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
NPHP4	261734	broad.mit.edu	37	1	5967195	5967195	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5967195G>C	uc001alq.1	-	13	1857	c.1591C>G	c.(1591-1593)CAG>GAG	p.Q531E	NPHP4_uc001als.1_RNA|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron|NPHP4_uc009vlu.1_5'Flank	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	531					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GGGGAGGCCTGAGAGCCATGG	0.617													6	7	---	---	---	---	PASS
CASZ1	54897	broad.mit.edu	37	1	10699644	10699644	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10699644G>A	uc001aro.2	-	21	4955	c.4635C>T	c.(4633-4635)GCC>GCT	p.A1545A		NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	1545					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		AGAAGCCCGCGGCGCTGATCA	0.662													7	28	---	---	---	---	PASS
PLEKHM2	23207	broad.mit.edu	37	1	16053734	16053734	+	Silent	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16053734C>T	uc010obo.1	+	9	1394	c.1167C>T	c.(1165-1167)TCC>TCT	p.S389S		NM_015164	NP_055979	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M	389					Golgi organization	cytoplasm	kinesin binding			ovary(1)	1		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GCGAGCGCTCCGAGCCGGGCC	0.672													3	5	---	---	---	---	PASS
PLA2G5	5322	broad.mit.edu	37	1	20412659	20412659	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20412659G>A	uc001bcy.2	+	3	392	c.124G>A	c.(124-126)GGC>AGC	p.G42S	PLA2G5_uc001bcw.2_RNA|PLA2G5_uc001bcx.2_Missense_Mutation_p.G73S	NM_000929	NP_000920	P39877	PA2G5_HUMAN	phospholipase A2, group V precursor	42					lipid catabolic process	extracellular region	calcium ion binding|calcium-dependent phospholipase A2 activity			skin(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)		GACAAACTACGGCTTCTACGG	0.557													17	72	---	---	---	---	PASS
C1orf128	57095	broad.mit.edu	37	1	24112837	24112837	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24112837C>T	uc001bhq.2	+	5	588	c.458C>T	c.(457-459)TCA>TTA	p.S153L	C1orf128_uc010oeb.1_Missense_Mutation_p.S60L	NM_020362	NP_065095	Q9GZP4	PITH1_HUMAN	chromosome 1 open reading frame 128	153	PITH.										0		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.0034)|all_lung(284;0.00519)|Breast(348;0.0222)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0561)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;1.97e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		TATCATCTCTCAATTCATATT	0.383													14	88	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34071503	34071503	+	Silent	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34071503G>T	uc001bxn.1	-	42	6338	c.6309C>A	c.(6307-6309)GTC>GTA	p.V2103V	CSMD2_uc001bxm.1_Intron|CSMD2_uc001bxo.1_Intron	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2103	Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				AGGAAGCGGCGACGGGAGGAG	0.328													6	55	---	---	---	---	PASS
DMRTB1	63948	broad.mit.edu	37	1	53925207	53925207	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53925207G>A	uc001cvq.1	+	1	136	c.81G>A	c.(79-81)GCG>GCA	p.A27A		NM_033067	NP_149056	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal,	27	DM.				sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2						AGGGACACGCGGGCAAATGCC	0.617													11	30	---	---	---	---	PASS
GBP2	2634	broad.mit.edu	37	1	89586879	89586879	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89586879G>A	uc001dmz.1	-	3	536	c.265C>T	c.(265-267)CCA>TCA	p.P89S	GBP2_uc001dmy.1_RNA	NM_004120	NP_004111	P32456	GBP2_HUMAN	guanylate binding protein 2,	89					interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)	1		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		GTGTGTTCTGGCTTCTTGGGA	0.428													42	168	---	---	---	---	PASS
GBP2	2634	broad.mit.edu	37	1	89587622	89587622	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89587622G>A	uc001dmz.1	-	2	299	c.28C>T	c.(28-30)CCA>TCA	p.P10S	GBP2_uc001dmy.1_RNA	NM_004120	NP_004111	P32456	GBP2_HUMAN	guanylate binding protein 2,	10					interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)	1		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		AGGCTCATTGGGCCCGGCAAG	0.488													42	188	---	---	---	---	PASS
DENND2D	79961	broad.mit.edu	37	1	111738540	111738540	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111738540C>T	uc001eak.1	-	6	843	c.643G>A	c.(643-645)GAG>AAG	p.E215K	DENND2D_uc001eal.1_Missense_Mutation_p.E212K	NM_024901	NP_079177	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	215	DENN.									ovary(1)	1		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		TAACCCACCTCAGTGCCTGAG	0.552													37	197	---	---	---	---	PASS
HIST2H2AB	317772	broad.mit.edu	37	1	149859299	149859299	+	Silent	SNP	G	C	C	rs140091148	byFrequency	TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149859299G>C	uc001ete.2	-	1	168	c.168C>G	c.(166-168)CTC>CTG	p.L56L	HIST2H2BE_uc001etc.2_5'Flank	NM_175065	NP_778235	Q8IUE6	H2A2B_HUMAN	histone cluster 2, H2ab	56					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)|breast(1)	2	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			TCAGGTACTCGAGGACCGCCG	0.667													17	97	---	---	---	---	PASS
HIST2H2AB	317772	broad.mit.edu	37	1	149859370	149859370	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149859370G>C	uc001ete.2	-	1	97	c.97C>G	c.(97-99)CGC>GGC	p.R33G	HIST2H2BE_uc001etc.2_5'Flank	NM_175065	NP_778235	Q8IUE6	H2A2B_HUMAN	histone cluster 2, H2ab	33					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)|breast(1)	2	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			CGCAGCAAGCGGTGCACTCGC	0.682													26	150	---	---	---	---	PASS
TARS2	80222	broad.mit.edu	37	1	150469036	150469036	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150469036G>A	uc001euq.2	+	8	860	c.853G>A	c.(853-855)GAA>AAA	p.E285K	TARS2_uc010pcd.1_RNA|TARS2_uc001eur.2_Intron|TARS2_uc009wlt.2_Intron|TARS2_uc009wls.2_Intron	NM_025150	NP_079426	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial	285					threonyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|threonine-tRNA ligase activity			ovary(1)	1	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	CCCCACAACAGAATTGCTGAG	0.547													38	185	---	---	---	---	PASS
THBS3	7059	broad.mit.edu	37	1	155171307	155171307	+	Silent	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155171307C>T	uc001fix.2	-	11	1253	c.1230G>A	c.(1228-1230)CAG>CAA	p.Q410Q	RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Silent_p.Q401Q|THBS3_uc001fiz.2_Silent_p.Q410Q|THBS3_uc001fiy.2_5'UTR|THBS3_uc010pfu.1_Silent_p.Q290Q|THBS3_uc010pfv.1_RNA|THBS3_uc001fja.2_RNA	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor	410	EGF-like 3; calcium-binding (Potential).				cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGAGGCAGCCCTGGCTCTGGT	0.627													12	65	---	---	---	---	PASS
C1orf61	10485	broad.mit.edu	37	1	156376974	156376974	+	Silent	SNP	A	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156376974A>G	uc001fou.1	-	6	438	c.321T>C	c.(319-321)CTT>CTC	p.L107L	C1orf61_uc001fot.1_3'UTR|C1orf61_uc001fov.1_Intron|C1orf61_uc001fow.1_Intron|C1orf61_uc001fox.1_Intron	NM_006365	NP_006356	Q13536	CROC4_HUMAN	transcriptional activator of the c-fos promoter	107						nucleus				skin(1)	1	Hepatocellular(266;0.158)					aggaataagcaagatcatgga	0.139													5	25	---	---	---	---	PASS
C1orf92	149499	broad.mit.edu	37	1	156897312	156897312	+	Silent	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156897312C>T	uc001fqm.2	+	7	859	c.687C>T	c.(685-687)AAC>AAT	p.N229N	C1orf92_uc001fql.2_Silent_p.N14N	NM_144702	NP_653303	Q8N4P6	LRC71_HUMAN	hypothetical protein LOC149499	229	LRR 3.										0	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTCTGCGGAACAATAACATCG	0.627													9	21	---	---	---	---	PASS
FCRL2	79368	broad.mit.edu	37	1	157737189	157737189	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157737189A>G	uc001fre.2	-	6	1053	c.994T>C	c.(994-996)TAC>CAC	p.Y332H	FCRL2_uc001frd.2_Missense_Mutation_p.Y79H|FCRL2_uc010phz.1_Missense_Mutation_p.Y332H|FCRL2_uc009wsp.2_Intron	NM_030764	NP_110391	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2 precursor	332	Ig-like C2-type 4.|Extracellular (Potential).				cell-cell signaling	integral to membrane|plasma membrane|soluble fraction	receptor activity|SH3/SH2 adaptor activity			ovary(1)|pancreas(1)	2	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TAAAATTGGTACAAGATTGGG	0.587													26	132	---	---	---	---	PASS
RGS4	5999	broad.mit.edu	37	1	163044272	163044272	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163044272G>A	uc009wuy.2	+	5	1051	c.540G>A	c.(538-540)CCG>CCA	p.P180P	RGS4_uc001gcl.3_Silent_p.P277P|RGS4_uc009wuz.2_3'UTR|RGS4_uc009wva.2_Silent_p.P162P	NM_005613	NP_005604	P49798	RGS4_HUMAN	regulator of G-protein signaling 4 isoform 2	180					inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	plasma membrane	calmodulin binding|GTPase activator activity|signal transducer activity			ovary(2)|central_nervous_system(1)	3						TGGTCAACCCGTCCAGCTGTG	0.517													8	349	---	---	---	---	PASS
ATP1B1	481	broad.mit.edu	37	1	169101419	169101419	+	RNA	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169101419C>G	uc001gfs.1	+	6		c.1663C>G						P05026	AT1B1_HUMAN	Synthetic construct DNA, clone: pF1KB8186, Homo sapiens ATP1B1 gene for ATPase, Na+/K+ transporting, beta 1 polypeptide, without stop codon, in Flexi system.						ATP biosynthetic process|blood coagulation|leukocyte migration	sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	all_hematologic(923;0.208)					GGGAACTGCCCTTTAAATTTT	0.413													5	17	---	---	---	---	PASS
C1orf49	84066	broad.mit.edu	37	1	178485756	178485756	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178485756G>T	uc001glt.1	+	5	335	c.223G>T	c.(223-225)GAT>TAT	p.D75Y	C1orf49_uc001glu.1_Missense_Mutation_p.D75Y|C1orf49_uc001glv.1_RNA|C1orf49_uc001glw.1_Missense_Mutation_p.D83Y	NM_032126	NP_115502	Q5T0J7	CA049_HUMAN	hypothetical protein LOC84066	75	Potential.					microtubule cytoskeleton					0						TTAGATAAAGGATCTAATGGA	0.299													7	58	---	---	---	---	PASS
IRF6	3664	broad.mit.edu	37	1	209964183	209964183	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209964183C>G	uc001hhq.1	-	7	980	c.717G>C	c.(715-717)CAG>CAC	p.Q239H	IRF6_uc010psm.1_Missense_Mutation_p.Q144H|IRF6_uc009xct.1_Missense_Mutation_p.Q239H	NM_006147	NP_006138	O14896	IRF6_HUMAN	interferon regulatory factor 6	239					cell cycle arrest|interferon-gamma-mediated signaling pathway|mammary gland epithelial cell differentiation|negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		CGGTCATGGTCTGCCCGTACT	0.577										HNSCC(57;0.16)			38	165	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228468045	228468045	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228468045G>A	uc009xez.1	+	29	7873	c.7829G>A	c.(7828-7830)CGG>CAG	p.R2610Q	OBSCN_uc001hsn.2_Missense_Mutation_p.R2610Q|OBSCN_uc001hsp.1_Missense_Mutation_p.R309Q|OBSCN_uc001hsq.1_5'Flank	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	2610	Ig-like 25.				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)				CACAAGGGCCGGCGCCACACG	0.622													6	10	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235866082	235866082	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235866082C>G	uc001hxj.2	-	45	10514	c.10339G>C	c.(10339-10341)GAG>CAG	p.E3447Q	LYST_uc001hxi.2_Missense_Mutation_p.E671Q	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	3447					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)			TCTCGGGTCTCCCTGAAAGCA	0.498									Chediak-Higashi_syndrome				4	243	---	---	---	---	PASS
VN1R5	317705	broad.mit.edu	37	1	247419665	247419665	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247419665C>G	uc010pyu.1	+	2	292	c.292C>G	c.(292-294)CAG>GAG	p.Q98E		NM_173858	NP_776257	Q7Z5H4	VN1R5_HUMAN	vomeronasal 1 receptor 5	98	Helical; Name=3; (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0	all_cancers(71;5.7e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)	all_cancers(173;0.0314)	OV - Ovarian serous cystadenocarcinoma(106;0.00854)			GCTCTTCACCCAGGCAATATT	0.413													33	170	---	---	---	---	PASS
ITGB1BP1	9270	broad.mit.edu	37	2	9558757	9558757	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9558757T>A	uc002qzj.2	-	2	247	c.70A>T	c.(70-72)AAG>TAG	p.K24*	ITGB1BP1_uc002qzk.2_Nonsense_Mutation_p.K24*|ITGB1BP1_uc002qzl.2_RNA|ITGB1BP1_uc002qzm.2_RNA|ITGB1BP1_uc010yiy.1_Intron|ITGB1BP1_uc002qzn.1_Nonsense_Mutation_p.K24*	NM_004763	NP_004754	O14713	ITBP1_HUMAN	integrin cytoplasmic domain-associated protein 1	24	Ser/Thr-rich.				cell migration|cell-matrix adhesion|intracellular protein kinase cascade	cytosol|lamellipodium|membrane|ruffle	protein binding|protein binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.23)		TTCCCTACCTTGCTCTTAGTA	0.428													81	388	---	---	---	---	PASS
NCOA1	8648	broad.mit.edu	37	2	24964741	24964741	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24964741G>C	uc002rfk.2	+	17	3650	c.3392G>C	c.(3391-3393)AGA>ACA	p.R1131T	NCOA1_uc010eye.2_Missense_Mutation_p.R1131T|NCOA1_uc002rfi.2_Missense_Mutation_p.R980T|NCOA1_uc002rfj.2_Missense_Mutation_p.R1131T|NCOA1_uc002rfl.2_Missense_Mutation_p.R1131T|NCOA1_uc010eyf.2_Missense_Mutation_p.R24T	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1	1131	Gln-rich.								PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGCAGCAAAGAGCCATGCTT	0.537			T	PAX3	alveolar rhadomyosarcoma								6	52	---	---	---	---	PASS
CDC42EP3	10602	broad.mit.edu	37	2	37873428	37873428	+	Silent	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37873428C>A	uc002rqi.1	-	2	1296	c.303G>T	c.(301-303)CCG>CCT	p.P101P		NM_006449	NP_006440	Q9UKI2	BORG2_HUMAN	Cdc42 effector protein 3	101					regulation of cell shape|signal transduction	actin cytoskeleton|cytoplasm|endomembrane system|membrane	cytoskeletal regulatory protein binding				0		all_hematologic(82;0.172)				TTTTGAGCACCGGGGAGGGCG	0.532													4	182	---	---	---	---	PASS
