---	PASS
RSBN1	54665	broad.mit.edu	37	1	114319949	114319949	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114319949G>C	uc001edq.2	-	4	1577	c.1541C>G	c.(1540-1542)TCT>TGT	p.S514C	RSBN1_uc001edr.2_RNA	NM_018364	NP_060834	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	514						nucleus				ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-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)		TCGGAGGCTAGAAAGTGTACC	0.428													40	188	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142803746	142803746	+	Intron	SNP	A	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142803746A>G	uc001eiw.1	+						uc001ejb.2_RNA|uc001ejc.2_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		actatggattagagctgatta	0.000													3	17	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145367739	145367739	+	Silent	SNP	A	G	G	rs146714035	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145367739A>G	uc001end.3	+	85	10595	c.10560A>G	c.(10558-10560)AAA>AAG	p.K3520K	NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	3445											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ggaaggggaaaaaaagaaggg	0.244													6	182	---	---	---	---	PASS
CFH	3075	broad.mit.edu	37	1	196695918	196695918	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196695918C>A	uc001gtj.3	+	14	2324	c.2084C>A	c.(2083-2085)CCT>CAT	p.P695H		NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	695	Sushi 12.				complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6						GGAGATATACCTGAACTTGAA	0.353													29	169	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197104365	197104365	+	Silent	SNP	G	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197104365G>C	uc001gtu.2	-	5	2291	c.2034C>G	c.(2032-2034)CCC>CCG	p.P678P	ASPM_uc001gtv.2_Silent_p.P678P|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	678					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						TCGGGTGTCTGGGAATATCTA	0.333													12	100	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228462137	228462137	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228462137C>T	uc009xez.1	+	19	5719	c.5675C>T	c.(5674-5676)ACC>ATC	p.T1892I	OBSCN_uc001hsn.2_Missense_Mutation_p.T1892I	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	1892	Ig-like 18.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				GCGCAGCTCACCGTCAGTGGT	0.642													6	32	---	---	---	---	PASS
GNPAT	8443	broad.mit.edu	37	1	231377146	231377146	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231377146A>G	uc001hup.3	+	1	228	c.22A>G	c.(22-24)AAC>GAC	p.N8D	C1orf131_uc001hul.2_5'Flank|C1orf131_uc001hum.2_5'Flank|C1orf131_uc001hun.1_5'Flank|C1orf131_uc010pwd.1_5'Flank|C1orf131_uc001huo.1_5'Flank|GNPAT_uc009xfo.1_5'UTR|GNPAT_uc009xfp.2_Missense_Mutation_p.N8D	NM_014236	NP_055051	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	8	Poly-Ser.				ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity			ovary(3)|breast(1)	4	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				CAGTTCATCTAACTCTTATTT	0.617													26	162	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235840808	235840808	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235840808C>T	uc001hxj.2	-	49	11087	c.10912G>A	c.(10912-10914)GGA>AGA	p.G3638R	LYST_uc001hxi.2_Missense_Mutation_p.G862R	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	3638	WD 4.				defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ATGCAGGTTCCGTCTCTGCTC	0.338									Chediak-Higashi_syndrome				34	237	---	---	---	---	PASS
FBXO11	80204	broad.mit.edu	37	2	48059590	48059590	+	Silent	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48059590C>T	uc010fbl.2	-	11	1158	c.1044G>A	c.(1042-1044)GCG>GCA	p.A348A	FBXO11_uc002rwe.2_Silent_p.A348A|FBXO11_uc002rwf.2_Silent_p.A348A|FBXO11_uc002rwg.1_Silent_p.A348A|FBXO11_uc010fbk.2_5'UTR	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1	432	PbH1 2.				ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCCCAGCTAACGCATTATTGG	0.328													18	128	---	---	---	---	PASS
SPTBN1	6711	broad.mit.edu	37	2	54785805	54785805	+	Intron	SNP	C	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54785805C>A	uc002rxu.2	+						SPTBN1_uc002rxv.1_Intron|SPTBN1_uc002rxx.2_5'UTR	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			CGGAATGGGGCTCGCCTAAGG	0.622													7	20	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61415488	61415488	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61415488C>A	uc002sbe.2	-	80	10412	c.10390G>T	c.(10390-10392)GAA>TAA	p.E3464*	USP34_uc002sbd.2_Nonsense_Mutation_p.E266*	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	3464					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			TCAGATTCTTCCTCAGCTAGG	0.463													4	157	---	---	---	---	PASS
FUNDC2P2	388965	broad.mit.edu	37	2	84518122	84518122	+	Silent	SNP	T	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84518122T>G	uc010ffz.1	+	1	317	c.180T>G	c.(178-180)GGT>GGG	p.G60G		NR_003663				RecName: Full=FUN14 domain-containing protein 2; AltName: Full=Hepatitis C virus core-binding protein 6; AltName: Full=Cervical cancer proto-oncogene 3 protein;          Short=HCC-3;												0						GGTGCACGGGTTTTATATTCC	0.488													9	150	---	---	---	---	PASS
KYNU	8942	broad.mit.edu	37	2	143790837	143790837	+	Nonsense_Mutation	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143790837C>T	uc002tvl.2	+	12	1118	c.988C>T	c.(988-990)CGA>TGA	p.R330*	KYNU_uc010fnm.2_Nonsense_Mutation_p.R330*	NM_003937	NP_003928	Q16719	KYNU_HUMAN	kynureninase (L-kynurenine hydrolase) isoform a	330					anthranilate metabolic process|NAD biosynthetic process|quinolinate biosynthetic process|response to interferon-gamma|response to vitamin B6	cytosol|mitochondrion|soluble fraction	kynureninase activity|protein homodimerization activity			skin(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.072)	L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)	CTGTGGATTCCGAATTTCAAA	0.373													63	486	---	---	---	---	PASS
BAZ2B	29994	broad.mit.edu	37	2	160289891	160289891	+	Intron	SNP	T	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160289891T>A	uc002uao.2	-						BAZ2B_uc002uap.2_Intron|BAZ2B_uc002uas.1_Intron|BAZ2B_uc002uaq.1_Intron|BAZ2B_uc002uar.1_5'UTR	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						AAACATAAGTTAAAAAACACA	0.289													6	192	---	---	---	---	PASS
TBR1	10716	broad.mit.edu	37	2	162272776	162272776	+	5'UTR	SNP	A	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162272776A>G	uc002ubw.1	+	1					TBR1_uc010foy.2_5'Flank	NM_006593	NP_006584	Q16650	TBR1_HUMAN	T-box, brain, 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						TCTCCCAGGGAAAAAAAAAAG	0.428													3	12	---	---	---	---	PASS
SP140L	93349	broad.mit.edu	37	2	231222557	231222557	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231222557G>T	uc010fxm.1	+	3	236	c.145G>T	c.(145-147)GTC>TTC	p.V49F	SP140_uc010zma.1_RNA|SP140L_uc010fxn.1_5'UTR	NM_138402	NP_612411	Q9H930	LY10L_HUMAN	SP140 nuclear body protein-like	49	HSR.					nucleus	DNA binding|metal ion binding			central_nervous_system(1)	1						TGAGGGACTTGTCTATGACAC	0.423													14	454	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47163433	47163433	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47163433A>C	uc003cqs.2	-	3	2746	c.2693T>G	c.(2692-2694)TTG>TGG	p.L898W	SETD2_uc003cqv.2_Missense_Mutation_p.L887W	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	898					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TCCGCATTTCAAGAGAGTTAG	0.378			N|F|S|Mis		clear cell renal carcinoma								8	273	---	---	---	---	PASS
C3orf38	285237	broad.mit.edu	37	3	88199141	88199141	+	5'UTR	SNP	G	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88199141G>T	uc003dqw.2	+	1					CGGBP1_uc003dqu.2_5'Flank	NM_173824	NP_776185	Q5JPI3	CC038_HUMAN	hypothetical protein LOC285237						apoptosis						0		Lung NSC(201;0.17)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		GTTGCCAGGCGCGGGCCCAGT	0.607													6	22	---	---	---	---	PASS
MYH15	22989	broad.mit.edu	37	3	108112995	108112995	+	Silent	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108112995G>A	uc003dxa.1	-	37	5259	c.5202C>T	c.(5200-5202)AGC>AGT	p.S1734S		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	1734	Potential.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						GGCTGAGGAGGCTTGTGTTCT	0.478													30	150	---	---	---	---	PASS
