Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	g.chr22:22786685T>C	uc011aim.1	+	67		c.6868T>C								Parts of antibodies, mostly variable regions.												0						CTCAGGGGTCTCTGACCGATT	0.532													4	222	---	---	---	---	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	---	---	---	---	
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	3b4e02da-87be-46e2-b4bd-555ca1440808	b8daddf3-4dbc-47b1-b5bf-777c46131bb8	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	---	---	---	---	