MEIS1	4211	broad.mit.edu	37	2	66796175	66796175	+	Intron	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66796175C>G	uc002sdu.2	+						MEIS1_uc002sdt.2_3'UTR|MEIS1_uc002sdv.2_Intron|MEIS1_uc010yqh.1_Intron|MEIS1_uc010yqi.1_Intron|MEIS1_uc002sdw.1_Intron	NM_002398	NP_002389	O00470	MEIS1_HUMAN	Meis homeobox 1								sequence-specific DNA binding transcription factor activity				0						TTTTATCTCCCTTCTAGGACC	0.433													37	248	---	---	---	---	PASS
ATP6V1B1	525	broad.mit.edu	37	2	71185479	71185479	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71185479C>A	uc002shj.2	+	4	377	c.290C>A	c.(289-291)TCA>TAA	p.S97*	ATP6V1B1_uc002shi.1_Nonsense_Mutation_p.S97*|ATP6V1B1_uc010fdv.2_Nonsense_Mutation_p.S97*|ATP6V1B1_uc010fdw.2_RNA|ATP6V1B1_uc010fdx.2_Nonsense_Mutation_p.S55*	NM_001692	NP_001683	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1	97					ATP hydrolysis coupled proton transport|calcium ion homeostasis|cellular iron ion homeostasis|excretion|inner ear morphogenesis|insulin receptor signaling pathway|ossification|pH reduction|sensory perception of sound|transferrin transport	apical plasma membrane|basolateral plasma membrane|cytosol|endomembrane system|lateral plasma membrane|microvillus|proton-transporting V-type ATPase, V1 domain|vacuolar proton-transporting V-type ATPase complex	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			skin(1)	1						GAAGGGACATCAGGGATCGAT	0.542													23	75	---	---	---	---	PASS
LOXL3	84695	broad.mit.edu	37	2	74761715	74761715	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74761715C>T	uc002smp.1	-	10	1838	c.1766G>A	c.(1765-1767)CGA>CAA	p.R589Q	LOXL3_uc002smo.1_Missense_Mutation_p.R228Q|LOXL3_uc010ffm.1_Missense_Mutation_p.R533Q|LOXL3_uc002smq.1_Missense_Mutation_p.R444Q|LOXL3_uc010ffn.1_Missense_Mutation_p.R444Q	NM_032603	NP_115992	P58215	LOXL3_HUMAN	lysyl oxidase-like 3 precursor	589	Lysyl-oxidase like.					extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0						GAAGTCAGCTCGTCCCAGGTT	0.642													14	51	---	---	---	---	PASS
PTCD3	55037	broad.mit.edu	37	2	86352933	86352933	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86352933T>G	uc002sqw.2	+	12	947	c.881T>G	c.(880-882)TTT>TGT	p.F294C	PTCD3_uc010ytc.1_RNA|PTCD3_uc002sqx.1_Translation_Start_Site	NM_017952	NP_060422	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3 precursor	294	PPR 4.					mitochondrion	protein binding			ovary(1)	1						GTATACACATTTAATGCATTG	0.313													9	54	---	---	---	---	PASS
KDM3A	55818	broad.mit.edu	37	2	86693609	86693609	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86693609G>A	uc002sri.3	+	10	1449	c.1122G>A	c.(1120-1122)CAG>CAA	p.Q374Q	KDM3A_uc010ytj.1_Silent_p.Q374Q|KDM3A_uc010ytk.1_Silent_p.Q322Q	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A	374					androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5						AGTCCTCTCAGATTGGAACTG	0.433													56	274	---	---	---	---	PASS
HNMT	3176	broad.mit.edu	37	2	138738926	138738926	+	Intron	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138738926G>C	uc002tvc.2	+						HNMT_uc002tve.2_Missense_Mutation_p.E111Q|HNMT_uc002tvf.2_Intron	NM_006895	NP_008826	P50135	HNMT_HUMAN	histamine N-methyltransferase isoform 1						respiratory gaseous exchange	cytoplasm	histamine N-methyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.125)	Amodiaquine(DB00613)|Histamine Phosphate(DB00667)|Quinacrine(DB01103)	TGCCCGTTTAGAAAGCAAatc	0.259													9	200	---	---	---	---	PASS
ZEB2	9839	broad.mit.edu	37	2	145156292	145156292	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145156292G>T	uc002tvu.2	-	8	2942	c.2462C>A	c.(2461-2463)CCA>CAA	p.P821Q	ZEB2_uc002tvv.2_Missense_Mutation_p.P815Q|ZEB2_uc010zbm.1_Missense_Mutation_p.P792Q|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Missense_Mutation_p.P850Q	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	821						cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)		CATTTGTTTTGGTAATGACAA	0.388													5	248	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152410492	152410492	+	Silent	SNP	G	A	A	rs113068669		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152410492G>A	uc010fnx.2	-	98	14564	c.14373C>T	c.(14371-14373)ATC>ATT	p.I4791I	NEB_uc002txr.2_Silent_p.I1214I	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	4791	Nebulin 131.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGTCGGGCACGATGTGGATTT	0.458													41	221	---	---	---	---	PASS
KIAA1715	80856	broad.mit.edu	37	2	176860294	176860294	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176860294G>C	uc002ukc.1	-	2	212	c.19C>G	c.(19-21)CGA>GGA	p.R7G	KIAA1715_uc010zer.1_Missense_Mutation_p.R7G|KIAA1715_uc010fqw.1_Missense_Mutation_p.S71W|KIAA1715_uc010zes.1_Missense_Mutation_p.S71W|KIAA1715_uc002ukd.1_5'UTR|KIAA1715_uc010zet.1_RNA	NM_030650	NP_085153	Q9C0E8	LNP_HUMAN	Lunapark	7	Cytoplasmic (Potential).					integral to membrane	protein binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0793)			ACCCTCCATCGAGAAAATAAT	0.333													3	96	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179476841	179476841	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179476841C>G	uc010zfg.1	-	216	42817	c.42593G>C	c.(42592-42594)CGA>CCA	p.R14198P	uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R7893P|TTN_uc010zfi.1_Missense_Mutation_p.R7826P|TTN_uc010zfj.1_Missense_Mutation_p.R7701P	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	15125							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCAACATGTCGTTTTGTCAC	0.398													6	44	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179593707	179593707	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179593707C>A	uc010zfg.1	-	62	15550	c.15326G>T	c.(15325-15327)AGT>ATT	p.S5109I	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.S1770I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6036							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATTATCCACACTTCTGATTTG	0.393													10	36	---	---	---	---	PASS
DNAJC10	54431	broad.mit.edu	37	2	183605123	183605123	+	Intron	SNP	T	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183605123T>G	uc002uow.1	+						DNAJC10_uc002uox.1_Intron|DNAJC10_uc002uoy.1_Intron|DNAJC10_uc002uoz.1_Intron|DNAJC10_uc010fro.1_Intron	NM_018981	NP_061854	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10						apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|ER-associated protein catabolic process|glycerol ether metabolic process|negative regulation of protein phosphorylation|protein folding|response to endoplasmic reticulum stress	endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|extracellular region	ATPase activator activity|ATPase binding|chaperone binding|electron carrier activity|heat shock protein binding|misfolded protein binding|protein disulfide oxidoreductase activity|unfolded protein binding			ovary(1)|large_intestine(1)|breast(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			GAGGTAATGTTTTTATTAATA	0.279													9	47	---	---	---	---	PASS
DNAJC10	54431	broad.mit.edu	37	2	183605127	183605127	+	Intron	SNP	A	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183605127A>T	uc002uow.1	+						DNAJC10_uc002uox.1_Intron|DNAJC10_uc002uoy.1_Intron|DNAJC10_uc002uoz.1_Intron|DNAJC10_uc010fro.1_Intron	NM_018981	NP_061854	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10						apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|ER-associated protein catabolic process|glycerol ether metabolic process|negative regulation of protein phosphorylation|protein folding|response to endoplasmic reticulum stress	endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|extracellular region	ATPase activator activity|ATPase binding|chaperone binding|electron carrier activity|heat shock protein binding|misfolded protein binding|protein disulfide oxidoreductase activity|unfolded protein binding			ovary(1)|large_intestine(1)|breast(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TAATGTTTTTATTAATAATGA	0.284													9	45	---	---	---	---	PASS
CASP10	843	broad.mit.edu	37	2	202060607	202060607	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202060607C>T	uc002uxl.1	+	5	1038	c.620C>T	c.(619-621)TCG>TTG	p.S207L	CASP10_uc002uxi.1_Missense_Mutation_p.S207L|CASP10_uc010zhn.1_RNA|CASP10_uc002uxj.1_Missense_Mutation_p.S207L|CASP10_uc002uxk.1_Missense_Mutation_p.S207L|CASP10_uc010fta.1_Missense_Mutation_p.S207L|CASP10_uc002uxm.1_Missense_Mutation_p.S207L|CASP10_uc010ftb.1_RNA	NM_032974	NP_116756	Q92851	CASPA_HUMAN	caspase 10 isoform b preproprotein	207					apoptosis|induction of apoptosis by extracellular signals|proteolysis	cytosol|plasma membrane	cysteine-type endopeptidase activity|identical protein binding|protein binding			skin(3)|ovary(1)|pancreas(1)|breast(1)	6						GAAGCCGAGTCGTATCAAGGA	0.333													48	270	---	---	---	---	PASS
PNKD	25953	broad.mit.edu	37	2	219137354	219137354	+	Intron	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219137354G>T	uc002vhn.2	+						AAMP_uc002vhj.2_5'Flank|AAMP_uc002vhk.2_5'Flank|AAMP_uc010fvo.2_5'Flank|AAMP_uc002vhl.2_5'Flank|PNKD_uc002vhm.1_Missense_Mutation_p.D100Y	NM_015488	NP_056303	Q8N490	PNKD_HUMAN	myofibrillogenesis regulator 1 isoform 1							membrane|mitochondrion|nucleus	hydroxyacylglutathione hydrolase activity|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;7.33e-07)|all cancers(144;0.000133)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGTGGACAAGGACCGTGTGAA	0.612											OREG0015199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	73	230	---	---	---	---	PASS
PAX3	5077	broad.mit.edu	37	2	223163256	223163256	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223163256G>A	uc010fwo.2	-	1	445	c.79C>T	c.(79-81)CTG>TTG	p.L27L	PAX3_uc002vmt.1_Silent_p.L27L|PAX3_uc002vmy.1_Silent_p.L27L|PAX3_uc002vmv.1_Silent_p.L27L|PAX3_uc002vmw.1_Silent_p.L27L|PAX3_uc002vmx.1_Silent_p.L27L|PAX3_uc002vmz.1_Silent_p.L27L|PAX3_uc002vna.1_Silent_p.L27L|CCDC140_uc002vnb.1_Intron	NM_181457	NP_852122	P23760	PAX3_HUMAN	paired box 3 isoform PAX3	27					apoptosis|organ morphogenesis|positive regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)|skin(1)	766		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTACCTTCCAGCGGGAACCCG	0.716			T	FOXO1A|NCOA1	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome						4	16	---	---	---	---	PASS
MYH15	22989	broad.mit.edu	37	3	108159979	108159979	+	Silent	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108159979C>T	uc003dxa.1	-	24	2901	c.2844G>A	c.(2842-2844)CTG>CTA	p.L948L		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	948	Potential.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						CCCTGGCAGTCAGCTCAGAAT	0.483													34	194	---	---	---	---	PASS
PHLDB2	90102	broad.mit.edu	37	3	111603564	111603564	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111603564C>T	uc010hqa.2	+	2	1051	c.640C>T	c.(640-642)CAG>TAG	p.Q214*	PHLDB2_uc003dyc.2_Nonsense_Mutation_p.Q241*|PHLDB2_uc003dyd.2_Nonsense_Mutation_p.Q214*|PHLDB2_uc003dyg.2_Nonsense_Mutation_p.Q214*|PHLDB2_uc003dyh.2_Nonsense_Mutation_p.Q214*|PHLDB2_uc003dye.3_Nonsense_Mutation_p.Q214*|PHLDB2_uc003dyf.3_Nonsense_Mutation_p.Q214*	NM_001134438	NP_001127910	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,	214						cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6						AATGAGCATTCAGGACAGCCT	0.517													17	101	---	---	---	---	PASS
RNF168	165918	broad.mit.edu	37	3	196198983	196198983	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196198983G>C	uc003fwq.2	-	6	1961	c.1423C>G	c.(1423-1425)CAC>GAC	p.H475D	RNF168_uc010iah.2_Missense_Mutation_p.H308D|uc010iag.1_5'Flank	NM_152617	NP_689830	Q8IYW5	RN168_HUMAN	ring finger protein 168	475					double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation	nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		GCGCGTAAGTGATACTCATCT	0.458													77	604	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	4	69403349	69403349	+	IGR	SNP	C	T	T	rs146629248	byFrequency	TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69403349C>T								YTHDC1 (187525 upstream) : UGT2B15 (108967 downstream)																							ATAACTAATCCCTTTTCTTCT	0.408													4	90	---	---	---	---	PASS
MRPL1	65008	broad.mit.edu	37	4	78870971	78870971	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78870971G>C	uc003hku.2	+	8	996	c.798G>C	c.(796-798)CAG>CAC	p.Q266H	MRPL1_uc010iji.1_Intron	NM_020236	NP_064621	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1 precursor	266							RNA binding				0						CAAGTGACCAGATAGCTGCCA	0.358													3	136	---	---	---	---	PASS
PPP3CA	5530	broad.mit.edu	37	4	102019574	102019574	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102019574C>A	uc011cen.1	-	5	1267	c.592G>T	c.(592-594)GTG>TTG	p.V198L	PPP3CA_uc003hvu.2_Missense_Mutation_p.V198L|PPP3CA_uc010ilj.2_Missense_Mutation_p.V198L|PPP3CA_uc003hvt.2_Missense_Mutation_p.V185L|PPP3CA_uc003hvs.2_Missense_Mutation_p.V131L|PPP3CA_uc010ilk.2_Intron	NM_000944	NP_000935	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha	198	Catalytic.				protein dephosphorylation	calcineurin complex|cytosol|nucleus	calcium ion binding|calmodulin binding			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		CCACCATGCACACACAGGAAC	0.393													24	92	---	---	---	---	PASS
CCRN4L	25819	broad.mit.edu	37	4	139966110	139966110	+	Silent	SNP	T	C	C	rs140314273		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139966110T>C	uc003ihl.2	+	3	971	c.778T>C	c.(778-780)TTG>CTG	p.L260L		NM_012118	NP_036250	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like	260					rhythmic process|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_hematologic(180;0.162)					AGCCATGACATTGAAAACCAA	0.478													18	65	---	---	---	---	PASS