LPP	4026	broad.mit.edu	37	3	188327128	188327128	+	Silent	SNP	T	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188327128T>C	uc003frs.1	+	6	855	c.609T>C	c.(607-609)CCT>CCC	p.P203P	LPP_uc011bsg.1_Silent_p.P203P|LPP_uc011bsi.1_Silent_p.P203P|LPP_uc003frt.2_Silent_p.P203P|LPP_uc011bsj.1_Silent_p.P40P	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation	203	Pro-rich.				cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		AACCCCAGCCTCAGCCAGTCC	0.567			T	HMGA2|MLL|C12orf9	lipoma|leukemia								11	96	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505835	195505835	+	Missense_Mutation	SNP	C	T	T	rs58500707	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505835C>T	uc011bto.1	-	3	12692	c.12232G>A	c.(12232-12234)GCC>ACC	p.A4078T	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGCGTGACCTGTG	0.597													3	14	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505838	195505838	+	Missense_Mutation	SNP	G	C	C	rs59101491		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505838G>C	uc011bto.1	-	3	12689	c.12229C>G	c.(12229-12231)CAC>GAC	p.H4077D	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGCGTGACCTGTGGAT	0.597													2	13	---	---	---	---	PASS
TM4SF19	116211	broad.mit.edu	37	3	196051041	196051041	+	Intron	SNP	G	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196051041G>T	uc003fwj.2	-						uc003fwk.1_Nonstop_Mutation_p.*102Y|TM4SF19_uc010iad.1_Intron|TM4SF19_uc003fwl.1_Intron|TM4SF19_uc011btv.1_Intron	NM_138461		Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19							integral to membrane					0	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		CAAGATGCTAGGATGTGTGAC	0.507													4	63	---	---	---	---	PASS
RGS12	6002	broad.mit.edu	37	4	3317854	3317854	+	5'UTR	SNP	A	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3317854A>C	uc003ggw.2	+	2					RGS12_uc003ggu.2_5'UTR|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_RNA|RGS12_uc003ggv.2_5'UTR|RGS12_uc003ggx.1_5'UTR	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ATATGGCTCCAAGGGAACAAT	0.488													14	130	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62812695	62812695	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62812695C>T	uc010ihh.2	+	13	2452	c.2279C>T	c.(2278-2280)GCC>GTC	p.A760V	LPHN3_uc003hcq.3_Missense_Mutation_p.A760V|LPHN3_uc003hct.2_Missense_Mutation_p.A153V	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	747	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding	p.A760G(1)		lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						ACGGAGAATGCCAGTATGAAG	0.403													5	473	---	---	---	---	PASS
AMBN	258	broad.mit.edu	37	4	71472377	71472377	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71472377C>T	uc003hfl.2	+	13	1349	c.1274C>T	c.(1273-1275)ACA>ATA	p.T425I		NM_016519	NP_057603	Q9NP70	AMBN_HUMAN	ameloblastin precursor	425					bone mineralization|cell adhesion|cell proliferation|odontogenesis of dentine-containing tooth	proteinaceous extracellular matrix	growth factor activity|structural constituent of tooth enamel			ovary(3)|skin(1)	4			Lung(101;0.235)			TCTCTGCAAACATCCATGCCA	0.488													22	93	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126242091	126242091	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126242091C>T	uc003ifj.3	+	1	4525	c.4525C>T	c.(4525-4527)CGG>TGG	p.R1509W		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	1509	Cadherin 14.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						AGAAACTAGACGGTATGCTTT	0.403													52	285	---	---	---	---	PASS
NSUN2	54888	broad.mit.edu	37	5	6604802	6604802	+	Intron	SNP	T	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6604802T>A	uc003jdu.2	-						NSUN2_uc003jds.2_Missense_Mutation_p.L24F|NSUN2_uc003jdt.2_Intron|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1						TAATAACCTGTAAGTAAAAAA	0.468													4	82	---	---	---	---	PASS
FAM134B	54463	broad.mit.edu	37	5	16475005	16475005	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16475005T>C	uc003jfs.2	-	9	1377	c.1339A>G	c.(1339-1341)ACA>GCA	p.T447A	FAM134B_uc003jfr.2_Missense_Mutation_p.T306A	NM_001034850	NP_001030022	Q9H6L5	F134B_HUMAN	hypothetical protein LOC54463 isoform 1	447					sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3						TCAGTGTCTGTGTCCTCTTCT	0.493													21	133	---	---	---	---	PASS
GUSBP1	728411	broad.mit.edu	37	5	21497235	21497235	+	3'UTR	SNP	C	T	T	rs141635554	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21497235C>T	uc010iub.2	+	6					GUSBP1_uc011cnn.1_RNA|GUSBP1_uc003jgh.3_Intron	NR_027028				SubName: Full=Putative uncharacterized protein GUSBL2;												0						AGTTTGAGAACTGGTGTAAGA	0.488													4	24	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	6	29230640	29230640	+	IGR	SNP	G	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29230640G>T								OR2J2 (88290 upstream) : OR14J1 (43827 downstream)																							GGTCCCAAATGCTTTTTGTCT	0.418													21	134	---	---	---	---	PASS
VARS2	57176	broad.mit.edu	37	6	30884893	30884893	+	Silent	SNP	G	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30884893G>T	uc003nsc.1	+	8	1397	c.765G>T	c.(763-765)GTG>GTT	p.V255V	VARS2_uc003nsd.2_Silent_p.V255V|VARS2_uc011dmx.1_Silent_p.V255V|VARS2_uc011dmy.1_Silent_p.V115V|VARS2_uc011dmz.1_Silent_p.V285V|VARS2_uc011dna.1_Silent_p.V255V|VARS2_uc011dnb.1_RNA|VARS2_uc011dnc.1_RNA|VARS2_uc011dnd.1_5'Flank|VARS2_uc010jsg.1_5'Flank	NM_020442	NP_065175	Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	255					valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4						GCTCCTCAGTGGCTGTGACTG	0.567													4	159	---	---	---	---	PASS
EHMT2	10919	broad.mit.edu	37	6	31850727	31850727	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31850727G>T	uc003nxz.1	-	24	3064	c.3054C>A	c.(3052-3054)AAC>AAA	p.N1018K	EHMT2_uc003nxv.1_Missense_Mutation_p.N57K|EHMT2_uc003nxw.1_Missense_Mutation_p.N57K|EHMT2_uc003nxx.1_Missense_Mutation_p.N216K|EHMT2_uc003nxy.1_Missense_Mutation_p.N816K|EHMT2_uc011don.1_Missense_Mutation_p.N1041K|EHMT2_uc003nya.1_Missense_Mutation_p.N984K	NM_006709	NP_006700	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	1018	Pre-SET.				DNA methylation|peptidyl-lysine dimethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			ovary(1)	1						AGCACGCCTGGTTACACTCGA	0.572													4	76	---	---	---	---	PASS
KIAA0240	23506	broad.mit.edu	37	6	42824964	42824964	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42824964C>A	uc003osn.1	+	10	2395	c.2244C>A	c.(2242-2244)GAC>GAA	p.D748E	KIAA0240_uc011duw.1_Missense_Mutation_p.D748E|KIAA0240_uc003osp.1_Missense_Mutation_p.D748E	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506	748										ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)			CTGAAGAAGACTTGAGAAAAG	0.542													20	131	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51889566	51889566	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51889566G>T	uc003pah.1	-	32	5318	c.5042C>A	c.(5041-5043)GCA>GAA	p.A1681E	PKHD1_uc003pai.2_Missense_Mutation_p.A1681E	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1681	IPT/TIG 12; atypical.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					GTCAATGTTTGCAGCTCCTGA	0.493													4	177	---	---	---	---	PASS
TAAR9	134860	broad.mit.edu	37	6	132859537	132859537	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132859537G>A	uc011eci.1	+	1	111	c.109G>A	c.(109-111)GCC>ACC	p.A37T		NM_175057	NP_778227	Q96RI9	TAAR9_HUMAN	trace amine associated receptor 9	37	Extracellular (Potential).					plasma membrane	G-protein coupled receptor activity				0	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.0042)|GBM - Glioblastoma multiforme(226;0.00816)		TATCCTCTACGCCGTCCTTGG	0.478													12	63	---	---	---	---	PASS
TBP	6908	broad.mit.edu	37	6	170881381	170881381	+	3'UTR	SNP	A	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170881381A>C	uc003qxt.2	+	8					TBP_uc003qxu.2_3'UTR|TBP_uc011ehf.1_3'UTR	NM_003194	NP_003185	P20226	TBP_HUMAN	TATA box binding protein						cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		TGCCTCCCCCACCCCCTTCTT	0.413													6	61	---	---	---	---	PASS
DPY19L2P1	554236	broad.mit.edu	37	7	35142675	35142675	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35142675C>T	uc003teq.1	-	19	1988	c.881G>A	c.(880-882)CGT>CAT	p.R294H	DPY19L2P1_uc003tep.1_Intron|DPY19L2P1_uc010kwz.1_Intron					RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						ATTATCAAAACGAACTCTGCG	0.338													3	73	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48327660	48327660	+	Silent	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48327660G>A	uc003toq.2	+	20	8965	c.8940G>A	c.(8938-8940)GCG>GCA	p.A2980A	ABCA13_uc010kys.1_Silent_p.A54A	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	2980					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						TCACTTTGGCGCAGGACCACT	0.438													55	221	---	---	---	---	PASS
PON1	5444	broad.mit.edu	37	7	94940824	94940824	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94940824A>C	uc003uns.2	-	5	533	c.436T>G	c.(436-438)TTT>GTT	p.F146V	PON1_uc011kih.1_Missense_Mutation_p.F146V	NM_000446	NP_000437	P27169	PON1_HUMAN	paraoxonase 1 precursor	146					aromatic compound catabolic process|carboxylic acid catabolic process|organophosphate catabolic process|phosphatidylcholine metabolic process|positive regulation of binding|positive regulation of cholesterol efflux|positive regulation of transporter activity|response to external stimulus	spherical high-density lipoprotein particle	aryldialkylphosphatase activity|arylesterase activity|calcium ion binding|phospholipid binding|protein homodimerization activity			pancreas(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Atorvastatin(DB01076)|Cefazolin(DB01327)	TCTTCTTGAAATTTAAACAAC	0.353													34	177	---	---	---	---	PASS
PIK3CG	5294	broad.mit.edu	37	7	106524649	106524649	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106524649T>C	uc003vdv.3	+	9	2895	c.2810T>C	c.(2809-2811)GTG>GCG	p.V937A	PIK3CG_uc003vdu.2_Missense_Mutation_p.V937A|PIK3CG_uc003vdw.2_Missense_Mutation_p.V937A	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	937	PI3K/PI4K.				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						GGCTACTGTGTGGCAACCTTT	0.353													48	267	---	---	---	---	PASS
TFEC	22797	broad.mit.edu	37	7	115581932	115581932	+	Intron	SNP	C	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115581932C>A	uc003vhj.1	-						TFEC_uc003vhk.1_Intron|TFEC_uc003vhl.3_Missense_Mutation_p.M197I|TFEC_uc011kmw.1_Missense_Mutation_p.M316I	NM_012252	NP_036384	O14948	TFEC_HUMAN	transcription factor EC isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			large_intestine(1)	1			STAD - Stomach adenocarcinoma(10;0.00878)			CTCATGGCTACATTCTTATAA	0.363													12	213	---	---	---	---	PASS
FEZF1	389549	broad.mit.edu	37	7	121943288	121943288	+	Silent	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121943288G>A	uc003vkd.2	-	2	953	c.879C>T	c.(877-879)TGC>TGT	p.C293C	FEZF1_uc003vkc.2_Silent_p.C243C|uc010lko.1_5'Flank|uc003vkf.1_5'Flank	NM_001024613	NP_001019784	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1 isoform 1	293	C2H2-type 2.				cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|breast(1)	3						AACCTTTTCCGCACACTTTGC	0.463													25	134	---	---	---	---	PASS
EPHB6	2051	broad.mit.edu	37	7	142561925	142561925	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142561925A>C	uc011kst.1	+	7	1154	c.367A>C	c.(367-369)ACC>CCC	p.T123P	EPHB6_uc011ksu.1_Missense_Mutation_p.T123P|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_5'UTR	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	123	Extracellular (Potential).					extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19	Melanoma(164;0.059)					GAGCGGCGGCACCTGCCGGGA	0.642													11	96	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149493511	149493511	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149493511G>A	uc010lpk.2	+	45	6587	c.6587G>A	c.(6586-6588)CGC>CAC	p.R2196H		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	2196	F5/8 type C.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			ACTTTCGGCCGCATGGTGCAG	0.607													4	155	---	---	---	---	PASS
FLJ10661	286042	broad.mit.edu	37	8	8095843	8095843	+	RNA	SNP	C	T	T	rs62495078		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8095843C>T	uc011kwt.1	+	8		c.1038C>T			FLJ10661_uc010lrq.2_Intron|FLJ10661_uc003wsf.3_Intron	NR_024362				Homo sapiens cDNA FLJ60033 complete cds, highly similar to Protein FAM86A.												0						GAAGAGCAGACACTGCCATGG	0.602													4	34	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55537506	55537506	+	Missense_Mutation	SNP	A	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55537506A>T	uc003xsd.1	+	4	1212	c.1064A>T	c.(1063-1065)AAA>ATA	p.K355I	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	355					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			ACTGTCAGTAAAACTGGTCCT	0.353													10	60	---	---	---	---	PASS
C8orf45	157777	broad.mit.edu	37	8	67809157	67809157	+	Missense_Mutation	SNP	C	T	T	rs142662778	byFrequency	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67809157C>T	uc003xwz.3	+	12	1760	c.1589C>T	c.(1588-1590)GCG>GTG	p.A530V	C8orf45_uc011lev.1_Missense_Mutation_p.A530V|C8orf45_uc011lew.1_Missense_Mutation_p.A461V|C8orf45_uc011lex.1_Missense_Mutation_p.A288V|C8orf45_uc003xwy.3_Missense_Mutation_p.A530V	NM_173518	NP_775789	Q4G0Z9	CH045_HUMAN	minichromosome maintenance complex	530					DNA replication		ATP binding|DNA binding			ovary(1)	1	Breast(64;0.186)		Epithelial(68;0.00384)|OV - Ovarian serous cystadenocarcinoma(28;0.00913)|all cancers(69;0.0175)|BRCA - Breast invasive adenocarcinoma(89;0.206)			CTGTTTTATGCGGCTTCTAGA	0.398													5	269	---	---	---	---	PASS
TRPS1	7227	broad.mit.edu	37	8	116426187	116426187	+	3'UTR	SNP	T	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116426187T>A	uc003ynz.2	-	6					TRPS1_uc011lhy.1_3'UTR|TRPS1_uc003yny.2_3'UTR|TRPS1_uc010mcy.2_3'UTR	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1						negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CATAAGACATTACAAGCTATT	0.313									Langer-Giedion_syndrome				11	70	---	---	---	---	PASS
TNC	3371	broad.mit.edu	37	9	117791638	117791638	+	Splice_Site	SNP	C	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117791638C>A	uc004bjj.3	-	25	6531	c.6169_splice	c.e25+1	p.G2057_splice	TNC_uc010mvf.2_Splice_Site_p.G1784_splice	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor						cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7						GGCTGCATTACCAAGCCAGAA	0.478													4	222	---	---	---	---	PASS
LCN12	286256	broad.mit.edu	37	9	139847394	139847394	+	Silent	SNP	G	A	A	rs62580418		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139847394G>A	uc004ckb.2	+	2	177	c.165G>A	c.(163-165)CCG>CCA	p.P55P	LCN12_uc004ckc.2_Silent_p.P55P	NM_178536	NP_848631	Q6JVE5	LCN12_HUMAN	lipocalcin 12 precursor	55					lipid metabolic process	extracellular region	binding|transporter activity				0	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		GCTTCAGGCCGGAGCACAGGG	0.637													39	233	---	---	---	---	PASS
PTPLA	9200	broad.mit.edu	37	10	17632152	17632152	+	3'UTR	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17632152C>T	uc001ipg.2	-	7						NM_014241	NP_055056	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like, member A						fatty acid biosynthetic process|multicellular organismal development|signal transduction	endoplasmic reticulum membrane|integral to membrane	lyase activity|protein tyrosine phosphatase activity			central_nervous_system(1)|skin(1)	2						CAATACCTACCCAAAAGTTAC	0.303													4	7	---	---	---	---	PASS
MLLT10	8028	broad.mit.edu	37	10	21962615	21962615	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21962615T>A	uc001iqs.2	+	11	1736	c.1388T>A	c.(1387-1389)GTA>GAA	p.V463E	MLLT10_uc001iqt.2_Missense_Mutation_p.V463E|MLLT10_uc001iqv.2_RNA|MLLT10_uc001iqy.2_Missense_Mutation_p.V463E|MLLT10_uc001ira.2_5'UTR|MLLT10_uc001irb.2_RNA|MLLT10_uc001iqz.2_Missense_Mutation_p.V218E	NM_004641	NP_004632	P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	463	DNA-binding.				positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2						GAAGAAACTGTAAAGGAAAAG	0.398			T	MLL|PICALM|CDK6	AL								7	340	---	---	---	---	PASS
LYZL2	119180	broad.mit.edu	37	10	30918597	30918597	+	Missense_Mutation	SNP	T	C	C	rs74551644	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30918597T>C	uc001ivk.2	-	1	51	c.38A>G	c.(37-39)AAG>AGG	p.K13R		NM_183058	NP_898881	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	Error:Variant_position_missing_in_Q7Z4W2_after_alignment					cell wall macromolecule catabolic process	extracellular region	lysozyme activity				0		Prostate(175;0.151)				ACTGCTCCACTTAGTCGGTGA	0.498													6	46	---	---	---	---	PASS
LRIT2	340745	broad.mit.edu	37	10	85981795	85981795	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85981795C>A	uc001kcy.2	-	3	1542	c.1534G>T	c.(1534-1536)GCA>TCA	p.A512S	LRIT2_uc010qmc.1_Missense_Mutation_p.A522S	NM_001017924	NP_001017924	A6NDA9	LRIT2_HUMAN	leucine rich repeat containing 22 precursor	512						integral to membrane				ovary(2)	2						TGCGGGGCTGCAGGGGTGCAG	0.627													4	157	---	---	---	---	PASS
SORCS3	22986	broad.mit.edu	37	10	106974254	106974254	+	Silent	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106974254C>T	uc001kyi.1	+	18	2657	c.2430C>T	c.(2428-2430)ACC>ACT	p.T810T	SORCS3_uc010qqz.1_RNA	NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	810	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		AGAAGTACACCGCCAAGGCCC	0.537													4	97	---	---	---	---	PASS