FSTL5	56884	broad.mit.edu	37	4	162307103	162307103	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162307103C>G	uc003iqh.2	-	16	2776	c.2340G>C	c.(2338-2340)AAG>AAC	p.K780N	FSTL5_uc003iqi.2_Missense_Mutation_p.K779N|FSTL5_uc010iqv.2_Missense_Mutation_p.K770N|uc010iqu.1_RNA	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	780						extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		CCTTGAGACTCTTTATCATCT	0.458													42	169	---	---	---	---	PASS
SPATA4	132851	broad.mit.edu	37	4	177116539	177116539	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177116539G>T	uc003iuo.1	-	1	284	c.175C>A	c.(175-177)CTT>ATT	p.L59I		NM_144644	NP_653245	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	59					apoptosis|spermatogenesis						0		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)		AGACCCTGAAGCCAACGCAGA	0.622													15	111	---	---	---	---	PASS
ADCY2	108	broad.mit.edu	37	5	7709351	7709351	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7709351T>C	uc003jdz.1	+	10	1496	c.1429T>C	c.(1429-1431)TTC>CTC	p.F477L	ADCY2_uc011cmo.1_Missense_Mutation_p.F297L	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	477	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						CCAGCATCTCTTCAGACCTCG	0.592													19	108	---	---	---	---	PASS
ADCY2	108	broad.mit.edu	37	5	7709429	7709429	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7709429G>A	uc003jdz.1	+	10	1574	c.1507G>A	c.(1507-1509)GCA>ACA	p.A503T	ADCY2_uc011cmo.1_Missense_Mutation_p.A323T	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	503	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						GTCCTGGGGGGCAGCCAAGCC	0.607													10	75	---	---	---	---	PASS
SEMA5A	9037	broad.mit.edu	37	5	9063029	9063029	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9063029A>G	uc003jek.2	-	18	3200	c.2488T>C	c.(2488-2490)TAC>CAC	p.Y830H		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	830	TSP type-1 5.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						CATTCCTGGTATTCCAGAGAT	0.512													4	134	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21802373	21802373	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21802373G>C	uc010iuc.2	-	7	1617	c.1159C>G	c.(1159-1161)CCG>GCG	p.P387A	CDH12_uc011cno.1_Missense_Mutation_p.P347A|CDH12_uc003jgk.2_Missense_Mutation_p.P387A	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	387	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						GTGTAGAGCGGCTTGCTGAAA	0.552										HNSCC(59;0.17)			40	41	---	---	---	---	PASS
GOLPH3	64083	broad.mit.edu	37	5	32143959	32143959	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32143959T>C	uc003jhp.1	-	2	538	c.253A>G	c.(253-255)ATA>GTA	p.I85V		NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3	85					cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1						CCAGATGATATACAGTCATTC	0.308													60	114	---	---	---	---	PASS
PRR16	51334	broad.mit.edu	37	5	120021831	120021831	+	Silent	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120021831C>G	uc003ksq.2	+	2	505	c.342C>G	c.(340-342)CTC>CTG	p.L114L	PRR16_uc003ksp.2_Silent_p.L91L|PRR16_uc003ksr.2_Silent_p.L44L	NM_016644	NP_057728	Q569H4	PRR16_HUMAN	proline rich 16	114	Pro-rich.									pancreas(2)|ovary(1)	3		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CTGCTATCCTCACGGTCCTGA	0.522													28	112	---	---	---	---	PASS
PKD2L2	27039	broad.mit.edu	37	5	137271531	137271531	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137271531G>T	uc003lby.2	+	13	1773	c.1717G>T	c.(1717-1719)GAG>TAG	p.E573*	PKD2L2_uc003lbw.1_Nonsense_Mutation_p.E573*|PKD2L2_uc003lbx.2_Nonsense_Mutation_p.E472*|PKD2L2_uc011cyi.1_Nonsense_Mutation_p.E181*	NM_014386	NP_055201	Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	573	Cytoplasmic (Potential).|Potential.					integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			AGAGAGGCTTGAGAAAAAGTA	0.383													7	56	---	---	---	---	PASS
MATR3	9782	broad.mit.edu	37	5	138661310	138661310	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138661310A>G	uc003ldu.2	+	16	2757	c.2330A>G	c.(2329-2331)GAT>GGT	p.D777G	MATR3_uc003ldt.2_Missense_Mutation_p.D439G|MATR3_uc003ldw.2_Missense_Mutation_p.D825G|MATR3_uc003ldx.2_Missense_Mutation_p.D777G|MATR3_uc010jfc.2_Missense_Mutation_p.D777G|MATR3_uc011czb.1_Missense_Mutation_p.D489G|MATR3_uc003ldz.2_Missense_Mutation_p.D777G|MATR3_uc003lea.2_Missense_Mutation_p.D777G|MATR3_uc003leb.2_Missense_Mutation_p.D439G|MATR3_uc003lec.2_Missense_Mutation_p.D454G	NM_199189	NP_954659	P43243	MATR3_HUMAN	matrin 3	777						nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACAATCCCAGATGAGTATAGA	0.418													20	47	---	---	---	---	PASS
PAIP2	51247	broad.mit.edu	37	5	138704469	138704469	+	Silent	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138704469G>T	uc003led.2	+	4	543	c.366G>T	c.(364-366)GTG>GTT	p.V122V	PAIP2_uc003lee.2_Silent_p.V122V|PAIP2_uc003lef.2_Silent_p.V122V|SLC23A1_uc003leh.2_Intron|SLC23A1_uc003leg.2_Intron	NM_016480	NP_057564	Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	122					negative regulation of translational initiation	cytoplasm	protein binding|translation repressor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTCCTGGGGTGAAGTACGGAA	0.393													18	113	---	---	---	---	PASS
PCDHB13	56123	broad.mit.edu	37	5	140594887	140594887	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140594887G>A	uc003lja.1	+	1	1379	c.1192G>A	c.(1192-1194)GAA>AAA	p.E398K		NM_018933	NP_061756	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13 precursor	398	Cadherin 4.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAAATCCGCGGAAAACTTTTA	0.453													22	89	---	---	---	---	PASS
HAVCR2	84868	broad.mit.edu	37	5	156514243	156514243	+	Missense_Mutation	SNP	C	A	A	rs138681649		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156514243C>A	uc003lwk.1	-	7	920	c.776G>T	c.(775-777)CGC>CTC	p.R259L		NM_032782	NP_116171	Q8TDQ0	HAVR2_HUMAN	T cell immunoglobulin mucin 3 precursor	259	Cytoplasmic (Potential).					integral to membrane					0	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTCTTCTGAGCGAATTCCCTC	0.458													11	59	---	---	---	---	PASS
DTNBP1	84062	broad.mit.edu	37	6	15627683	15627683	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15627683C>T	uc003nbm.2	-	5	417	c.246G>A	c.(244-246)ATG>ATA	p.M82I	DTNBP1_uc003nbl.2_Missense_Mutation_p.M1I|DTNBP1_uc003nbn.2_RNA|DTNBP1_uc003nbo.2_RNA|DTNBP1_uc003nbp.2_Missense_Mutation_p.M82I|DTNBP1_uc010jph.2_Missense_Mutation_p.M69I	NM_032122	NP_115498	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1 isoform a	82					actin cytoskeleton reorganization|cellular membrane organization|neuron projection morphogenesis|post-Golgi vesicle-mediated transport|regulation of dopamine receptor signaling pathway	axon part|BLOC-1 complex|cell junction|dendritic spine|endoplasmic reticulum membrane|endosome membrane|growth cone|melanosome membrane|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|synaptic vesicle membrane|synaptosome	identical protein binding				0	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			GCGCAGAAAGCATGACCACCT	0.488									Hermansky-Pudlak_syndrome				12	76	---	---	---	---	PASS
HIST1H2BH	8345	broad.mit.edu	37	6	26252107	26252107	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26252107G>A	uc003nhh.2	+	1	229	c.229G>A	c.(229-231)GAG>AAG	p.E77K	HIST1H3F_uc003nhg.1_5'Flank	NM_003524	NP_003515	Q93079	H2B1H_HUMAN	histone cluster 1, H2bh	77					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(3)	3						CATCGCCGGCGAGGCTTCCCG	0.592													8	197	---	---	---	---	PASS
HIST1H2BK	85236	broad.mit.edu	37	6	27114419	27114419	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27114419G>A	uc003nix.1	-	1	201	c.159C>T	c.(157-159)ACC>ACT	p.T53T	HIST1H2AH_uc003niz.2_5'Flank|hsa-mir-3143|MI0014167_5'Flank	NM_080593	NP_542160	O60814	H2B1K_HUMAN	histone cluster 1, H2bk	53					defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding				0						AGGAGATGCCGGTGTCGGGGT	0.577													47	282	---	---	---	---	PASS
ZNF184	7738	broad.mit.edu	37	6	27420015	27420015	+	Silent	SNP	A	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27420015A>T	uc003njj.2	-	5	2134	c.1323T>A	c.(1321-1323)ACT>ACA	p.T441T	ZNF184_uc010jqv.2_Silent_p.T441T|ZNF184_uc003nji.2_Silent_p.T441T	NM_007149	NP_009080	Q99676	ZN184_HUMAN	zinc finger protein 184	441					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GTTTCTCCCCAGTATGAGTTT	0.403													37	194	---	---	---	---	PASS
MDC1	9656	broad.mit.edu	37	6	30671677	30671677	+	Silent	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30671677C>T	uc003nrg.3	-	10	5723	c.5283G>A	c.(5281-5283)GTG>GTA	p.V1761V	MDC1_uc003nrf.3_Intron|MDC1_uc011dmp.1_Silent_p.V1368V	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1761	Required for nuclear localization (NLS2).				cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4						CAGCTGCTCTCACTGCTCCCC	0.557								Other_conserved_DNA_damage_response_genes					6	107	---	---	---	---	PASS
PBX2	5089	broad.mit.edu	37	6	32155509	32155509	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32155509T>A	uc003oav.1	-	5	1056	c.785A>T	c.(784-786)TAT>TTT	p.Y262F	PBX2_uc003oaw.2_Missense_Mutation_p.Y262F	NM_002586	NP_002577	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	262	Homeobox; TALE-type.						transcription factor binding			ovary(1)	1						GGAGTAGAAATACTCATTTAG	0.517													4	24	---	---	---	---	PASS
HLA-DRA	3122	broad.mit.edu	37	6	32410335	32410335	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32410335G>A	uc003obh.2	+	2	274	c.193G>A	c.(193-195)GAG>AAG	p.E65K	HLA-DRA_uc003obi.2_Missense_Mutation_p.E65K	NM_019111	NP_061984	P01903	DRA_HUMAN	major histocompatibility complex, class II, DR	65	Extracellular (Potential).|Alpha-1.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|Golgi apparatus|integral to plasma membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity			ovary(1)|skin(1)	2						GGCAAAGAAGGAGACGGTCTG	0.468									T-cell_Lymphoma_(Cutaneous)__Familial_Clustering_of|Kaposi_Sarcoma_Familial_Clustering_of				32	146	---	---	---	---	PASS
SYNGAP1	8831	broad.mit.edu	37	6	33405597	33405597	+	Silent	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33405597C>A	uc011dri.1	+	8	1110	c.915C>A	c.(913-915)ACC>ACA	p.T305T	SYNGAP1_uc003oeo.1_Silent_p.T290T|SYNGAP1_uc010juy.2_Silent_p.T290T|SYNGAP1_uc010juz.2_Silent_p.T17T	NM_006772	NP_006763	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	305	C2.				negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity|SH3 domain binding			ovary(4)	4						CTGGGGACACCGTCTTCTGGG	0.602													3	95	---	---	---	---	PASS
KCNK17	89822	broad.mit.edu	37	6	39271753	39271753	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39271753C>A	uc003ooo.2	-	4	808	c.668G>T	c.(667-669)GGC>GTC	p.G223V	KCNK17_uc003oop.2_Missense_Mutation_p.G223V	NM_031460	NP_113648	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	223						integral to membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2						GTCGCCGAAGCCCACGGTGCT	0.617													18	128	---	---	---	---	PASS
MOCS1	4337	broad.mit.edu	37	6	39874531	39874531	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39874531C>A	uc003opb.2	-	10	1651	c.1513G>T	c.(1513-1515)GTG>TTG	p.V505L	MOCS1_uc003opa.2_3'UTR|MOCS1_uc003opc.2_Missense_Mutation_p.V489L|MOCS1_uc003opd.2_3'UTR|MOCS1_uc003ope.2_Missense_Mutation_p.V402L	NM_005942	NP_005933	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis-step 1 protein	505	Molybdenum cofactor biosynthesis protein C.				Mo-molybdopterin cofactor biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding			ovary(1)|liver(1)|central_nervous_system(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					GCCACAGCCACCCGCTCTGTG	0.592													3	78	---	---	---	---	PASS
COL9A1	1297	broad.mit.edu	37	6	70942343	70942343	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70942343G>C	uc003pfg.3	-	36	2605	c.2446C>G	c.(2446-2448)CGT>GGT	p.R816G	COL9A1_uc003pfe.3_Missense_Mutation_p.R365G|COL9A1_uc003pff.3_Missense_Mutation_p.R573G	NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor	816	Triple-helical region (COL1).				axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding			ovary(4)	4						GGAAGGCCACGAATTCCCATC	0.592													33	209	---	---	---	---	PASS
SESN1	27244	broad.mit.edu	37	6	109322510	109322510	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109322510C>A	uc003pst.3	-	3	442	c.350G>T	c.(349-351)CGT>CTT	p.R117L	SESN1_uc003psu.2_Missense_Mutation_p.R176L	NM_014454	NP_055269	Q9Y6P5	SESN1_HUMAN	sestrin 1	117					cell cycle arrest|negative regulation of cell proliferation|response to DNA damage stimulus	nucleus				ovary(1)	1		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		AATGTAGTGACGATAATGTAG	0.333													18	117	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152782727	152782727	+	Intron	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152782727C>A	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qow.2_Intron|SYNE1_uc003qox.1_Intron|SYNE1_uc003qoz.2_Intron|SYNE1_uc003qoy.2_Intron	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AAATTATTTTCGCACCTTGGT	0.443										HNSCC(10;0.0054)			30	153	---	---	---	---	PASS
PDE10A	10846	broad.mit.edu	37	6	165808737	165808737	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165808737C>A	uc003qun.2	-	16	1649	c.1408G>T	c.(1408-1410)GGT>TGT	p.G470C	PDE10A_uc011egj.1_RNA|PDE10A_uc011egk.1_Missense_Mutation_p.G400C|PDE10A_uc003quo.2_Missense_Mutation_p.G480C	NM_006661	NP_006652	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 2	470					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	TCAAAAGGACCAATGTCAAAG	0.333													7	56	---	---	---	---	PASS