RAB38	23682	broad.mit.edu	37	11	87847074	87847074	+	3'UTR	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87847074C>T	uc001pcj.1	-	3						NM_022337	NP_071732	P57729	RAB38_HUMAN	RAB38						protein transport|small GTPase mediated signal transduction	melanosome|plasma membrane	GTP binding|GTPase activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TCTATCCTGACGTTTACCCAA	0.423													13	70	---	---	---	---	PASS
CAPZA3	93661	broad.mit.edu	37	12	18891209	18891209	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18891209C>G	uc001rdy.2	+	1	165	c.7C>G	c.(7-9)CTT>GTT	p.L3V	PLCZ1_uc001rdv.3_5'Flank|PLCZ1_uc001rdw.3_5'Flank|PLCZ1_uc010sid.1_5'Flank	NM_033328	NP_201585	Q96KX2	CAZA3_HUMAN	capping protein alpha 3	3					actin cytoskeleton organization|actin filament capping	F-actin capping protein complex	actin binding			ovary(1)|central_nervous_system(1)	2	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				AAACATGACACTTAGCGTGCT	0.438													4	201	---	---	---	---	PASS
KRT3	3850	broad.mit.edu	37	12	53189692	53189692	+	Silent	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53189692G>A	uc001say.2	-	1	201	c.135C>T	c.(133-135)TTC>TTT	p.F45F		NM_057088	NP_476429	P12035	K2C3_HUMAN	keratin 3	45	Gly-rich.|Head.				epithelial cell differentiation|intermediate filament cytoskeleton organization	keratin filament	structural molecule activity				0						CTCCGCTCCGGAAGCCATAGG	0.677													4	37	---	---	---	---	PASS
OR6C76	390326	broad.mit.edu	37	12	55820712	55820712	+	Silent	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55820712C>T	uc010spm.1	+	1	675	c.675C>T	c.(673-675)ATC>ATT	p.I225I		NM_001005183	NP_001005183	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C,	225	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TTCTGAGAATCCCCTCAGCAC	0.363													18	108	---	---	---	---	PASS
KITLG	4254	broad.mit.edu	37	12	88928477	88928477	+	Intron	SNP	C	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88928477C>G	uc001tav.2	-						KITLG_uc001taw.2_Intron|KITLG_uc009zso.1_5'Flank	NM_000899	NP_000890	P21583	SCF_HUMAN	KIT ligand isoform b precursor						cell adhesion|cell proliferation|hemopoiesis|male gonad development|positive regulation of DNA replication|signal transduction	cytoplasm|cytoskeleton|integral to membrane|plasma membrane	growth factor activity|identical protein binding|stem cell factor receptor binding			ovary(1)	1						CCTGAGCTGCCAGACATGACG	0.259									Testicular_Cancer_Familial_Clustering_of				6	38	---	---	---	---	PASS
MCF2L	23263	broad.mit.edu	37	13	113729393	113729393	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113729393C>T	uc001vsu.2	+	11	1391	c.1369C>T	c.(1369-1371)CGC>TGC	p.R457C	MCF2L_uc001vsq.2_Missense_Mutation_p.R457C|MCF2L_uc010tjr.1_Missense_Mutation_p.R400C|MCF2L_uc001vsr.2_Missense_Mutation_p.R404C|MCF2L_uc001vss.3_Missense_Mutation_p.R398C|MCF2L_uc010tjs.1_Missense_Mutation_p.R398C|MCF2L_uc001vst.1_Missense_Mutation_p.R362C	NM_001112732	NP_001106203	O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming	430	Spectrin.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				AGACTCCATCCGCCCAAAGTG	0.662													21	138	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64557603	64557603	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64557603G>A	uc001xgm.2	+	60	12043	c.11813G>A	c.(11812-11814)CGT>CAT	p.R3938H	SYNE2_uc001xgl.2_Missense_Mutation_p.R3938H|SYNE2_uc010apy.2_Missense_Mutation_p.R323H|SYNE2_uc010apx.1_Missense_Mutation_p.R330H	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3938	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GAAAATATACGTCCCATGAAG	0.353													16	98	---	---	---	---	PASS
KIAA0284	283638	broad.mit.edu	37	14	105354293	105354293	+	Silent	SNP	A	G	G	rs2582548	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105354293A>G	uc010axb.2	+	12	3941	c.3717A>G	c.(3715-3717)TCA>TCG	p.S1239S	INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Silent_p.S1169S|KIAA0284_uc001yps.2_Silent_p.S1145S|KIAA0284_uc001ypt.2_5'Flank	NM_001112726	NP_001106197	Q9Y4F5	K0284_HUMAN	hypothetical protein LOC283638 isoform 1	1239						cytoplasm|microtubule				breast(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.178)		GGGCCCGCTCAGGCAGTGCCC	0.682													5	4	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	33954939	33954939	+	Silent	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33954939C>T	uc001zhi.2	+	35	5278	c.5208C>T	c.(5206-5208)GGC>GGT	p.G1736G	RYR3_uc010bar.2_Silent_p.G1736G	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	1736	4 X approximate repeats.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGGTCATGGGCGTGTTTGATG	0.567													20	115	---	---	---	---	PASS
GOLGA6B	55889	broad.mit.edu	37	15	72954595	72954595	+	Missense_Mutation	SNP	A	G	G	rs143576794	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72954595A>G	uc010uks.1	+	11	891	c.850A>G	c.(850-852)AAG>GAG	p.K284E		NM_018652	NP_061122	A6NDN3	GOG6B_HUMAN	golgi autoantigen, golgin subfamily a, 6B	284	Potential.										0						TTTCTCAGCTAAGCCCCCATC	0.522													4	49	---	---	---	---	PASS
BTBD12	84464	broad.mit.edu	37	16	3652056	3652056	+	Intron	SNP	C	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3652056C>A	uc002cvp.2	-						BTBD12_uc002cvq.1_3'UTR	NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12						DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0						GCACTCCAGCCCTGGGGTGCT	0.493								Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				3	42	---	---	---	---	PASS
CCDC102A	92922	broad.mit.edu	37	16	57552177	57552177	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57552177G>C	uc002elw.2	-	6	1264	c.1051C>G	c.(1051-1053)CAG>GAG	p.Q351E		NM_033212	NP_149989	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	351	Potential.									ovary(1)	1						TTTTCGGCCTGCAGCCGCTCC	0.682													6	46	---	---	---	---	PASS
FAM57A	79850	broad.mit.edu	37	17	644587	644587	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:644587C>A	uc002frp.2	+	5	592	c.551C>A	c.(550-552)ACG>AAG	p.T184K	FAM57A_uc002frq.2_Missense_Mutation_p.T152K|FAM57A_uc002frr.2_Missense_Mutation_p.T94K	NM_024792	NP_079068	Q8TBR7	FA57A_HUMAN	family with sequence similarity 57, member A	184	TLC.|Helical; (Potential).					integral to membrane|plasma membrane					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0217)		GGAATCCTCACGCTGGCCACC	0.537													4	163	---	---	---	---	PASS
C17orf63	55731	broad.mit.edu	37	17	27085367	27085367	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27085367G>T	uc002hct.1	-	3	1877	c.1610C>A	c.(1609-1611)GCC>GAC	p.A537D	C17orf63_uc010wax.1_Missense_Mutation_p.A537D|C17orf63_uc010way.1_Missense_Mutation_p.A537D|C17orf63_uc002hcw.2_Missense_Mutation_p.A409D	NM_018182	NP_060652	Q8WU58	CQ063_HUMAN	hypothetical protein LOC55731	537										ovary(1)	1	all_epithelial(6;5.06e-20)|Lung NSC(42;0.01)		Epithelial(11;3.38e-06)|all cancers(11;2.46e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.104)			GGCTCGGTGGGCCTTGCTCAG	0.577													6	57	---	---	---	---	PASS
CLTC	1213	broad.mit.edu	37	17	57737855	57737855	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57737855C>T	uc002ixq.1	+	7	1516	c.1073C>T	c.(1072-1074)GCC>GTC	p.A358V	CLTC_uc002ixp.2_Missense_Mutation_p.A358V|CLTC_uc002ixr.1_Missense_Mutation_p.A362V	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	358	Globular terminal domain.				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					AATAACTTAGCCGGTGCTGAA	0.433			T	ALK|TFE3	ALCL|renal 								6	443	---	---	---	---	PASS
USP32	84669	broad.mit.edu	37	17	58288802	58288802	+	Silent	SNP	A	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58288802A>G	uc002iyo.1	-	20	2539	c.2253T>C	c.(2251-2253)TGT>TGC	p.C751C	USP32_uc002iyn.1_Silent_p.C421C	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32	751					protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			TGTTACTAACACACTGGATGC	0.433													4	224	---	---	---	---	PASS
FAM38B	63895	broad.mit.edu	37	18	10691323	10691323	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10691323C>A	uc002kor.3	-	6	921	c.781G>T	c.(781-783)GGG>TGG	p.G261W	FAM38B_uc002koq.2_Missense_Mutation_p.G159W	NM_022068	NP_071351	Q9H5I5	PIEZ2_HUMAN	family with sequence similarity 38, member B	2304	Helical; (Potential).					integral to membrane	ion channel activity			ovary(1)	1						GCAGACAACCCGAAGTAAACA	0.443													3	137	---	---	---	---	PASS
KIAA1632	57724	broad.mit.edu	37	18	43505804	43505804	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43505804G>A	uc002lbm.2	-	14	2718	c.2618C>T	c.(2617-2619)GCG>GTG	p.A873V	KIAA1632_uc002lbo.1_Missense_Mutation_p.A873V	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	873					autophagy						0						CCGAATCACCGCTATCTCAGA	0.353													18	170	---	---	---	---	PASS
TSPAN16	26526	broad.mit.edu	37	19	11417404	11417404	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11417404A>G	uc002mqv.1	+	5	725	c.575A>G	c.(574-576)GAT>GGT	p.D192G	TSPAN16_uc002mqu.1_RNA|uc002mqw.1_RNA	NM_012466	NP_036598	Q9UKR8	TSN16_HUMAN	transmembrane 4 superfamily member 16	192	Cytoplasmic (Potential).					integral to membrane				skin(1)	1						GACGGACGCGATGTGTCTCCA	0.468													5	78	---	---	---	---	PASS
CYP2A13	1553	broad.mit.edu	37	19	41596036	41596036	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41596036G>A	uc002opt.2	+	3	437	c.428G>A	c.(427-429)CGC>CAC	p.R143H		NM_000766	NP_000757	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A,	143					xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|heme binding			ovary(2)|skin(1)	3					Clomipramine(DB01242)|Nicotine(DB00184)	GTGGGCAAGCGCGGCATCGAG	0.697													10	50	---	---	---	---	PASS
PSG2	5670	broad.mit.edu	37	19	43579780	43579780	+	Silent	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43579780C>T	uc002ovr.2	-	3	528	c.435G>A	c.(433-435)GAG>GAA	p.E145E	PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG2_uc002ovq.3_Silent_p.E145E|PSG2_uc010eiq.1_Silent_p.E145E|PSG2_uc002ovs.3_Silent_p.E145E|PSG2_uc002ovt.3_Silent_p.E145E	NM_031246	NP_112536	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	145					cell migration|female pregnancy	extracellular region					0		Prostate(69;0.00682)				GCTTGGGAGTCTCCACTGTGC	0.512													5	304	---	---	---	---	PASS
ZNF283	284349	broad.mit.edu	37	19	44352238	44352238	+	Silent	SNP	C	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44352238C>G	uc002oxr.3	+	7	1753	c.1485C>G	c.(1483-1485)ACC>ACG	p.T495T	ZNF283_uc002oxp.3_Silent_p.T356T	NM_181845	NP_862828	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	495	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)				GCGGAAAGACCTTTTGTAGTG	0.413													15	218	---	---	---	---	PASS
MYBPC2	4606	broad.mit.edu	37	19	50939044	50939044	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50939044G>A	uc002psf.2	+	3	172	c.121G>A	c.(121-123)GAG>AAG	p.E41K		NM_004533	NP_004524	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	41					cell adhesion|muscle filament sliding	cytosol|myosin filament	actin binding|structural constituent of muscle			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		AGCCCCACCCGAGGACCAGTC	0.567													8	20	---	---	---	---	PASS
ZNF579	163033	broad.mit.edu	37	19	56090151	56090151	+	Silent	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56090151C>T	uc002qlh.2	-	2	908	c.855G>A	c.(853-855)CTG>CTA	p.L285L		NM_152600	NP_689813	Q8NAF0	ZN579_HUMAN	zinc finger protein 579	285	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.106)		GGTGGCGCGACAGGGACCAGG	0.731													4	38	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57329201	57329201	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57329201G>T	uc002qnu.2	-	6	1126	c.775C>A	c.(775-777)CAG>AAG	p.Q259K	ZIM2_uc010ygq.1_5'UTR|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Intron|PEG3_uc002qnv.2_Missense_Mutation_p.Q259K|PEG3_uc002qnw.2_Missense_Mutation_p.Q135K|PEG3_uc002qnx.2_Missense_Mutation_p.Q133K|PEG3_uc010etr.2_Missense_Mutation_p.Q259K	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	259					apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TCAGCAAGCTGCACTCCTGGT	0.488													5	41	---	---	---	---	PASS
PRND	23627	broad.mit.edu	37	20	4705797	4705797	+	3'UTR	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4705797C>T	uc002wkz.2	+	2						NM_012409	NP_036541	Q9UKY0	PRND_HUMAN	prion-like protein doppel preproprotein						protein homooligomerization	anchored to membrane|plasma membrane					0						CAGCTCTTCTCCCCCAAACCC	0.582													4	11	---	---	---	---	PASS
RBL1	5933	broad.mit.edu	37	20	35668590	35668590	+	Silent	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35668590C>T	uc002xgi.2	-	14	1948	c.1869G>A	c.(1867-1869)AAG>AAA	p.K623K	RBL1_uc010zvt.1_RNA|RBL1_uc002xgj.1_Silent_p.K623K	NM_002895	NP_002886	P28749	RBL1_HUMAN	retinoblastoma-like protein 1 isoform a	623	Pocket; binds T and E1A.|Spacer.				cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)				TTCGAACTTCCTTGACTCTTG	0.418													22	222	---	---	---	---	PASS
ZNF334	55713	broad.mit.edu	37	20	45129919	45129919	+	3'UTR	SNP	A	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45129919A>T	uc002xsc.2	-	5					ZNF334_uc002xsa.2_3'UTR|ZNF334_uc002xsb.2_3'UTR|ZNF334_uc002xsd.2_3'UTR|ZNF334_uc010ghl.2_3'UTR	NM_018102	NP_060572	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)				GTTGGAATTTATTACTTTGTT	0.289													4	216	---	---	---	---	PASS
JAM2	58494	broad.mit.edu	37	21	27078323	27078323	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27078323G>A	uc002ylp.1	+	7	1275	c.730G>A	c.(730-732)GTA>ATA	p.V244I	JAM2_uc011ace.1_Missense_Mutation_p.V244I|JAM2_uc002ylq.1_RNA|JAM2_uc011acf.1_Missense_Mutation_p.V208I|JAM2_uc010glh.1_RNA|JAM2_uc002ylr.1_Missense_Mutation_p.V244I|JAM2_uc010gli.1_Missense_Mutation_p.V244I	NM_021219	NP_067042	P57087	JAM2_HUMAN	junctional adhesion molecule 2 precursor	244	Helical; (Potential).				blood coagulation|cell-cell adhesion|leukocyte migration	integral to plasma membrane|tight junction					0						CATAGCAGCCGTAGTAGTTGT	0.393													16	121	---	---	---	---	PASS
DSCAM	1826	broad.mit.edu	37	21	41684282	41684282	+	Silent	SNP	C	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41684282C>T	uc002yyq.1	-	9	2240	c.1788G>A	c.(1786-1788)CCG>CCA	p.P596P	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	596	Extracellular (Potential).|Ig-like C2-type 7.				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GTATGAAAGGCGGAACTGCAA	0.448													5	26	---	---	---	---	PASS
ADARB1	104	broad.mit.edu	37	21	46645452	46645452	+	3'UTR	SNP	T	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46645452T>C	uc002zgy.2	+	12					ADARB1_uc002zgr.2_Intron|ADARB1_uc002zgs.2_Intron|ADARB1_uc002zgw.2_Intron|ADARB1_uc002zgv.2_Intron|ADARB1_uc002zgt.2_3'UTR|ADARB1_uc010gpx.2_Intron|ADARB1_uc002zgq.2_Intron|ADARB1_uc002zgu.2_Intron	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2						adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)		CTCCTTGTAATCTCACACAGG	0.458													31	135	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22662971	22662971	+	Intron	SNP	A	G	G			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22662971A>G	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_RNA|LOC96610_uc010gto.2_RNA					Parts of antibodies, mostly variable regions.												0						TGTAAGTAAAATTCACTTTGG	0.323													4	14	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22662995	22662995	+	Intron	SNP	C	T	T	rs79792109	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22662995C>T	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_RNA|LOC96610_uc010gto.2_RNA					Parts of antibodies, mostly variable regions.												0						TTTATTGTGTCACATAGAATT	0.348													4	25	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22786685	22786685	+	RNA	SNP	T	C	C	rs61735472		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22786685T>C	uc011aim.1	+	67		c.6868T>C								Parts of antibodies, mostly variable regions.												0						CTCAGGGGTCTCTGACCGATT	0.532													4	222	---	---	---	---	PASS
PPARA	5465	broad.mit.edu	37	22	46594256	46594256	+	5'UTR	SNP	G	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46594256G>A	uc003bgw.1	+	4					PPARA_uc003bgx.1_5'UTR|PPARA_uc010hab.1_5'UTR|PPARA_uc003bgy.1_RNA|PPARA_uc003bgz.1_RNA|PPARA_uc003bha.2_5'UTR|PPARA_uc003bhb.1_5'UTR|PPARA_uc010hac.1_5'UTR	NM_005036	NP_005027	Q07869	PPARA_HUMAN	peroxisome proliferative activated receptor,						fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)	GAGCTCGGCGGCACAACCAGC	0.488													5	214	---	---	---	---	PASS
ARHGAP6	395	broad.mit.edu	37	X	11204545	11204545	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11204545T>C	uc004cup.1	-	5	1957	c.1084A>G	c.(1084-1086)ATG>GTG	p.M362V	ARHGAP6_uc004cuo.1_RNA|ARHGAP6_uc004cur.1_Missense_Mutation_p.M362V|ARHGAP6_uc004cum.1_Missense_Mutation_p.M159V|ARHGAP6_uc004cun.1_Missense_Mutation_p.M182V|ARHGAP6_uc010neb.1_Missense_Mutation_p.M184V|ARHGAP6_uc011mif.1_Missense_Mutation_p.M159V	NM_013427	NP_038286	O43182	RHG06_HUMAN	Rho GTPase activating protein 6 isoform 1	362					actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2						TCCACTGACATGGCACCCTGC	0.443													58	123	---	---	---	---	PASS