EIF3B	8662	broad.mit.edu	37	7	2402315	2402315	+	Missense_Mutation	SNP	C	A	A	rs150739455		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2402315C>A	uc003slx.2	+	3	811	c.728C>A	c.(727-729)GCT>GAT	p.A243D	EIF3B_uc003sly.2_Missense_Mutation_p.A243D|EIF3B_uc003slz.1_Missense_Mutation_p.A204D|EIF3B_uc003sma.2_Translation_Start_Site	NM_003751	NP_003742	P55884	EIF3B_HUMAN	eukaryotic translation initiation factor 3,	243	Sufficient for interaction with EIF3E.|RRM.|Sufficient for interaction with EIF3J.				regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	nucleotide binding|protein complex scaffold|translation initiation factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		CCTGCCCACgctgtggatgct	0.408													4	76	---	---	---	---	PASS
TTYH3	80727	broad.mit.edu	37	7	2701348	2701348	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2701348G>A	uc003smp.2	+	14	1734	c.1547G>A	c.(1546-1548)CGC>CAC	p.R516H	TTYH3_uc010ksn.2_Missense_Mutation_p.R236H|TTYH3_uc003smq.2_Missense_Mutation_p.R345H	NM_025250	NP_079526	Q9C0H2	TTYH3_HUMAN	tweety 3	516	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	chloride channel activity				0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		AGCCAGCCTCGCCCTGACTCC	0.692													3	13	---	---	---	---	PASS
SAMD9	54809	broad.mit.edu	37	7	92731019	92731019	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92731019G>C	uc003umf.2	-	3	4648	c.4392C>G	c.(4390-4392)TTC>TTG	p.F1464L	SAMD9_uc003umg.2_Missense_Mutation_p.F1464L	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1464						cytoplasm				ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			ATTGCCCCTTGAAAGAATTTT	0.343													35	200	---	---	---	---	PASS
LAMB1	3912	broad.mit.edu	37	7	107599767	107599767	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107599767C>A	uc003vew.2	-	20	2952	c.2617G>T	c.(2617-2619)GCC>TCC	p.A873S	LAMB1_uc003vev.2_Missense_Mutation_p.A897S	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	873	Laminin EGF-like 8.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CAGTCATCGGCGTGGCCATTG	0.557													41	203	---	---	---	---	PASS
LAMB1	3912	broad.mit.edu	37	7	107615434	107615434	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107615434G>A	uc003vew.2	-	12	1814	c.1479C>T	c.(1477-1479)TGC>TGT	p.C493C	LAMB1_uc003vev.2_Silent_p.C517C|LAMB1_uc003vex.2_Silent_p.C493C|LAMB1_uc010ljn.1_Silent_p.C579C	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	493	Laminin EGF-like 4.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TACTTACCAGGCACTGGTCAC	0.498													27	114	---	---	---	---	PASS
LMOD2	442721	broad.mit.edu	37	7	123302662	123302662	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123302662G>C	uc003vky.2	+	2	1179	c.1022G>C	c.(1021-1023)AGA>ACA	p.R341T		NM_207163	NP_997046	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	341						cytoskeleton	actin binding|tropomyosin binding				0						CCAGGACCAAGAATGAGCATG	0.483													5	183	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131853158	131853158	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131853158C>G	uc003vra.3	-	22	4420	c.4191G>C	c.(4189-4191)AAG>AAC	p.K1397N		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1397	Cytoplasmic (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						CGTACTCCAGCTTGCTCTGCA	0.587													13	43	---	---	---	---	PASS
MKRN1	23608	broad.mit.edu	37	7	140154376	140154376	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140154376C>T	uc003vvt.2	-	8	1615	c.1390G>A	c.(1390-1392)GAA>AAA	p.E464K	MKRN1_uc003vvs.2_Missense_Mutation_p.E400K|MKRN1_uc011krd.1_Missense_Mutation_p.E198K	NM_013446	NP_038474	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1 isoform 1	464							ligase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.00956)					CACTCATCTTCAGAGTCTGTT	0.488													12	65	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151960110	151960110	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151960110C>G	uc003wla.2	-	9	1509	c.1290G>C	c.(1288-1290)TGG>TGC	p.W430C		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	430	PHD-type 2.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		CTTTGCATTTCCAGCCATTGG	0.348			N		medulloblastoma								37	159	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	2796131	2796131	+	Silent	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2796131C>T	uc011kwk.1	-	70	11064	c.10674G>A	c.(10672-10674)CTG>CTA	p.L3558L	CSMD1_uc011kwj.1_Silent_p.L2872L|CSMD1_uc010lrg.2_Silent_p.L1449L	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	3558	Cytoplasmic (Potential).					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		AGACTGTGTTCAGAGTTGTGT	0.458													5	40	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	2830790	2830790	+	Silent	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2830790C>G	uc011kwk.1	-	57	9165	c.8775G>C	c.(8773-8775)GGG>GGC	p.G2925G	CSMD1_uc011kwj.1_Silent_p.G2254G|CSMD1_uc010lrg.2_Silent_p.G935G	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2925	Extracellular (Potential).|Sushi 22.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GTGCTGGGGTCCCCGGATCAC	0.483													48	279	---	---	---	---	PASS
XKR5	389610	broad.mit.edu	37	8	6690416	6690416	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6690416T>A	uc003wqp.2	-	2	87	c.65A>T	c.(64-66)TAC>TTC	p.Y22F	XKR5_uc003wqq.2_5'UTR|XKR5_uc003wqr.1_RNA	NM_207411	NP_997294	Q6UX68	XKR5_HUMAN	XK-related protein 5a	22						integral to membrane					0			STAD - Stomach adenocarcinoma(24;0.0984)	READ - Rectum adenocarcinoma(644;0.137)|COAD - Colon adenocarcinoma(149;0.166)		AGCCACGGTGTAAAGGCCTGG	0.532													12	15	---	---	---	---	PASS
GPR124	25960	broad.mit.edu	37	8	37686463	37686463	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37686463G>A	uc003xkj.2	+	3	759	c.396G>A	c.(394-396)GGG>GGA	p.G132G	GPR124_uc003xki.2_Silent_p.G132G|GPR124_uc010lvy.2_Silent_p.G132G	NM_032777	NP_116166	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124 precursor	132	Extracellular (Potential).				central nervous system development|endothelial cell migration|neuropeptide signaling pathway|regulation of angiogenesis|regulation of chemotaxis|sprouting angiogenesis	integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(2)|ovary(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			TGGGCCTGGGGGAGCTGAAGC	0.667													6	66	---	---	---	---	PASS
STAR	6770	broad.mit.edu	37	8	38005810	38005810	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38005810C>T	uc003xkv.1	-	3	478	c.214G>A	c.(214-216)GAG>AAG	p.E72K	STAR_uc010lwc.1_Missense_Mutation_p.E34K	NM_001007243	NP_001007244	P49675	STAR_HUMAN	steroidogenic acute regulatory protein isoform	72	START.				C21-steroid hormone biosynthetic process	mitochondrial intermembrane space	cholesterol transporter activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.0151)|Lung NSC(58;0.0295)		READ - Rectum adenocarcinoma(644;0.188)		TAGGCCAGCTCCTGGTCACTG	0.572													9	26	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77765105	77765105	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77765105G>A	uc003yav.2	+	10	6200	c.5813G>A	c.(5812-5814)CGT>CAT	p.R1938H	ZFHX4_uc003yau.1_Missense_Mutation_p.R1983H|ZFHX4_uc003yaw.1_Missense_Mutation_p.R1938H	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1938						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAATTTGCTCGTCAATACAGG	0.299										HNSCC(33;0.089)			21	41	---	---	---	---	PASS
RNF19A	25897	broad.mit.edu	37	8	101287334	101287334	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101287334C>G	uc003yjj.1	-	4	1047	c.730G>C	c.(730-732)GAG>CAG	p.E244Q	RNF19A_uc003yjk.1_Missense_Mutation_p.E244Q	NM_015435	NP_056250	Q9NV58	RN19A_HUMAN	ring finger protein 19	244	IBR-type.				microtubule cytoskeleton organization|protein modification process	centrosome|integral to membrane	ligase activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			CCACAGCCCTCTCGCCCACAA	0.433													22	141	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113697923	113697923	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113697923C>G	uc003ynu.2	-	15	2353	c.2194G>C	c.(2194-2196)GTT>CTT	p.V732L	CSMD3_uc003yns.2_Missense_Mutation_p.V4L|CSMD3_uc003ynt.2_Missense_Mutation_p.V692L|CSMD3_uc011lhx.1_Missense_Mutation_p.V628L	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	732	Extracellular (Potential).|CUB 4.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						GGAGAAAGAACTGTTCCCATT	0.353										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			68	147	---	---	---	---	PASS
PTPRD	5789	broad.mit.edu	37	9	8485848	8485848	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8485848T>A	uc003zkk.2	-	27	3680	c.2969A>T	c.(2968-2970)TAC>TTC	p.Y990F	PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Missense_Mutation_p.Y981F|PTPRD_uc003zkm.2_Missense_Mutation_p.Y977F|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	990	Fibronectin type-III 7.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TTTTACATCGTATGTGGTATC	0.488										TSP Lung(15;0.13)			12	71	---	---	---	---	PASS
SPINK4	27290	broad.mit.edu	37	9	33246680	33246680	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33246680G>C	uc003zsh.2	+	3	180	c.169G>C	c.(169-171)GAT>CAT	p.D57H	SUGT1P1_uc010mjq.1_Intron	NM_014471	NP_055286	O60575	ISK4_HUMAN	serine peptidase inhibitor, Kazal type 4	57	Kazal-like.					extracellular region	serine-type endopeptidase inhibitor activity				0			LUSC - Lung squamous cell carcinoma(29;0.00506)			CTGCGGCACTGATGGGCTCAC	0.572													33	262	---	---	---	---	PASS
FRMPD1	22844	broad.mit.edu	37	9	37746211	37746211	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37746211G>A	uc004aag.1	+	16	4226	c.4182G>A	c.(4180-4182)TCG>TCA	p.S1394S	FRMPD1_uc004aah.1_Silent_p.S1394S	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1394						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		CACCCCTGTCGAGGAAAAGCC	0.657													6	70	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	84675878	84675878	+	Nonstop_Mutation	SNP	A	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84675878A>T	uc010mpu.1	-	3	550	c.547T>A	c.(547-549)TGA>AGA	p.*183R		NM_001164339	NP_001157811			hypothetical protein LOC404770																		TGGAGTTATCAGAGTGGAGTC	0.562													69	284	---	---	---	---	PASS
OR2K2	26248	broad.mit.edu	37	9	114089856	114089856	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114089856G>A	uc011lwp.1	-	1	858	c.858C>T	c.(856-858)CCC>CCT	p.P286P		NM_205859	NP_995581	Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K,	315	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						TGTAAATTATGGGGTTCAACA	0.388													34	129	---	---	---	---	PASS
C10orf18	54906	broad.mit.edu	37	10	5772786	5772786	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5772786C>G	uc001iij.2	+	11	1449	c.824C>G	c.(823-825)TCT>TGT	p.S275C	C10orf18_uc001iik.2_5'UTR	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	275										ovary(1)|central_nervous_system(1)	2						TTGGAAGTGTCTACTGCTTTG	0.423													26	587	---	---	---	---	PASS
DHTKD1	55526	broad.mit.edu	37	10	12142178	12142178	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12142178C>G	uc001ild.3	+	9	1772	c.1673C>G	c.(1672-1674)TCC>TGC	p.S558C		NM_018706	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain	558					glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			ATTTTACAGTCCAGAATGGAG	0.353													44	319	---	---	---	---	PASS
PHYH	5264	broad.mit.edu	37	10	13330464	13330464	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13330464C>T	uc001imf.2	-	6	662	c.574G>A	c.(574-576)GCC>ACC	p.A192T	PHYH_uc001ime.2_Missense_Mutation_p.A92T|PHYH_uc001img.2_Missense_Mutation_p.A175T	NM_006214	NP_006205	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase isoform a precursor	192			A -> AA (in RD).		fatty acid alpha-oxidation|nervous system development	peroxisomal matrix	electron carrier activity|L-ascorbic acid binding|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|phytanoyl-CoA dioxygenase activity|protein binding				0		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	GCCGTCCAGGCGCAAACGATG	0.582													31	125	---	---	---	---	PASS
WAC	51322	broad.mit.edu	37	10	28900789	28900789	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28900789C>G	uc001iuf.2	+	10	1460	c.1375C>G	c.(1375-1377)CAA>GAA	p.Q459E	WAC_uc001iud.2_Missense_Mutation_p.Q414E|WAC_uc001iue.2_Missense_Mutation_p.Q149E|WAC_uc001iug.2_Missense_Mutation_p.Q356E|WAC_uc001iuh.2_Missense_Mutation_p.Q411E	NM_016628	NP_057712	Q9BTA9	WAC_HUMAN	WW domain-containing adapter with a coiled-coil	459					cell cycle checkpoint|histone H2B conserved C-terminal lysine ubiquitination|histone monoubiquitination|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nuclear speck	chromatin binding|RNA polymerase II core binding			large_intestine(1)|ovary(1)	2						AAGCACACCTCAAACTAACAC	0.433													20	282	---	---	---	---	PASS
PARD3	56288	broad.mit.edu	37	10	34806096	34806096	+	Intron	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34806096G>C	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixp.1_5'Flank|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				AGCTAGAAATGAAAGGTAAAT	0.393													9	74	---	---	---	---	PASS
ECD	11319	broad.mit.edu	37	10	74920183	74920183	+	Intron	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74920183C>A	uc001jtn.2	-						ECD_uc009xqx.2_Intron|ECD_uc009xqy.2_Intron|ECD_uc001jto.2_Intron	NM_007265	NP_009196	O95905	SGT1_HUMAN	suppressor of S. cerevisiae gcr2 isoform 1						regulation of glycolysis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	transcription coactivator activity			pancreas(1)	1	Prostate(51;0.0119)					ATTAAAATAACTACAATACCT	0.294													27	66	---	---	---	---	PASS
RGR	5995	broad.mit.edu	37	10	86017684	86017684	+	Silent	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86017684C>A	uc001kdc.1	+	6	704	c.666C>A	c.(664-666)CTC>CTA	p.L222L	RGR_uc001kdd.1_Silent_p.L226L|RGR_uc001kde.1_Intron	NM_001012720	NP_001012738	P47804	RGR_HUMAN	retinal G-protein coupled receptor isoform 2	222	Helical; Name=6; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity|protein binding			ovary(1)	1						CGCTGCTGCTCGGCTGGGGCC	0.547													30	80	---	---	---	---	PASS