NXF4	55999	broad.mit.edu	37	X	101826202	101826202	+	RNA	SNP	G	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101826202G>T	uc004ejf.1	+	16		c.3342G>T				NR_002216				Homo sapiens cDNA FLJ42710 fis, clone BRAMY3007609, moderately similar to Homo sapiens nuclear RNA export factor 2 (NXF2).												0						CTATTCTCCAGGTGAGATCTG	0.498													6	9	---	---	---	---	PASS
TARDBP	23435	broad.mit.edu	37	1	11080808	11080808	+	Intron	DEL	A	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11080808delA	uc001art.2	+						TARDBP_uc010oap.1_Intron	NM_007375	NP_031401	Q13148	TADBP_HUMAN	TAR DNA binding protein						3'-UTR-mediated mRNA stabilization|cell death|mRNA processing|negative regulation by host of viral transcription|RNA splicing|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0578)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.37e-07)|COAD - Colon adenocarcinoma(227;7.38e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)		attaaaatacaaaaaaaaaaa	0.000													5	4	---	---	---	---	
CLCNKB	1188	broad.mit.edu	37	1	16383329	16383330	+	Intron	INS	-	C	C	rs138507185	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16383329_16383330insC	uc001axw.3	+						FAM131C_uc010obz.1_Intron|CLCNKB_uc001axx.3_Intron|CLCNKB_uc001axy.3_Intron	NM_000085	NP_000076	P51801	CLCKB_HUMAN	chloride channel Kb isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			skin(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CTCCTCTACATCCCCCCGCACC	0.545													3	5	---	---	---	---	
EPHA8	2046	broad.mit.edu	37	1	22913273	22913274	+	Intron	INS	-	GG	GG	rs66713995		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22913273_22913274insGG	uc001bfx.1	+						EPHA8_uc001bfw.2_Intron	NM_020526	NP_065387	P29322	EPHA8_HUMAN	ephrin receptor EphA8 isoform 1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CAGTCTGAGGTGGGGGGGGTGA	0.658													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	74420085	74420086	+	IGR	INS	-	TCC	TCC	rs58825552		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74420085_74420086insTCC								None (None upstream) : LRRIQ3 (71618 downstream)																							cctcccttccttccttccttcc	0.000													4	2	---	---	---	---	
UBAP2L	9898	broad.mit.edu	37	1	154200024	154200025	+	Intron	INS	-	TT	TT	rs140500910	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154200024_154200025insTT	uc001fep.3	+						UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc001fen.1_Intron|UBAP2L_uc010pem.1_Intron|UBAP2L_uc010pen.1_5'Flank	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CCtttgttttgttttttgtttt	0.139													4	2	---	---	---	---	
ERO1LB	56605	broad.mit.edu	37	1	236395979	236395980	+	Intron	INS	-	T	T	rs34039166		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236395979_236395980insT	uc001hxt.2	-							NM_019891	NP_063944	Q86YB8	ERO1B_HUMAN	endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			ataaaataatcttttttttttt	0.243													7	4	---	---	---	---	
CKAP2L	150468	broad.mit.edu	37	2	113513316	113513316	+	Intron	DEL	A	-	-	rs150191453		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113513316delA	uc002tie.2	-						CKAP2L_uc002tif.2_Intron|CKAP2L_uc010yxp.1_Intron|CKAP2L_uc010yxq.1_Intron	NM_152515	NP_689728	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like							centrosome					0						TCTTAAAAAGAAAAAAAAAAA	0.343													6	3	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	132905835	132905836	+	Intron	INS	-	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132905835_132905836insT	uc002tti.3	-						NCRNA00164_uc002ttj.3_Intron	NR_027019				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						AATTTTCCTTCGCTAAATATCA	0.406													7	4	---	---	---	---	
RQCD1	9125	broad.mit.edu	37	2	219447953	219447978	+	Intron	DEL	TGTGTCTCTCTCTCTCTCTCTCTCTC	-	-	rs36210927	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219447953_219447978delTGTGTCTCTCTCTCTCTCTCTCTCTC	uc010zkh.1	+						RQCD1_uc002vih.1_Intron|RQCD1_uc010zki.1_Intron	NM_005444	NP_005435	Q92600	RCD1_HUMAN	RCD1 required for cell differentiation1 homolog						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|sex differentiation|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(1)|skin(1)	2		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000192)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		tgtgtgtgtgtgtgtctctctctctctctctctctctctctctctc	0.226													2	5	---	---	---	---	
BCHE	590	broad.mit.edu	37	3	165515095	165515099	+	Intron	DEL	CCCTT	-	-	rs142594104		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165515095_165515099delCCCTT	uc003fem.3	-						BCHE_uc003fen.3_Intron	NM_000055	NP_000046	P06276	CHLE_HUMAN	butyrylcholinesterase precursor						choline metabolic process|cocaine metabolic process|synaptic transmission, cholinergic	endoplasmic reticulum lumen|extracellular space|membrane	acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|enzyme binding			ovary(3)|pancreas(1)	4					Ambenonium(DB01122)|Atropine(DB00572)|Bambuterol(DB01408)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinnarizine(DB00568)|Demecarium bromide(DB00944)|Dibucaine(DB00527)|Donepezil(DB00843)|Echothiophate Iodide(DB01057)|Edrophonium(DB01010)|Ethopropazine(DB00392)|Etomidate(DB00292)|Galantamine(DB00674)|Hexafluronium bromide(DB00941)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Mivacurium(DB01226)|Neostigmine(DB01400)|Pancuronium(DB01337)|Pralidoxime(DB00733)|Procainamide(DB01035)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Terbutaline(DB00871)|Trimethaphan(DB01116)	ctccctcccccccttccttccttcc	0.034													4	4	---	---	---	---	
IQCG	84223	broad.mit.edu	37	3	197639506	197639506	+	Intron	DEL	A	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197639506delA	uc003fyo.2	-						IQCG_uc003fyn.2_Intron|IQCG_uc003fyp.2_Intron|IQCG_uc003fym.2_Intron	NM_001134435	NP_001127907	Q9H095	IQCG_HUMAN	IQ motif containing G												0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		AGCAGAGTACAAAAAAAAAGT	0.398													340	8	---	---	---	---	
GRK4	2868	broad.mit.edu	37	4	2965874	2965875	+	Intron	INS	-	C	C	rs142156088	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2965874_2965875insC	uc003ggn.1	+						GRK4_uc003ggo.1_Intron|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron|NOP14_uc003ggj.1_5'Flank|NOP14_uc003ggk.3_5'Flank|NOP14_uc003ggl.2_5'Flank|NOP14_uc010icq.1_5'Flank|GRK4_uc003ggm.2_Intron	NM_182982	NP_892027	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4 isoform							cell cortex	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GGCGCCCCCGACCCCCCCCCCA	0.708													5	5	---	---	---	---	
BST1	683	broad.mit.edu	37	4	15709457	15709458	+	Intron	INS	-	CTCTCTCTCT	CTCTCTCTCT	rs146353876	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15709457_15709458insCTCTCTCTCT	uc003goh.3	+							NM_004334	NP_004325	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1 precursor						humoral immune response|multicellular organismal development	anchored to membrane|extrinsic to membrane|plasma membrane	binding|NAD+ nucleosidase activity			central_nervous_system(1)	1						CAGTCTAAGCActctctctctc	0.084													4	3	---	---	---	---	
UGT2B4	7363	broad.mit.edu	37	4	70351409	70351410	+	Intron	DEL	AT	-	-	rs33914959		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70351409_70351410delAT	uc003hek.3	-						UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_Intron	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor						estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2						aggaaacatcatgtgcagaAAA	0.084													3	3	---	---	---	---	
USO1	8615	broad.mit.edu	37	4	76734266	76734267	+	Intron	INS	-	A	A	rs74649498		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76734266_76734267insA	uc003hiu.2	+						USO1_uc003hiv.2_Intron|USO1_uc003hiw.2_Intron	NM_003715	NP_003706	O60763	USO1_HUMAN	USO1 homolog, vesicle docking protein						intracellular protein transport|vesicle fusion with Golgi apparatus	cytosol|Golgi membrane	protein binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			ctccatctcagaaaaaaaaaaa	0.119													9	4	---	---	---	---	