C10orf79	80217	broad.mit.edu	37	10	105906076	105906076	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105906076C>G	uc001kxw.2	-	30	3916	c.3800G>C	c.(3799-3801)AGA>ACA	p.R1267T	C10orf79_uc009xxq.2_Intron	NM_025145	NP_079421	Q8NDM7	WDR96_HUMAN	hypothetical protein LOC80217	1267											0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)		CAGGTCTTCTCTAGATTTCCG	0.413													10	184	---	---	---	---	PASS
TPH1	7166	broad.mit.edu	37	11	18062260	18062260	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18062260C>G	uc001mnp.2	-	1	76	c.50G>C	c.(49-51)AGA>ACA	p.R17T	TPH1_uc009yhe.2_RNA	NM_004179	NP_004170	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	17					aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity				0					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	GAGACTTGCTCTTCCCCTTTC	0.333													22	70	---	---	---	---	PASS
NELL1	4745	broad.mit.edu	37	11	20869208	20869208	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20869208G>T	uc001mqe.2	+	4	568	c.415G>T	c.(415-417)GCA>TCA	p.A139S	NELL1_uc001mqf.2_Missense_Mutation_p.A139S|NELL1_uc009yid.2_Missense_Mutation_p.A167S|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor	139	TSP N-terminal.				cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						AAGGACAGAGGCACTTCCTTA	0.478													10	51	---	---	---	---	PASS
ZNF408	79797	broad.mit.edu	37	11	46726988	46726988	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46726988C>T	uc001nde.1	+	5	1968	c.1738C>T	c.(1738-1740)CCC>TCC	p.P580S	ZNF408_uc010rgw.1_Missense_Mutation_p.P572S	NM_024741	NP_079017	Q9H9D4	ZN408_HUMAN	zinc finger protein 408	580	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|identical protein binding|zinc ion binding				0						GAGGCCCTTTCCCTGTCCCCA	0.672													11	54	---	---	---	---	PASS
CKAP5	9793	broad.mit.edu	37	11	46832582	46832582	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46832582G>T	uc001ndi.1	-	5	715	c.605C>A	c.(604-606)CCA>CAA	p.P202Q	CKAP5_uc009ylg.1_Missense_Mutation_p.P88Q|CKAP5_uc001ndj.1_Missense_Mutation_p.P202Q	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein	202					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						ATTTTGTAATGGGGGTCTCAG	0.388													33	149	---	---	---	---	PASS
OR5AR1	219493	broad.mit.edu	37	11	56431560	56431560	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56431560C>A	uc010rjm.1	+	1	399	c.399C>A	c.(397-399)AGC>AGA	p.S133R		NM_001004730	NP_001004730	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR,	133	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TCCACTATAGCACCTTCATGT	0.512													59	338	---	---	---	---	PASS
ZDHHC5	25921	broad.mit.edu	37	11	57464264	57464264	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57464264G>A	uc001nkx.1	+	10	2297	c.1041G>A	c.(1039-1041)CCG>CCA	p.P347P	ZDHHC5_uc001nky.1_Silent_p.P294P|ZDHHC5_uc001nkz.1_Silent_p.P161P	NM_015457	NP_056272	Q9C0B5	ZDHC5_HUMAN	zinc finger, DHHC domain containing 5	347						integral to membrane	acyltransferase activity|zinc ion binding			skin(1)	1						ACAGCCCCCCGACACCTACCA	0.458													15	69	---	---	---	---	PASS
OR5B12	390191	broad.mit.edu	37	11	58206915	58206915	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58206915G>C	uc010rkh.1	-	1	710	c.710C>G	c.(709-711)TCT>TGT	p.S237C		NM_001004733	NP_001004733	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B,	237	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AGCACAAGTAGAAAAGGCCTT	0.418													5	120	---	---	---	---	PASS
SLC22A10	387775	broad.mit.edu	37	11	63058004	63058004	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63058004G>A	uc009yor.2	+	1	575	c.367G>A	c.(367-369)GAT>AAT	p.D123N	SLC22A10_uc010rmo.1_Intron|SLC22A10_uc001nwu.3_RNA|SLC22A10_uc010rmp.1_Missense_Mutation_p.D71N	NM_001039752	NP_001034841	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	123	Extracellular (Potential).					integral to membrane	transmembrane transporter activity			ovary(2)	2						CTGGGTATATGATCAAAGCTA	0.468													5	130	---	---	---	---	PASS
FAM86C	55199	broad.mit.edu	37	11	71500881	71500881	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71500881T>C	uc001oqv.3	+	2	175	c.149T>C	c.(148-150)ATT>ACT	p.I50T	FAM86C_uc009ysr.2_Missense_Mutation_p.I50T|FAM86C_uc001oqw.3_Missense_Mutation_p.I50T|FAM86C_uc009yss.2_RNA|FAM86C_uc010rqq.1_RNA	NM_018172	NP_060642	Q9NVL1	FA86C_HUMAN	hypothetical protein LOC55199 isoform 1	50											0						CTGCGGGATATTTTGCAGAAG	0.493													16	114	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92533601	92533601	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92533601G>A	uc001pdj.3	+	9	7439	c.7422G>A	c.(7420-7422)GGG>GGA	p.G2474G		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2474	Cadherin 22.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TCTCTGATGGGTTGTTCACCA	0.498										TCGA Ovarian(4;0.039)			30	97	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108224619	108224619	+	Intron	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108224619G>A	uc001pkb.1	+						ATM_uc009yxr.1_Intron|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		TAAGTGATATGAAGTAAAGGA	0.289			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			23	167	---	---	---	---	PASS
BCO2	83875	broad.mit.edu	37	11	112065424	112065424	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112065424C>T	uc001pnf.2	+	5	799	c.682C>T	c.(682-684)CAT>TAT	p.H228Y	BCO2_uc001pne.1_Missense_Mutation_p.H55Y|BCO2_uc001png.2_Intron|BCO2_uc001pnh.2_Missense_Mutation_p.H194Y|BCO2_uc010rwt.1_Missense_Mutation_p.H123Y|BCO2_uc009yyn.2_Missense_Mutation_p.H194Y|BCO2_uc001pni.2_Missense_Mutation_p.H194Y	NM_031938	NP_114144	Q9BYV7	BCDO2_HUMAN	beta-carotene dioxygenase 2 isoform a	228					carotene metabolic process|retinal metabolic process|retinoic acid metabolic process		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						TGCACATCCTCATTATGACCT	0.398													39	160	---	---	---	---	PASS
NFRKB	4798	broad.mit.edu	37	11	129758544	129758544	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129758544A>C	uc001qfi.2	-	4	483	c.282T>G	c.(280-282)AGT>AGG	p.S94R	NFRKB_uc001qfg.2_Missense_Mutation_p.S107R|NFRKB_uc001qfh.2_Missense_Mutation_p.S117R|NFRKB_uc010sbw.1_Missense_Mutation_p.S94R	NM_001143835	NP_001137307	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	94					DNA recombination|DNA repair|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Ino80 complex	DNA binding|protease binding			ovary(3)	3	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		AGTTCTCCCCACTGAACAAGG	0.498													28	159	---	---	---	---	PASS
OPCML	4978	broad.mit.edu	37	11	132307140	132307140	+	Silent	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132307140G>T	uc001qgs.2	-	4	690	c.640C>A	c.(640-642)CGG>AGG	p.R214R	OPCML_uc001qgu.2_Silent_p.R207R|OPCML_uc010sck.1_Silent_p.R214R|OPCML_uc001qgt.2_Silent_p.R213R|OPCML_uc010scl.1_Silent_p.R173R	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion	214	Ig-like C2-type 2.				cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		TTTACTTTCCGCACATCGGGC	0.537													22	188	---	---	---	---	PASS
KDM5A	5927	broad.mit.edu	37	12	475139	475139	+	Silent	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:475139G>C	uc001qif.1	-	4	861	c.498C>G	c.(496-498)CTC>CTG	p.L166L	KDM5A_uc001qie.1_Silent_p.L166L|KDM5A_uc010sdn.1_Silent_p.L125L|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	166	ARID.				chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						CATATGGGTAGAGAATTCTTT	0.393			T 	NUP98	AML								80	395	---	---	---	---	PASS
KDM5A	5927	broad.mit.edu	37	12	475168	475168	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:475168G>C	uc001qif.1	-	4	832	c.469C>G	c.(469-471)CTT>GTT	p.L157V	KDM5A_uc001qie.1_Missense_Mutation_p.L157V|KDM5A_uc010sdn.1_Missense_Mutation_p.L116V|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	157	ARID.				chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						GACTTCAAAAGAGACCCAGTT	0.408			T 	NUP98	AML								99	515	---	---	---	---	PASS
PLCZ1	89869	broad.mit.edu	37	12	18841147	18841147	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18841147G>A	uc010sid.1	-	13	1658	c.1467C>T	c.(1465-1467)ATC>ATT	p.I489I	PLCZ1_uc001rdv.3_Silent_p.I385I|PLCZ1_uc001rdw.3_Silent_p.I230I|PLCZ1_uc001rdu.1_Silent_p.I271I|PLCZ1_uc009zil.1_RNA	NM_033123	NP_149114	Q86YW0	PLCZ1_HUMAN	phospholipase C, zeta 1	489	C2.			I -> T (in Ref. 2; AAK61372).	intracellular signal transduction|lipid catabolic process|multicellular organismal development	nucleus|perinuclear region of cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)					GGATACCACTGATGAGCTGCA	0.294													42	209	---	---	---	---	PASS
H1FNT	341567	broad.mit.edu	37	12	48723703	48723703	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48723703C>A	uc001rrm.2	+	1	941	c.629C>A	c.(628-630)GCG>GAG	p.A210E		NM_181788	NP_861453	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	210					chromosome condensation|multicellular organismal development|sperm chromatin condensation|spermatid nucleus elongation	nuclear chromatin	ATP binding|DNA binding			pancreas(1)	1						GAAGCGGGAGCGACAGCGGCA	0.662													7	9	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39266156	39266156	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39266156G>A	uc001uwv.2	+	1	4984	c.4675G>A	c.(4675-4677)GAA>AAA	p.E1559K		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	1559	Extracellular (Potential).|CSPG 11.				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GCTCACTGTCGAAGACAGAGA	0.443													39	122	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77657221	77657221	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77657221G>A	uc001vkf.2	-	64	10959	c.10868C>T	c.(10867-10869)TCA>TTA	p.S3623L	MYCBP2_uc010aev.2_Missense_Mutation_p.S3027L|MYCBP2_uc001vke.2_Missense_Mutation_p.S243L	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	3623					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		CATAAGGTCTGAGATGGTCTG	0.473													43	116	---	---	---	---	PASS
RNF219	79596	broad.mit.edu	37	13	79213126	79213126	+	Silent	SNP	A	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79213126A>G	uc001vkw.1	-	4	440	c.381T>C	c.(379-381)ATT>ATC	p.I127I	RNF219_uc010afb.1_5'UTR|RNF219_uc010afc.2_Silent_p.I127I	NM_024546	NP_078822	Q5W0B1	RN219_HUMAN	ring finger protein 219	127	Potential.						zinc ion binding			large_intestine(2)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		AAGGATCCAGAATAGTTTTGA	0.373													61	188	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22592224	22592224	+	Intron	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22592224C>G	uc001wbw.2	+						uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Nonsense_Mutation_p.Y103*|uc010ajj.1_Nonsense_Mutation_p.Y103*|uc001wde.1_Nonsense_Mutation_p.Y77*|uc010aji.1_Nonsense_Mutation_p.Y103*					SubName: Full=Alpha-chain C region; Flags: Fragment;																		CTGCTGTGTACTATTGCATCG	0.522													9	52	---	---	---	---	PASS
HAUS4	54930	broad.mit.edu	37	14	23419520	23419520	+	Intron	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23419520C>T	uc001whp.2	-						HAUS4_uc001who.2_Intron|HAUS4_uc001whq.2_Intron|HAUS4_uc001whr.2_Intron|HAUS4_uc001whs.2_Intron|HAUS4_uc001wht.2_Intron|HAUS4_uc001whu.2_Intron|HAUS4_uc001whv.2_Intron|HAUS4_uc001whw.2_Intron|HAUS4_uc001whx.2_Intron	NM_017815	NP_060285	Q9H6D7	HAUS4_HUMAN	HAUS augmin-like complex, subunit 4						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle				ovary(1)	1						AGCTAGCACTCACCTGAATTG	0.438													13	59	---	---	---	---	PASS
KLHL28	54813	broad.mit.edu	37	14	45400541	45400541	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45400541C>G	uc001wvq.2	-	4	1793	c.1547G>C	c.(1546-1548)AGA>ACA	p.R516T	KLHL28_uc001wvr.2_Missense_Mutation_p.R516T	NM_017658	NP_060128	Q9NXS3	KLH28_HUMAN	BTB (POZ) domain containing 5	516	Kelch 5.									ovary(1)	1						ATTACCTGTTCTAGGTTCTTT	0.358													13	61	---	---	---	---	PASS
FANCM	57697	broad.mit.edu	37	14	45645812	45645812	+	Silent	SNP	T	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45645812T>C	uc001wwd.3	+	14	3954	c.3855T>C	c.(3853-3855)CAT>CAC	p.H1285H	FANCM_uc010anf.2_Silent_p.H1259H|FANCM_uc001wwe.3_Silent_p.H821H|FANCM_uc010ang.2_Silent_p.H499H	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1285					DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7						CAAGAGATCATAGTAAAAATT	0.328								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				25	107	---	---	---	---	PASS
KLHDC2	23588	broad.mit.edu	37	14	50247037	50247037	+	Silent	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50247037C>T	uc001wwx.2	+	9	1280	c.880C>T	c.(880-882)CTA>TTA	p.L294L	SDCCAG1_uc010anj.1_Intron|KLHDC2_uc001wwy.2_Silent_p.L294L|KLHDC2_uc010anp.2_Silent_p.L294L	NM_014315	NP_055130	Q9Y2U9	KLDC2_HUMAN	kelch domain containing 2	294	Kelch 5.					nucleus	protein binding			ovary(1)	1	all_epithelial(31;0.000959)|Breast(41;0.0117)					TAAACAGCCACTAAGTAAGTC	0.368													29	92	---	---	---	---	PASS
DCAF5	8816	broad.mit.edu	37	14	69521476	69521476	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69521476G>A	uc001xkp.2	-	9	2146	c.1927C>T	c.(1927-1929)CAA>TAA	p.Q643*	DCAF5_uc001xkq.2_Nonsense_Mutation_p.Q642*	NM_003861	NP_003852	Q96JK2	DCAF5_HUMAN	WD repeat domain 22	643						CUL4 RING ubiquitin ligase complex				ovary(1)|central_nervous_system(1)	2						CGGCTTGGTTGAATCTCTAGC	0.473													10	135	---	---	---	---	PASS
SPATA7	55812	broad.mit.edu	37	14	88883116	88883116	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88883116C>G	uc001xwq.2	+	5	451	c.300C>G	c.(298-300)TTC>TTG	p.F100L	SPATA7_uc001xwr.2_Missense_Mutation_p.F68L|SPATA7_uc001xws.2_Missense_Mutation_p.F36L|SPATA7_uc001xwt.2_5'UTR	NM_018418	NP_060888	Q9P0W8	SPAT7_HUMAN	spermatogenesis-associated protein 7 isoform a	100					response to stimulus|visual perception					ovary(1)	1						AAAAAGAGTTCAAATTAACTA	0.279													5	92	---	---	---	---	PASS