FRG1	2483	broad.mit.edu	37	4	190874371	190874372	+	Intron	DEL	AG	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190874371_190874372delAG	uc003izs.2	+							NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1						rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TTAAGCCCACAGGGTAATTTTG	0.252													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3324082	3324086	+	IGR	DEL	GTATC	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3324082_3324086delGTATC								C5orf38 (568570 upstream) : IRX1 (272082 downstream)																							gtgttgtgtggtatctgtggtgtgt	0.015													4	2	---	---	---	---	
NUDT12	83594	broad.mit.edu	37	5	102886822	102886823	+	Intron	INS	-	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102886822_102886823insT	uc003koi.2	-						NUDT12_uc011cvb.1_Intron	NM_031438	NP_113626	Q9BQG2	NUD12_HUMAN	nudix-type motif 12							nucleus|peroxisome	metal ion binding|NAD+ diphosphatase activity				0		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		TACATGCAAAGttttttttttt	0.139													5	3	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127680393	127680393	+	Intron	DEL	T	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127680393delT	uc003kuu.2	-						FBN2_uc003kuv.2_Intron	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TCTTATAttcttttttttttt	0.164													3	4	---	---	---	---	
EXOC2	55770	broad.mit.edu	37	6	499431	499432	+	Intron	DEL	AC	-	-	rs4061197		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:499431_499432delAC	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		TCACAGTTAAacacacacacac	0.267													5	3	---	---	---	---	
C6orf146	222826	broad.mit.edu	37	6	4077904	4077908	+	Intron	DEL	CAGAA	-	-	rs139948157		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4077904_4077908delCAGAA	uc003mvx.2	-						C6orf146_uc010jnq.1_Intron|C6orf146_uc003mvy.2_Intron|C6orf201_uc003mwa.3_5'Flank|C6orf201_uc003mvz.3_5'Flank	NM_173563	NP_775834	Q8IXS0	CF146_HUMAN	hypothetical protein LOC222826											ovary(1)	1	Ovarian(93;0.0925)	all_hematologic(90;0.108)				TGGCAGATCTCAGAACAGAAGATTA	0.444													3	4	---	---	---	---	
RNF144B	255488	broad.mit.edu	37	6	18406292	18406292	+	Intron	DEL	A	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18406292delA	uc003ncs.2	+							NM_182757	NP_877434	Q7Z419	R144B_HUMAN	IBR domain containing 2						apoptosis|positive regulation of anti-apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			ttatttattcaacaaatattt	0.139													405	13	---	---	---	---	
GPR126	57211	broad.mit.edu	37	6	142630883	142630883	+	Intron	DEL	T	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142630883delT	uc010khc.2	+						GPR126_uc010khd.2_Intron|GPR126_uc010khe.2_Intron|GPR126_uc010khf.2_Intron|GPR126_uc003qix.2_Intron	NM_020455	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		ACTTACTGCCTTTTTTTTTTT	0.323													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	158195281	158195281	+	IGR	DEL	G	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158195281delG								ZDHHC14 (100305 upstream) : SNX9 (49013 downstream)																							tggaggaggtgggggagtgga	0.313													4	2	---	---	---	---	
ACAT2	39	broad.mit.edu	37	6	160199454	160199455	+	Intron	DEL	TT	-	-	rs71808548		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160199454_160199455delTT	uc010kjy.2	+						ACAT2_uc011efw.1_Intron	NM_005891	NP_005882	Q9BWD1	THIC_HUMAN	acetyl-Coenzyme A acetyltransferase 2							mitochondrion|nucleolus	acetyl-CoA C-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CTTCCCAAGGTTTaaaaaaaaa	0.317													6	3	---	---	---	---	
CHN2	1124	broad.mit.edu	37	7	29438231	29438232	+	Intron	INS	-	G	G	rs140510730	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29438231_29438232insG	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058	P52757	CHIO_HUMAN	beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2						ttatgttatgaggggggggtcc	0.084													3	4	---	---	---	---	
STAG3L1	54441	broad.mit.edu	37	7	74991539	74991539	+	Intron	DEL	C	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74991539delC	uc003ucu.1	+						STAG3L1_uc010lcz.1_Intron|STAG3L1_uc003ucv.1_Intron|STAG3L1_uc011kfw.1_Intron|STAG3L1_uc011kfx.1_Intron	NM_018991	NP_061864	P0CL83	ST3L1_HUMAN	stromal antigen 3-like 1 isoform 1							nucleus	binding				0						AGAGCATGttctttttttttt	0.179													3	3	---	---	---	---	
TFR2	7036	broad.mit.edu	37	7	100230356	100230357	+	Intron	DEL	AG	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100230356_100230357delAG	uc003uvv.1	-						TFR2_uc010lhc.1_Intron|TFR2_uc003uvu.1_Intron	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN	transferrin receptor 2						cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					aaaaaaaaaaagaacctttttt	0.000													4	2	---	---	---	---	
LUC7L2	51631	broad.mit.edu	37	7	139091747	139091748	+	Intron	INS	-	TTT	TTT	rs10254132		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139091747_139091748insTTT	uc003vux.2	+						LUC7L2_uc011kqs.1_Intron|LUC7L2_uc011kqt.1_Intron|LUC7L2_uc003vuy.2_Intron|LUC7L2_uc003vuz.1_Intron|LUC7L2_uc003vva.2_Intron	NM_016019	NP_057103	Q9Y383	LC7L2_HUMAN	LUC7-like 2								enzyme binding|metal ion binding				0	Melanoma(164;0.242)					TGCTTTTGTGGttttttttttt	0.371													4	2	---	---	---	---	
BRAF	673	broad.mit.edu	37	7	140476673	140476674	+	Intron	INS	-	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140476673_140476674insA	uc003vwc.3	-							NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf						activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	CAATGGTCTTCAAAAATAATTT	0.356		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				93	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141036751	141036752	+	IGR	INS	-	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141036751_141036752insA								MRPS33 (321970 upstream) : AGK (214326 downstream)																							accatcaccaccaccaccatca	0.000													5	3	---	---	---	---	
MAK16	84549	broad.mit.edu	37	8	33355789	33355790	+	Intron	INS	-	AA	AA			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33355789_33355790insAA	uc003xjj.2	+						C8orf41_uc010lvu.1_Intron	NM_032509	NP_115898	Q9BXY0	MAK16_HUMAN	MAK16 homolog							nucleolus				ovary(1)	1						gaccccgtctcaaaaaaaaaaa	0.153													4	2	---	---	---	---	
ADAM32	203102	broad.mit.edu	37	8	39141290	39141291	+	Intron	INS	-	T	T	rs67530415		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39141290_39141291insT	uc003xmt.3	+						ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron|ADAM32_uc003xmv.2_Intron	NM_145004	NP_659441	Q8TC27	ADA32_HUMAN	a disintegrin and metalloprotease domain 32						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			TTCttttattcttttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101438935	101438936	+	IGR	INS	-	A	A			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101438935_101438936insA								RNF19A (116608 upstream) : ANKRD46 (83051 downstream)																							ccaccaccaccactaccaccac	0.000													4	3	---	---	---	---	
COL15A1	1306	broad.mit.edu	37	9	101822425	101822425	+	Intron	DEL	A	-	-	rs10709284		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101822425delA	uc004azb.1	+							NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor						angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)				AAAAGACGTGAAAAAACAAAA	0.294													6	3	---	---	---	---	
SLIT1	6585	broad.mit.edu	37	10	98780878	98780879	+	Intron	INS	-	CCTTGTTC	CCTTGTTC	rs140758802	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98780878_98780879insCCTTGTTC	uc001kmw.2	-							NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		AGCCGCAGGTGCCTTGTTCCTG	0.604													4	3	---	---	---	---	
SFXN4	119559	broad.mit.edu	37	10	120914415	120914415	+	Intron	DEL	T	-	-	rs34654417		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120914415delT	uc001leb.2	-						SFXN4_uc001ldy.2_Intron|SFXN4_uc001ldz.2_Intron|SFXN4_uc001lea.2_Intron	NM_213649	NP_998814	Q6P4A7	SFXN4_HUMAN	sideroflexin 4						iron ion homeostasis	integral to membrane|mitochondrial membrane	cation transmembrane transporter activity			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		atgcCCCATCTTATCAGGGGG	0.239													3	3	---	---	---	---	
MKI67	4288	broad.mit.edu	37	10	129911471	129911472	+	Intron	INS	-	C	C	rs145393258	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129911471_129911472insC	uc001lke.2	-						MKI67_uc001lkf.2_Intron|MKI67_uc009yav.1_Intron|MKI67_uc009yaw.1_Intron	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67						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)				CATCAAGGACTCCCCCGACTCG	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	27505351	27505351	+	IGR	DEL	C	-	-	rs11030023	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27505351delC								LGR4 (11017 upstream) : LIN7C (10620 downstream)																							aacaaacaaacaaaaaaacaC	0.214													4	2	---	---	---	---	