CATSPERB	79820	broad.mit.edu	37	14	92091277	92091277	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92091277G>T	uc001xzs.1	-	18	1957	c.1817C>A	c.(1816-1818)GCA>GAA	p.A606E	CATSPERB_uc010aub.1_Missense_Mutation_p.A128E	NM_024764	NP_079040	Q9H7T0	CTSRB_HUMAN	cation channel, sperm-associated, beta	606					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				breast(2)|skin(2)|ovary(1)	5		all_cancers(154;0.0663)|all_epithelial(191;0.236)				TTTCATTTCTGCAATAACTGA	0.343													19	113	---	---	---	---	PASS
SERPINA11	256394	broad.mit.edu	37	14	94914713	94914713	+	Silent	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94914713G>C	uc001ydd.1	-	2	459	c.399C>G	c.(397-399)CTC>CTG	p.L133L		NM_001080451	NP_001073920	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1	133					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			kidney(1)	1				COAD - Colon adenocarcinoma(157;0.211)		CTTTTAGTTCGAGTTTGGGGC	0.537													52	264	---	---	---	---	PASS
ATP10A	57194	broad.mit.edu	37	15	25947152	25947152	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25947152C>T	uc010ayu.2	-	13	2777	c.2671G>A	c.(2671-2673)GAC>AAC	p.D891N		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	891	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TCTTGTTTGTCACCAGTGAGA	0.532													6	236	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34034598	34034598	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34034598G>A	uc001zhi.2	+	52	7922	c.7852G>A	c.(7852-7854)GTC>ATC	p.V2618I	RYR3_uc010bar.2_Missense_Mutation_p.V2618I	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2618	3.|Cytoplasmic (By similarity).|4 X approximate repeats.				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)		GGAATACATCGTCACCAAGTA	0.413													11	67	---	---	---	---	PASS
SLC12A6	9990	broad.mit.edu	37	15	34551037	34551037	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34551037C>T	uc001zhw.2	-	4	684	c.520G>A	c.(520-522)GAA>AAA	p.E174K	SLC12A6_uc001zhv.2_Missense_Mutation_p.E123K|SLC12A6_uc001zhx.2_Missense_Mutation_p.E159K|SLC12A6_uc001zhy.2_RNA|SLC12A6_uc001zhz.2_RNA|SLC12A6_uc001zia.2_Missense_Mutation_p.E115K|SLC12A6_uc001zib.2_Missense_Mutation_p.E165K|SLC12A6_uc001zic.2_Missense_Mutation_p.E174K|SLC12A6_uc010bau.2_Missense_Mutation_p.E174K|SLC12A6_uc001zid.2_Missense_Mutation_p.E115K|SLC12A6_uc001zhu.2_Missense_Mutation_p.E35K	NM_133647	NP_598408	Q9UHW9	S12A6_HUMAN	solute carrier family 12, member 6 isoform a	174	Cytoplasmic (Potential).				angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity			central_nervous_system(5)|ovary(1)|skin(1)	7		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	TTTTTCCCTTCAGTGATGTTT	0.453													65	375	---	---	---	---	PASS
C15orf52	388115	broad.mit.edu	37	15	40627419	40627419	+	Silent	SNP	C	G	G	rs144372797		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40627419C>G	uc001zlh.3	-	11	1561	c.1545G>C	c.(1543-1545)TCG>TCC	p.S515S	C15orf52_uc010ucn.1_Silent_p.S305S	NM_207380	NP_997263	Q6ZUT6	CO052_HUMAN	hypothetical protein LOC388115	515										large_intestine(1)	1		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		CTGTGCCTCTCGACCTTTGGC	0.692													76	343	---	---	---	---	PASS
GATM	2628	broad.mit.edu	37	15	45658353	45658353	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45658353C>T	uc001zvc.2	-	6	1198	c.869G>A	c.(868-870)AGA>AAA	p.R290K	GATM_uc001zvb.2_Missense_Mutation_p.R161K|GATM_uc010uev.1_Missense_Mutation_p.R343K	NM_001482	NP_001473	P50440	GATM_HUMAN	L-arginine:glycine amidinotransferase precursor	290					creatine biosynthetic process	mitochondrial inner membrane|mitochondrial intermembrane space	glycine amidinotransferase activity|protein binding				0		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Creatine(DB00148)|Glycine(DB00145)|L-Ornithine(DB00129)	GATATGCACTCTGTAGTCTGG	0.413													21	92	---	---	---	---	PASS
AP4E1	23431	broad.mit.edu	37	15	51242119	51242119	+	Silent	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51242119G>C	uc001zyx.1	+	12	1443	c.1413G>C	c.(1411-1413)CTG>CTC	p.L471L		NM_007347	NP_031373	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1	471					intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		ATAACTTTCTGAGACTACTAG	0.333													7	215	---	---	---	---	PASS
SIN3A	25942	broad.mit.edu	37	15	75682167	75682167	+	Intron	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75682167G>A	uc002bai.2	-						SIN3A_uc002baj.2_Intron|SIN3A_uc010uml.1_Intron	NM_015477	NP_056292	Q96ST3	SIN3A_HUMAN	transcriptional co-repressor Sin3A						blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5						CATCCACTGTGGGAGAGATGG	0.468													13	151	---	---	---	---	PASS
HOMER2	9455	broad.mit.edu	37	15	83561500	83561500	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83561500G>A	uc002bjg.2	-	2	285	c.99C>T	c.(97-99)ACC>ACT	p.T33T	HOMER2_uc002bjh.2_Silent_p.T33T|HOMER2_uc002bjj.2_Silent_p.T33T|HOMER2_uc002bji.2_Silent_p.T33T	NM_199330	NP_955362	Q9NSB8	HOME2_HUMAN	homer 2 isoform 2	33	WH1.				metabotropic glutamate receptor signaling pathway	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane					0						AGTAGGAAACGGTGACCGCCT	0.522													50	237	---	---	---	---	PASS
SV2B	9899	broad.mit.edu	37	15	91795168	91795168	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91795168C>G	uc002bqv.2	+	2	962	c.571C>G	c.(571-573)CTC>GTC	p.L191V	SV2B_uc002bqt.2_Missense_Mutation_p.L191V|SV2B_uc010uqv.1_Missense_Mutation_p.L40V|SV2B_uc002bqu.3_RNA	NM_014848	NP_055663	Q7L1I2	SV2B_HUMAN	synaptic vesicle protein 2B homolog	191	Helical; (Potential).				neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			CTTCGCCTCCCTCTCTTCCTT	0.587													5	147	---	---	---	---	PASS
NME4	4833	broad.mit.edu	37	16	450284	450284	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:450284G>T	uc002cgz.2	+	5	537	c.506G>T	c.(505-507)AGC>ATC	p.S169I	NME4_uc002cgy.2_Missense_Mutation_p.S99I|NME4_uc002cha.2_RNA|DECR2_uc002chb.2_5'Flank|DECR2_uc002chc.2_5'Flank|DECR2_uc010bqv.2_5'Flank|DECR2_uc002chd.2_5'Flank	NM_005009	NP_005000	O00746	NDKM_HUMAN	nucleoside diphosphate kinase 4 precursor	169					CTP biosynthetic process|GTP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|UTP biosynthetic process	mitochondrial inner membrane|mitochondrial intermembrane space	ATP binding|metal ion binding|nucleoside diphosphate kinase activity				0		Hepatocellular(16;0.00015)				TGGTTCCAGAGCAGTGAGCTG	0.652													13	103	---	---	---	---	PASS
CHD9	80205	broad.mit.edu	37	16	53358634	53358634	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53358634G>C	uc002ehb.2	+	38	8685	c.8521G>C	c.(8521-8523)GAA>CAA	p.E2841Q	CHD9_uc002egy.2_Missense_Mutation_p.E2825Q|CHD9_uc002ehc.2_Missense_Mutation_p.E2826Q|CHD9_uc002ehf.2_Missense_Mutation_p.E1939Q|CHD9_uc010cbw.2_Missense_Mutation_p.E907Q	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2841					cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)				TAAGTCTGTAGAAGTAAAAGA	0.393													5	29	---	---	---	---	PASS
NUP93	9688	broad.mit.edu	37	16	56878437	56878437	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56878437G>A	uc002eka.2	+	22	2497	c.2376G>A	c.(2374-2376)CTG>CTA	p.L792L	NUP93_uc002ekb.2_Silent_p.L669L|NUP93_uc010vhi.1_Silent_p.L669L	NM_014669	NP_055484	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	792					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(1)|lung(1)	2						CCCGCACTCTGATTACCTTTG	0.498													10	53	---	---	---	---	PASS
PRMT7	54496	broad.mit.edu	37	16	68349904	68349904	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68349904G>A	uc002evy.1	+	3	298	c.22G>A	c.(22-24)GCC>ACC	p.A8T	PRMT7_uc002evx.1_Missense_Mutation_p.A8T|PRMT7_uc010vlg.1_Missense_Mutation_p.A8T	NM_019023	NP_061896	Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	8					cell differentiation|DNA methylation involved in gamete generation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|spliceosomal snRNP assembly|transcription, DNA-dependent	cytosol|nucleus	[myelin basic protein]-arginine N-methyltransferase activity|histone methyltransferase activity (H4-R3 specific)|protein-arginine omega-N monomethyltransferase activity|protein-arginine omega-N symmetric methyltransferase activity|ribonucleoprotein binding				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		CTGCAGTCGGGCCAATCCGAC	0.532													3	44	---	---	---	---	PASS
ZC3H18	124245	broad.mit.edu	37	16	88697587	88697587	+	Silent	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88697587C>A	uc002fky.2	+	18	2942	c.2742C>A	c.(2740-2742)GCC>GCA	p.A914A	ZC3H18_uc010voz.1_Silent_p.A938A|ZC3H18_uc010chw.2_RNA|ZC3H18_uc002fkz.2_Silent_p.A184A	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	914						nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		ATCCCGGCGCCGCCAGCACCA	0.652													3	63	---	---	---	---	PASS
MVD	4597	broad.mit.edu	37	16	88722562	88722562	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88722562T>C	uc002flg.1	-	5	561	c.554A>G	c.(553-555)CAA>CGA	p.Q185R	MVD_uc002flf.1_Missense_Mutation_p.Q54R	NM_002461	NP_002452	P53602	MVD1_HUMAN	diphosphomevalonate decarboxylase	185					cholesterol biosynthetic process|positive regulation of cell proliferation	cytosol	ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity				0				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GGGGGCCACTTGCCGAGCGAT	0.687													21	82	---	---	---	---	PASS
GP1BA	2811	broad.mit.edu	37	17	4836835	4836835	+	Silent	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4836835C>T	uc010vsq.1	+	2	1011	c.936C>T	c.(934-936)GTC>GTT	p.V312V	uc002fzn.1_RNA	NM_000173	NP_000164	P07359	GP1BA_HUMAN	platelet glycoprotein Ib alpha polypeptide	312											0						GGACTGTGGTCAAGTTCCCCA	0.537													23	129	---	---	---	---	PASS
DHRS7C	201140	broad.mit.edu	37	17	9680518	9680518	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9680518C>A	uc010vvb.1	-	4	566	c.566G>T	c.(565-567)CGT>CTT	p.R189L	DHRS7C_uc010cof.2_Missense_Mutation_p.R188L	NM_001105571	NP_001099041	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	189						extracellular region	binding|oxidoreductase activity				0						ACAAGTCGTACGGAACGGGAT	0.423													15	51	---	---	---	---	PASS
KLHL10	317719	broad.mit.edu	37	17	39998268	39998268	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39998268G>A	uc010cxr.2	+	2	530	c.388G>A	c.(388-390)GAG>AAG	p.E130K	KLHL10_uc010wfv.1_Missense_Mutation_p.E124K|KLHL10_uc010wfw.1_Missense_Mutation_p.E42K	NM_152467	NP_689680	Q6JEL2	KLH10_HUMAN	kelch-like 10	130						cytoplasm				ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		Breast(137;0.000162)				GGGTTGCTGCGAGTTCCTCAA	0.507													5	145	---	---	---	---	PASS
KLHL10	317719	broad.mit.edu	37	17	39998457	39998457	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39998457G>C	uc010cxr.2	+	2	719	c.577G>C	c.(577-579)GAT>CAT	p.D193H	KLHL10_uc010wfv.1_Missense_Mutation_p.D187H|KLHL10_uc010wfw.1_Missense_Mutation_p.D105H	NM_152467	NP_689680	Q6JEL2	KLH10_HUMAN	kelch-like 10	193						cytoplasm				ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		Breast(137;0.000162)				CATTGAGAAAGATGAGCTCAA	0.403													4	163	---	---	---	---	PASS
KLHL10	317719	broad.mit.edu	37	17	40004407	40004407	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40004407G>C	uc010cxr.2	+	5	1817	c.1675G>C	c.(1675-1677)GAC>CAC	p.D559H	KLHL10_uc010wfw.1_Missense_Mutation_p.D471H	NM_152467	NP_689680	Q6JEL2	KLH10_HUMAN	kelch-like 10	559	Kelch 6.			D -> G (in Ref. 2; BAB71387).		cytoplasm				ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		Breast(137;0.000162)				TGATGCTCATGACATGAGTAT	0.473													6	155	---	---	---	---	PASS
TTC25	83538	broad.mit.edu	37	17	40087031	40087031	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40087031G>A	uc002hyj.3	+	1	144	c.55G>A	c.(55-57)GAA>AAA	p.E19K	TTC25_uc010cxt.2_RNA|TTC25_uc010cxs.1_Missense_Mutation_p.E19K	NM_031421	NP_113609	Q96NG3	TTC25_HUMAN	tetratricopeptide repeat domain 25	19	TPR 1.					cytoplasm	protein binding			ovary(1)	1		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)				TTATATGGCCGAAGGCGAGCG	0.542													5	17	---	---	---	---	PASS
C17orf71	55181	broad.mit.edu	37	17	57289136	57289136	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57289136A>G	uc002ixi.2	+	1	1766	c.1724A>G	c.(1723-1725)CAC>CGC	p.H575R		NM_018149	NP_060619	Q8ND04	SMG8_HUMAN	SMG8 protein	575					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of protein kinase activity		protein binding				0	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)					ACTGATCAACACTGTGTGCAC	0.373													13	92	---	---	---	---	PASS
C17orf86	654434	broad.mit.edu	37	17	75085560	75085560	+	Intron	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75085560G>A	uc002jtk.3	+						SCARNA16_uc002jtl.2_RNA	NR_027058				Homo sapiens clone FLB3442 PRO0872 mRNA, complete cds.												0						GATCATGTATGATACTGCAAA	0.378													8	158	---	---	---	---	PASS
AZI1	22994	broad.mit.edu	37	17	79176050	79176050	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79176050C>T	uc002jzp.1	-	7	978	c.778G>A	c.(778-780)GAG>AAG	p.E260K	AZI1_uc002jzn.1_Missense_Mutation_p.E260K|AZI1_uc002jzo.1_Missense_Mutation_p.E260K|AZI1_uc010wum.1_Missense_Mutation_p.E260K	NM_014984	NP_055799	Q9UPN4	AZI1_HUMAN	5-azacytidine induced 1 isoform a	260					cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centrosome|cytosol|intracellular membrane-bounded organelle				central_nervous_system(2)|large_intestine(1)|ovary(1)	4	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CTCTCAGCCTCCTCCTCCGTC	0.662													4	88	---	---	---	---	PASS
L3MBTL4	91133	broad.mit.edu	37	18	6241381	6241381	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6241381C>A	uc002kmz.3	-	8	688	c.528G>T	c.(526-528)AAG>AAT	p.K176N	L3MBTL4_uc010dkt.2_Missense_Mutation_p.K176N|L3MBTL4_uc002kmy.3_Missense_Mutation_p.K14N	NM_173464	NP_775735	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4	176	MBT 2.				chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)				TGAATAATTTCTTTGGAGCAT	0.303													40	229	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56278980	56278980	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56278980G>A	uc002lhj.3	-	2	264	c.50C>T	c.(49-51)ACA>ATA	p.T17I		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	17	Ig-like 1.						ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						GGAAAGCAATGTAGATAAAAA	0.463													36	157	---	---	---	---	PASS
TLE2	7089	broad.mit.edu	37	19	3028720	3028720	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3028720G>A	uc002lww.2	-	2	369	c.106C>T	c.(106-108)CAG>TAG	p.Q36*	TLE2_uc010dth.2_Nonsense_Mutation_p.Q36*|TLE2_uc010xhc.1_5'UTR|TLE2_uc010dti.2_Nonsense_Mutation_p.Q49*|TLE2_uc010xhd.1_Nonsense_Mutation_p.Q36*	NM_003260	NP_003251	Q04725	TLE2_HUMAN	transducin-like enhancer protein 2 isoform 1	36	Gln-rich.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TATTGAGCCTGAAGAAACTGG	0.672													19	101	---	---	---	---	PASS
TLE2	7089	broad.mit.edu	37	19	3028909	3028909	+	5'UTR	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3028909G>T	uc002lww.2	-	1					TLE2_uc010dth.2_5'UTR|TLE2_uc010xhc.1_Intron|TLE2_uc010dti.2_Intron|TLE2_uc010xhd.1_5'UTR	NM_003260	NP_003251	Q04725	TLE2_HUMAN	transducin-like enhancer protein 2 isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACATCCTGCCGATCCGAAAAG	0.667													7	37	---	---	---	---	PASS
MATK	4145	broad.mit.edu	37	19	3783854	3783854	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3783854G>A	uc002lyt.2	-	6	940	c.540C>T	c.(538-540)ATC>ATT	p.I180I	MATK_uc002lyv.2_Silent_p.I181I|MATK_uc002lyu.2_Silent_p.I139I|MATK_uc010dtq.2_Silent_p.I180I	NM_139355	NP_647612	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase isoform	180	SH2.				cell proliferation|mesoderm development|positive regulation of cell proliferation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			stomach(2)|ovary(1)|lung(1)|large_intestine(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGCCTCATCGATTGTGAGGT	0.682													13	54	---	---	---	---	PASS
MPND	84954	broad.mit.edu	37	19	4355107	4355107	+	Silent	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4355107C>G	uc002mae.2	+	8	1000	c.933C>G	c.(931-933)CTC>CTG	p.L311L	MPND_uc010dtx.2_RNA|MPND_uc002mag.2_Intron|MPND_uc002maf.2_Silent_p.L311L|MPND_uc002mah.2_Silent_p.L199L|MPND_uc002mai.2_Silent_p.L199L	NM_032868	NP_116257	Q8N594	MPND_HUMAN	MPN domain containing isoform 1	311	MPN.						peptidase activity			breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		TGACGGTGCTCAGAGCCTTCC	0.677													9	72	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8175749	8175749	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8175749C>G	uc002mjf.2	-	33	4334	c.4313G>C	c.(4312-4314)CGA>CCA	p.R1438P		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1438	EGF-like 22; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						GCCACCCCCTCGGTCCAGTTC	0.532													27	161	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9009681	9009681	+	Silent	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9009681G>C	uc002mkp.2	-	39	39249	c.39045C>G	c.(39043-39045)CTC>CTG	p.L13015L	MUC16_uc010dwi.2_5'Flank|MUC16_uc010dwj.2_5'Flank|MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	13017	Extracellular (Potential).|SEA 7.				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGGTAAAGTTGAGGGTGAACG	0.498													4	168	---	---	---	---	PASS
QTRT1	81890	broad.mit.edu	37	19	10812667	10812667	+	Silent	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10812667C>T	uc002mpr.2	+	2	310	c.285C>T	c.(283-285)TTC>TTT	p.F95F		NM_031209	NP_112486	Q9BXR0	TGT_HUMAN	queuine tRNA-ribosyltransferase 1	95					queuosine biosynthetic process	mitochondrion|nucleus|ribosome	metal ion binding|queuine tRNA-ribosyltransferase activity			skin(1)	1			Epithelial(33;1.55e-05)|all cancers(31;3.42e-05)			TCCACGGCTTCATGAATTGGC	0.572													37	142	---	---	---	---	PASS
CCDC105	126402	broad.mit.edu	37	19	15132721	15132721	+	Missense_Mutation	SNP	G	A	A	rs144636554		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15132721G>A	uc002nae.2	+	6	1340	c.1241G>A	c.(1240-1242)CGC>CAC	p.R414H		NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	414					microtubule cytoskeleton organization	microtubule				ovary(1)	1						GAGGCTGCGCGCCTCGCACAG	0.622													11	68	---	---	---	---	PASS
PRX	57716	broad.mit.edu	37	19	40902362	40902362	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40902362C>T	uc002onr.2	-	7	2166	c.1897G>A	c.(1897-1899)GAG>AAG	p.E633K	PRX_uc002onq.2_Missense_Mutation_p.E494K|PRX_uc002ons.2_3'UTR	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2	633	32.|55 X 5 AA approximate tandem repeats of [LVMAG]-[PSREQC]-[EDKL]-[LIVMAP]- [AQKHRPE]; that may have a tripeptide spacer of [LV]-P-[KER].				axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AGTTTCATCTCAGGGAGCTTC	0.587													54	285	---	---	---	---	PASS
PRX	57716	broad.mit.edu	37	19	40902675	40902675	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40902675C>A	uc002onr.2	-	7	1853	c.1584G>T	c.(1582-1584)ATG>ATT	p.M528I	PRX_uc002onq.2_Missense_Mutation_p.M389I|PRX_uc002ons.2_3'UTR	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2	528	15.|55 X 5 AA approximate tandem repeats of [LVMAG]-[PSREQC]-[EDKL]-[LIVMAP]- [AQKHRPE]; that may have a tripeptide spacer of [LV]-P-[KER].				axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TTGGGAGTTTCATCTCCGACA	0.567													35	186	---	---	---	---	PASS
TMEM145	284339	broad.mit.edu	37	19	42818842	42818842	+	Silent	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42818842C>T	uc002otk.1	+	4	403	c.351C>T	c.(349-351)TCC>TCT	p.S117S		NM_173633	NP_775904	Q8NBT3	TM145_HUMAN	transmembrane protein 145	117						integral to membrane					0		Prostate(69;0.00682)				ATGCCTGGTCCGGCTGTCAGG	0.622													37	166	---	---	---	---	PASS
LYPD3	27076	broad.mit.edu	37	19	43969729	43969729	+	5'UTR	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43969729C>T	uc002owl.1	-	1					LYPD3_uc002owm.2_5'UTR	NM_014400	NP_055215	O95274	LYPD3_HUMAN	GPI-anchored metastasis-associated protein							anchored to plasma membrane				pancreas(1)	1		Prostate(69;0.0153)				TCCATGGCTCCGTCCTGCTCC	0.687													20	66	---	---	---	---	PASS
PPP1R13L	10848	broad.mit.edu	37	19	45895149	45895149	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45895149G>C	uc002pbn.2	-	8	1881	c.1804C>G	c.(1804-1806)CCG>GCG	p.P602A	PPP1R13L_uc002pbm.2_Missense_Mutation_p.P181A|PPP1R13L_uc002pbo.2_Missense_Mutation_p.P602A	NM_006663	NP_006654	Q8WUF5	IASPP_HUMAN	protein phosphatase 1, regulatory subunit 13	602	Pro-rich.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	transcription corepressor activity|transcription factor binding			skin(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0182)		ATGCTCTGCGGCTGCTCTGGT	0.547													19	61	---	---	---	---	PASS
BBC3	27113	broad.mit.edu	37	19	47725147	47725147	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47725147G>A	uc002pgf.3	-	4	775	c.494C>T	c.(493-495)CCC>CTC	p.P165L	BBC3_uc010xyl.1_Silent_p.P199P|BBC3_uc010eky.2_Missense_Mutation_p.P103L|BBC3_uc010ekz.2_Silent_p.P39P	NM_014417	NP_055232	Q9BXH1	BBC3_HUMAN	BCL2 binding component 3 isoform 4	165					activation of caspase activity|activation of pro-apoptotic gene products|cellular response to hypoxia|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|negative regulation of growth|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|positive regulation of thymocyte apoptosis|protein insertion into mitochondrial membrane involved in induction of apoptosis|reduction of endoplasmic reticulum calcium ion concentration|release of cytochrome c from mitochondria|release of sequestered calcium ion into cytosol	cytosol|mitochondrial outer membrane	protein binding|protein binding				0		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.000179)|OV - Ovarian serous cystadenocarcinoma(262;0.00029)|Epithelial(262;0.0103)|GBM - Glioblastoma multiforme(486;0.0234)		CCAGGGTGAGGGGCGGTGCCG	0.612													16	52	---	---	---	---	PASS
C19orf75	284369	broad.mit.edu	37	19	51770708	51770708	+	Silent	SNP	A	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51770708A>G	uc002pwb.1	+	5	873	c.492A>G	c.(490-492)CAA>CAG	p.Q164Q	C19orf75_uc010eov.1_RNA|C19orf75_uc010ycw.1_Silent_p.Q70Q	NM_173635	NP_775906	Q8N7X8	CS075_HUMAN	hypothetical protein LOC284369	164						integral to membrane				ovary(1)|pancreas(1)	2						GAGCAAGCCAAGAACTTGAGA	0.453													42	197	---	---	---	---	PASS
PPP2R1A	5518	broad.mit.edu	37	19	52723032	52723032	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52723032C>G	uc002pyp.2	+	10	1376	c.1217C>G	c.(1216-1218)CCT>CGT	p.P406R	PPP2R1A_uc010ydk.1_Missense_Mutation_p.P351R|PPP2R1A_uc002pyq.2_Missense_Mutation_p.P227R	NM_014225	NP_055040	P30153	2AAA_HUMAN	alpha isoform of regulatory subunit A, protein	406	HEAT 11.|PP2A subunit C binding.				ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity			endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		TCCCTGCTCCCTGCCATTGTG	0.612			Mis		clear cell ovarian carcinoma								21	67	---	---	---	---	PASS
PYGB	5834	broad.mit.edu	37	20	25239951	25239951	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25239951G>T	uc002wup.2	+	2	431	c.322G>T	c.(322-324)GCC>TCC	p.A108S		NM_002862	NP_002853	P11216	PYGB_HUMAN	brain glycogen phosphorylase	108					glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					Pyridoxal Phosphate(DB00114)	CCTTCAGAATGCCTGCGATGA	0.522													8	101	---	---	---	---	PASS
DUSP15	128853	broad.mit.edu	37	20	30454959	30454959	+	Intron	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30454959G>A	uc002wwu.1	-						DUSP15_uc002wwv.1_Intron|DUSP15_uc002www.1_Intron|DUSP15_uc002wwx.1_Intron			Q9H1R2	DUS15_HUMAN	RecName: Full=Dual specificity protein phosphatase 15;          EC=3.1.3.48;          EC=3.1.3.16; AltName: Full=Vaccinia virus VH1-related dual-specific protein phosphatase Y; AltName: Full=VH1-related member Y;							cytoplasm|plasma membrane	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			TTTGGCATCTGAAAGAAACAG	0.567													3	16	---	---	---	---	PASS
BLCAP	10904	broad.mit.edu	37	20	36147493	36147493	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36147493G>T	uc002xha.2	-	2	287	c.84C>A	c.(82-84)TTC>TTA	p.F28L	BLCAP_uc002xhb.2_Missense_Mutation_p.F28L|BLCAP_uc002xhc.2_Missense_Mutation_p.F28L|NNAT_uc002xhd.2_5'Flank|NNAT_uc002xhe.2_5'Flank	NM_006698	NP_006689	P62952	BLCAP_HUMAN	bladder cancer associated protein	28	Helical; (Potential).				apoptosis|cell cycle	integral to membrane					0		Myeloproliferative disorder(115;0.00878)				AGAAGCCCATGAACATGGAGT	0.577													8	31	---	---	---	---	PASS
C20orf43	51507	broad.mit.edu	37	20	55048360	55048360	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55048360G>A	uc002xxt.2	+	2	180	c.73G>A	c.(73-75)GAC>AAC	p.D25N	C20orf43_uc010zzf.1_Missense_Mutation_p.D55N|C20orf43_uc002xxu.2_Missense_Mutation_p.D25N|C20orf43_uc002xxv.2_Missense_Mutation_p.D25N	NM_016407	NP_057491	Q9BY42	CT043_HUMAN	hypothetical protein LOC51507	25										ovary(1)	1			Colorectal(105;0.202)			TTATTAGGTCGACAAAGATGC	0.338													16	103	---	---	---	---	PASS
RBM38	55544	broad.mit.edu	37	20	55967737	55967737	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55967737G>A	uc010zzj.1	+	2	440	c.265G>A	c.(265-267)GAG>AAG	p.E89K	RBM38_uc010zzk.1_Missense_Mutation_p.E89K	NM_017495	NP_059965	Q9H0Z9	RBM38_HUMAN	RNA-binding region containing protein 1 isoform	89	RRM.				3'-UTR-mediated mRNA stabilization|cell cycle|cell cycle arrest|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mRNA processing|negative regulation of cell proliferation|regulation of RNA splicing|RNA splicing	cytosol|cytosol|nucleus|nucleus	mRNA 3'-UTR binding|mRNA binding|nucleotide binding|RNA binding				0	Lung NSC(12;0.00242)|all_lung(29;0.00767)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.55e-12)|Epithelial(14;9.49e-09)|all cancers(14;5.01e-08)			GGCGGCAGCTGAGAGGGCTTG	0.677													15	48	---	---	---	---	PASS
TAF4	6874	broad.mit.edu	37	20	60578311	60578311	+	Silent	SNP	G	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60578311G>A	uc002ybs.2	-	9	2391	c.2391C>T	c.(2389-2391)GCC>GCT	p.A797A		NM_003185	NP_003176	O00268	TAF4_HUMAN	TBP-associated factor 4	797					interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			CAGGTAACACGGCGGGTTTCA	0.488													16	94	---	---	---	---	PASS
DNMT3L	29947	broad.mit.edu	37	21	45674549	45674549	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45674549G>C	uc002zeg.1	-	8	1128	c.644C>G	c.(643-645)CCG>CGG	p.P215R	DNMT3L_uc002zeh.1_Missense_Mutation_p.P215R	NM_175867	NP_787063	Q9UJW3	DNM3L_HUMAN	cytosine-5-methyltransferase 3-like protein	215					DNA methylation|negative regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|spermatogenesis	cytosol	enzyme activator activity|enzyme binding|metal ion binding			skin(2)	2				Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)		CAGTTGTCCCGGGTCAGAACC	0.572													3	98	---	---	---	---	PASS
SF3A1	10291	broad.mit.edu	37	22	30735139	30735139	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30735139T>A	uc003ahl.2	-	10	1609	c.1477A>T	c.(1477-1479)ATC>TTC	p.I493F		NM_005877	NP_005868	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa isoform 1	493					nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|U2-type spliceosomal complex	protein binding|RNA binding			ovary(3)|large_intestine(1)|pancreas(1)	5						GGCTTCTGGATCTCCTCCTCA	0.512													6	291	---	---	---	---	PASS
LGALS1	3956	broad.mit.edu	37	22	38075647	38075647	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38075647A>G	uc003atn.2	+	4	396	c.299A>G	c.(298-300)AAG>AGG	p.K100R		NM_002305	NP_002296	P09382	LEG1_HUMAN	galectin-1	100	Galectin.				apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of apoptosis	cytoplasm|extracellular space|proteinaceous extracellular matrix	galactoside binding|signal transducer activity				0	Melanoma(58;0.0574)					CTGACCGTCAAGCTGCCAGAT	0.582													16	54	---	---	---	---	PASS