CKAP5	9793	broad.mit.edu	37	11	46780265	46780265	+	Intron	DEL	A	-	-	rs138844869		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46780265delA	uc001ndi.1	-						CKAP5_uc009ylg.1_Intron|CKAP5_uc001ndj.1_Intron|CKAP5_uc001ndh.1_Intron	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2						tcaaaagaggaaaaaaaaaaa	0.189													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48441736	48441736	+	IGR	DEL	T	-	-	rs147108249		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48441736delT								OR4C45 (67737 upstream) : OR4A47 (68609 downstream)																							TTTTTTTTCATTTTTTTTTTC	0.323													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74363782	74363782	+	IGR	DEL	C	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74363782delC								POLD3 (10017 upstream) : CHRDL2 (43693 downstream)																							AAAAGTAACTCCAACTTGGAA	0.413													4	2	---	---	---	---	
ERBB3	2065	broad.mit.edu	37	12	56492212	56492212	+	Intron	DEL	G	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56492212delG	uc001sjh.2	+						ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Intron|ERBB3_uc009zok.2_Intron|ERBB3_uc001sjk.2_Intron|ERBB3_uc001sjl.2_5'UTR	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor						cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			aaaaaaaaaagaaTTTGGGAC	0.189													99	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	101892566	101892567	+	IGR	DEL	GT	-	-	rs71648254		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101892566_101892567delGT								SPIC (11792 upstream) : MYBPC1 (96180 downstream)																							TTTGTTTGTCgtgtgtgtgtgt	0.168													4	2	---	---	---	---	
RILPL2	196383	broad.mit.edu	37	12	123900706	123900707	+	Intron	INS	-	A	A	rs144225262		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123900706_123900707insA	uc001uey.1	-							NM_145058	NP_659495	Q969X0	RIPL2_HUMAN	Rab interacting lysosomal protein-like 2							cytosol|plasma membrane	identical protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000546)|Epithelial(86;0.00179)|all cancers(50;0.0168)		accccatctctaaaaaaaaaaa	0.000													7	4	---	---	---	---	
SEL1L	6400	broad.mit.edu	37	14	81943647	81943648	+	Intron	INS	-	TGTGTGTGTG	TGTGTGTGTG	rs140905448	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81943647_81943648insTGTGTGTGTG	uc010tvv.1	-							NM_005065	NP_005056	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like precursor						Notch signaling pathway	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0299)		ACGTTTTGCAAtgtgtgtgtgt	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	100419367	100419368	+	IGR	INS	-	TGG	TGG	rs113676314		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100419367_100419368insTGG								EML1 (10974 upstream) : EVL (18783 downstream)																							gatggtggtgatggtgatggtg	0.119													4	2	---	---	---	---	
C16orf13	84326	broad.mit.edu	37	16	685626	685626	+	Frame_Shift_Del	DEL	G	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:685626delG	uc002chv.1	-	2	403	c.346delC	c.(346-348)CTGfs	p.L116fs	C16orf13_uc002chw.1_Frame_Shift_Del_p.L116fs|C16orf13_uc002chz.1_Frame_Shift_Del_p.L116fs|C16orf13_uc002cia.1_Intron|C16orf13_uc002cib.1_Intron|uc010uuk.1_5'Flank	NM_032366	NP_115742	Q96S19	CP013_HUMAN	hypothetical protein LOC84326 isoform a	116											0		Hepatocellular(780;0.00335)				GTGCAGCGCAGGGGGCTGACA	0.657													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20605022	20605023	+	IGR	INS	-	T	T			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20605022_20605023insT								ACSM2B (17327 upstream) : ACSM1 (29536 downstream)																							TTGTTATCGGCTTCTCCCCTGG	0.406													4	2	---	---	---	---	
PFAS	5198	broad.mit.edu	37	17	8171691	8171691	+	Intron	DEL	A	-	-	rs76845148		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8171691delA	uc002gkr.2	+						PFAS_uc010vuv.1_Intron|PFAS_uc002gks.2_Intron	NM_012393	NP_036525	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase						'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	attccatctcaaaaaaaaaaa	0.065													4	3	---	---	---	---	
AMZ2P1	201283	broad.mit.edu	37	17	62968909	62968909	+	RNA	DEL	T	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62968909delT	uc002jez.3	-	3		c.513delA			AMZ2P1_uc002jfa.3_RNA|AMZ2P1_uc002jfb.3_RNA|AMZ2P1_uc010del.2_RNA					Homo sapiens cDNA FLJ32065 fis, clone OCBBF1000086, weakly similar to Archeobacterial metalloproteinase-like protein 2 (EC 3.-.-.-).												0						TCTCATTGACTCTAAAGGAAC	0.358													56	11	---	---	---	---	
GPRC5C	55890	broad.mit.edu	37	17	72437119	72437120	+	Intron	INS	-	T	T	rs141781708		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72437119_72437120insT	uc002jks.2	+						GPRC5C_uc002jkp.2_Intron|GPRC5C_uc002jkq.2_Intron|GPRC5C_uc002jkr.2_Intron|GPRC5C_uc002jkt.2_Intron|GPRC5C_uc002jku.2_5'Flank	NM_018653	NP_061123	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor family C, group 5,							cytoplasmic vesicle membrane|integral to plasma membrane	G-protein coupled receptor activity|protein binding			ovary(2)|prostate(1)|central_nervous_system(1)|pancreas(1)	5						TAATTTAAAGATTTTTTTTTTT	0.198													3	7	---	---	---	---	
VAV1	7409	broad.mit.edu	37	19	6771753	6771753	+	5'Flank	DEL	A	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6771753delA	uc002mfu.1	+						VAV1_uc010xjh.1_5'Flank|VAV1_uc010dva.1_5'Flank	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16						actccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	21145362	21145364	+	IGR	DEL	TGC	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21145362_21145364delTGC								ZNF85 (11861 upstream) : ZNF430 (58133 downstream)																							caGTCCATCTTGCTGCTGATGAC	0.271													4	3	---	---	---	---	
TNNT1	7138	broad.mit.edu	37	19	55652874	55652874	+	Intron	DEL	T	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55652874delT	uc002qjb.3	-						TNNT1_uc002qiz.3_Intron|TNNT1_uc002qja.3_Intron|TNNT1_uc002qjc.3_Intron|TNNT1_uc002qje.3_Intron|TNNT1_uc002qjd.3_Intron|TNNT1_uc002qjf.2_Intron	NM_003283	NP_003274	P13805	TNNT1_HUMAN	troponin T1, skeletal, slow isoform a						muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		GACCGGCGCCTTTTTTTTTTT	0.308													4	2	---	---	---	---	
C20orf117	140710	broad.mit.edu	37	20	35423173	35423173	+	Intron	DEL	T	-	-	rs79620367		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35423173delT	uc002xgd.1	-						C20orf117_uc002xge.1_Intron	NM_199181	NP_954650	O94964	K0889_HUMAN	hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)				CTGCAttttcttttttttttt	0.104													6	3	---	---	---	---	
C20orf117	140710	broad.mit.edu	37	20	35445688	35445688	+	Intron	DEL	G	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35445688delG	uc002xgd.1	-						C20orf117_uc002xge.1_5'Flank	NM_199181	NP_954650	O94964	K0889_HUMAN	hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)				aaaaaaaaaagaaaagaaaaa	0.229													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	24474307	24474307	+	IGR	DEL	A	-	-	rs72441902		TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24474307delA								None (None upstream) : None (None downstream)																							catttctactaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SLC2A11	66035	broad.mit.edu	37	22	24204625	24204626	+	Intron	INS	-	G	G	rs140916169	by1000genomes	TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24204625_24204626insG	uc002zyn.3	+						SLC2A11_uc002zyl.1_Intron|SLC2A11_uc002zym.3_Intron|SLC2A11_uc002zyo.3_Intron|SLC2A11_uc011ajc.1_Intron|SLC2A11_uc011ajd.1_Intron|SLC2A11_uc002zyp.3_Intron	NM_001024938	NP_001020109	Q9BYW1	GTR11_HUMAN	glucose transporter protein 10 isoform c							integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1						cacctagtgatggggggtcagc	0.000													1	5	---	---	---	---	
SFI1	9814	broad.mit.edu	37	22	31985765	31985768	+	Intron	DEL	TTTA	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31985765_31985768delTTTA	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron|SFI1_uc010gwi.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						TTTGTCCATCTTTATTTATTTATT	0.333													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	70183298	70183302	+	IGR	DEL	AGGGA	-	-			TCGA-EJ-5498-01A-01D-1576-08	TCGA-EJ-5498-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70183298_70183302delAGGGA								SLC7A3 (32339 upstream) : SNX12 (26062 downstream)																							aaaaaaaaggagggaagggaaggga	0.249													5	4	---	---	---	---	