ASMTL	8623	broad.mit.edu	37	X	1546948	1546948	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1546948G>C	uc004cpx.1	-	7	687	c.576C>G	c.(574-576)GAC>GAG	p.D192E	ASMTL_uc011mhe.1_Missense_Mutation_p.D116E|ASMTL_uc004cpy.1_Missense_Mutation_p.D176E|ASMTL_uc011mhf.1_Missense_Mutation_p.D134E	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	192	MAF-like.				melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CGTTCAGAAAGTCCCCGTGTA	0.637													10	44	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	26179686	26179686	+	IGR	SNP	A	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26179686A>G								MAGEB18 (20834 upstream) : MAGEB6 (30871 downstream)																							TCCTGCATTCAATCTATGGGG	0.488													67	265	---	---	---	---	PASS
FAM47C	442444	broad.mit.edu	37	X	37026697	37026697	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37026697C>T	uc004ddl.1	+	1	228	c.214C>T	c.(214-216)CGC>TGC	p.R72C		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	72										ovary(3)	3						GCTTGTTTGTCGCCGTGACGA	0.532													22	99	---	---	---	---	PASS
USP11	8237	broad.mit.edu	37	X	47102014	47102014	+	Intron	SNP	C	G	G			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47102014C>G	uc004dhp.2	+						USP11_uc004dhq.2_Intron	NM_004651	NP_004642	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11						protein deubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)|lung(1)|central_nervous_system(1)	3						CTCTCCATATCCCATTCCTAG	0.547													10	80	---	---	---	---	PASS
KIAA2022	340533	broad.mit.edu	37	X	73960686	73960686	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73960686T>C	uc004eby.2	-	3	4323	c.3706A>G	c.(3706-3708)AAA>GAA	p.K1236E		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	1236					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15						ATTTGCATTTTCTCTCCATTG	0.493													17	79	---	---	---	---	PASS
PNMA5	114824	broad.mit.edu	37	X	152159319	152159319	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152159319T>A	uc010ntw.2	-	3	1163	c.824A>T	c.(823-825)CAC>CTC	p.H275L	PNMA5_uc004fha.3_Missense_Mutation_p.H275L|PNMA5_uc010ntx.2_Missense_Mutation_p.H275L|PNMA5_uc004fgy.3_Missense_Mutation_p.H275L	NM_001103151	NP_001096621	Q96PV4	PNMA5_HUMAN	paraneoplastic antigen like 5	275					apoptosis					ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)					GGGGCTCTTGTGCACGGCTTT	0.567													112	196	---	---	---	---	PASS
PDZD4	57595	broad.mit.edu	37	X	153072220	153072220	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153072220C>A	uc004fiz.1	-	4	713	c.463G>T	c.(463-465)GAC>TAC	p.D155Y	PDZD4_uc004fiy.1_Missense_Mutation_p.D80Y|PDZD4_uc004fix.2_Missense_Mutation_p.D59Y|PDZD4_uc004fja.1_Missense_Mutation_p.D161Y|PDZD4_uc011mze.1_Missense_Mutation_p.D46Y	NM_032512	NP_115901	Q76G19	PDZD4_HUMAN	PDZ domain containing 4	155	PDZ.					cell cortex				breast(1)	1	all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ATGCCCAGGTCCTCCTCGTCG	0.627													48	78	---	---	---	---	PASS
CDK11B	984	broad.mit.edu	37	1	1650497	1650498	+	Intron	INS	-	AG	AG	rs111891151		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1650497_1650498insAG	uc001agv.1	-						CDK11B_uc001ags.1_5'Flank|CDK11B_uc001agt.1_5'Flank|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc009vkr.2_Intron|CDK11A_uc009vks.2_Intron|CDK11A_uc010nys.1_Intron|CDK11A_uc010nyt.1_Intron|CDK11A_uc010nyu.1_Intron|CDK11A_uc009vkt.1_Intron|CDK11A_uc009vku.1_Intron|CDK11A_uc009vkv.1_Intron|CDK11A_uc001aht.1_Intron|CDK11B_uc001ahu.1_Intron|CDK11B_uc001ahv.1_Intron|CDK11B_uc001ahw.1_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						TGCTTTCAGCTAGTTTGCTCTC	0.485													3	3	---	---	---	---	
FNBP1L	54874	broad.mit.edu	37	1	93989788	93989789	+	Intron	INS	-	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93989788_93989789insT	uc001dpw.2	+						FNBP1L_uc001dpv.2_Intron	NM_001024948	NP_001020119	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like isoform 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	lipid binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		ttttatttttatttttTTTGGC	0.282													4	2	---	---	---	---	
SYCP1	6847	broad.mit.edu	37	1	115399757	115399758	+	Intron	INS	-	A	A	rs71582509		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115399757_115399758insA	uc001efr.2	+						SYCP1_uc010owt.1_Intron|SYCP1_uc001efq.2_Intron|SYCP1_uc009wgw.2_Intron	NM_003176	NP_003167	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1						cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ctctctctctcaaaaaaaaaaa	0.084													4	3	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	186115161	186115162	+	Intron	INS	-	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186115161_186115162insA	uc001grq.1	+						HMCN1_uc001grs.1_Intron	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						GGTGGAATTAGAAAAAAAAAAA	0.317													4	2	---	---	---	---	
DPYSL5	56896	broad.mit.edu	37	2	27169638	27169638	+	Intron	DEL	C	-	-	rs3835821		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27169638delC	uc002rhu.3	+						DPYSL5_uc002rhv.3_Intron	NM_020134	NP_064519	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					gagcctctgtctcctcatcta	0.129													6	4	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	138000234	138000234	+	Intron	DEL	T	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138000234delT	uc002tva.1	+						THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		TGTGAGCACCTTTTTTTTTTT	0.393													10	5	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	159992541	159992562	+	Intron	DEL	GTGTGTGTGTGTGTGTGTGTGC	-	-	rs55994009	by1000genomes	TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159992541_159992562delGTGTGTGTGTGTGTGTGTGTGC	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron|TANC1_uc002uah.1_5'Flank	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						gtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgCGCGCGCGCGC	0.396													5	7	---	---	---	---	
FKBP7	51661	broad.mit.edu	37	2	179334696	179334697	+	Intron	INS	-	T	T	rs7582280	by1000genomes	TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179334696_179334697insT	uc002umk.2	-						FKBP7_uc002umm.2_Intron|FKBP7_uc002uml.2_Intron|FKBP7_uc010zff.1_Intron	NM_181342	NP_851939	Q9Y680	FKBP7_HUMAN	FK506 binding protein 7 isoform a precursor						protein folding	endoplasmic reticulum lumen|membrane	calcium ion binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			tttcttttttgtttttttttct	0.223													4	2	---	---	---	---	
NDUFS1	4719	broad.mit.edu	37	2	207006522	207006523	+	Intron	INS	-	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207006522_207006523insA	uc002vbe.2	-						NDUFS1_uc010ziq.1_Intron|NDUFS1_uc010zir.1_Intron|NDUFS1_uc010zis.1_Intron|NDUFS1_uc010zit.1_Intron|NDUFS1_uc010ziu.1_Intron	NM_005006	NP_004997	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)	tccgtcccaccaaaaaaaaaaa	0.124													3	3	---	---	---	---	
MFF	56947	broad.mit.edu	37	2	228207712	228207712	+	Intron	DEL	A	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228207712delA	uc002vos.2	+						MFF_uc002vot.2_Intron|MFF_uc002vou.2_Intron|MFF_uc002vov.2_Intron|MFF_uc002vow.2_Intron|MFF_uc002vox.2_Intron|MFF_uc002voy.2_Intron|MFF_uc002voz.2_Intron	NM_020194	NP_064579	Q9GZY8	MFF_HUMAN	mitochondrial fission factor							integral to membrane|mitochondrial outer membrane				large_intestine(1)	1						TTTATTAAGGAAAAAAAAAAA	0.338													4	2	---	---	---	---	
RUVBL1	8607	broad.mit.edu	37	3	127823955	127823955	+	Intron	DEL	T	-	-	rs71615963		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127823955delT	uc003ekh.2	-						RUVBL1_uc003ekf.2_Intron|RUVBL1_uc010hss.2_Intron	NM_003707	NP_003698	Q9Y265	RUVB1_HUMAN	RuvB-like 1						cell division|CenH3-containing nucleosome assembly at centromere|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|mitosis|regulation of growth|regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription, DNA-dependent	Golgi apparatus|Ino80 complex|membrane|microtubule organizing center|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|DNA helicase activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.181)		GAAATGCAACttttttttttt	0.169													3	3	---	---	---	---	
ZBBX	79740	broad.mit.edu	37	3	167000473	167000486	+	Intron	DEL	TCATAAAGAACACT	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167000473_167000486delTCATAAAGAACACT	uc003fep.2	-						ZBBX_uc011bpc.1_Intron|ZBBX_uc003feq.2_Intron	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing							intracellular	zinc ion binding			ovary(2)	2						TTTTCCAATGTCATAAAGAACACTTCTGTGTATT	0.276													3	3	---	---	---	---	
ADAMTS3	9508	broad.mit.edu	37	4	73174950	73174951	+	Intron	INS	-	T	T	rs76753805		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73174950_73174951insT	uc003hgk.1	-						ADAMTS3_uc003hgl.2_Intron	NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAAGTGATTTCTTTTTTTTTTT	0.252													9	6	---	---	---	---	
KIF13A	63971	broad.mit.edu	37	6	17785982	17785982	+	Intron	DEL	A	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17785982delA	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			catctctaccaaaaaaaaaaa	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	53219904	53219905	+	IGR	INS	-	A	A			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53219904_53219905insA								ELOVL5 (5962 upstream) : GCLC (142235 downstream)																							TATAAAACTGCAAAAAAAAAAG	0.342													4	2	---	---	---	---	
TBX18	9096	broad.mit.edu	37	6	85472511	85472511	+	Intron	DEL	A	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85472511delA	uc003pkl.1	-						TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		AGGGAAACAGAGGGGAAGCCA	0.612													4	4	---	---	---	---	
AIM1	202	broad.mit.edu	37	6	106966842	106966843	+	Intron	DEL	AT	-	-	rs9486376	byFrequency	TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106966842_106966843delAT	uc003prh.2	+							NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1								sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		ttaaaaaCACATGTGTGCGcac	0.109													5	4	---	---	---	---	
SYNE1	23345	broad.mit.edu	37	6	152786901	152786902	+	Intron	INS	-	AC	AC	rs10549697		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152786901_152786902insAC	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_Intron|SYNE1_uc003qow.2_5'Flank|SYNE1_uc003qox.1_Intron|SYNE1_uc003qoz.2_Intron|SYNE1_uc003qoy.2_Intron	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GAAGAacacatacacacacaca	0.297										HNSCC(10;0.0054)			2	4	---	---	---	---	
SNX13	23161	broad.mit.edu	37	7	17854572	17854573	+	Intron	INS	-	AA	AA			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17854572_17854573insAA	uc003stw.1	-						SNX13_uc003stv.2_Intron|SNX13_uc010kuc.2_Intron|SNX13_uc010kub.2_Intron			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;						cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)					CAGTAACTAACAAGAAAAAAAA	0.317													4	2	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23827361	23827362	+	Intron	DEL	AC	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23827361_23827362delAC	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron|STK31_uc003swv.1_5'Flank	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						gtATGATTGTacacacacacac	0.094													4	2	---	---	---	---	
BLK	640	broad.mit.edu	37	8	11361876	11361877	+	Intron	INS	-	A	A	rs55809628		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11361876_11361877insA	uc003wty.2	+						BLK_uc003wtz.2_Intron|BLK_uc003wtx.2_Intron	NM_001715	NP_001706	P51451	BLK_HUMAN	B lymphoid tyrosine kinase						intracellular protein kinase cascade|positive regulation of insulin secretion		ATP binding|non-membrane spanning protein tyrosine kinase activity			large_intestine(1)|stomach(1)|ovary(1)	3			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		aaggaaggaagaaagaaaagaa	0.109													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68430364	68430365	+	IGR	INS	-	A	A	rs140332329		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68430364_68430365insA								FAM27B (636175 upstream) : MIR1299 (571874 downstream)																							TTATGCAGAAGAAAAAATTAAC	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3325617	3325624	+	IGR	DEL	TTCTTTCC	-	-	rs72763757		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3325617_3325624delTTCTTTCC								PITRM1 (110614 upstream) : KLF6 (492565 downstream)																							ctttctttctttctttccttccttcctt	0.000													3	3	---	---	---	---	
MTPAP	55149	broad.mit.edu	37	10	30638287	30638287	+	5'Flank	DEL	G	-	-	rs112277654		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30638287delG	uc001iva.3	-						MTPAP_uc001ivb.3_Intron|MTPAP_uc001ivc.2_5'Flank	NM_018109	NP_060579	Q9NVV4	PAPD1_HUMAN	PAP associated domain containing 1 precursor						cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1						TCGGGGGGGAGGGGGGGGGCA	0.507													5	6	---	---	---	---	
VPS26A	9559	broad.mit.edu	37	10	70917620	70917620	+	Intron	DEL	T	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70917620delT	uc001jpb.2	+						VPS26A_uc001jpc.2_Intron|VPS26A_uc009xqa.2_Intron|VPS26A_uc001jpd.2_Intron	NM_004896	NP_004887	O75436	VP26A_HUMAN	vacuolar protein sorting 26 A isoform 1						retrograde transport, endosome to Golgi|vacuolar transport	cytosol|endosome membrane|retromer complex|vesicle	protein binding|protein transporter activity				0						GAACTTTGTATTTTTTTTCAT	0.378													4	2	---	---	---	---	
PSD	5662	broad.mit.edu	37	10	104164124	104164125	+	Intron	DEL	AT	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104164124_104164125delAT	uc001kvg.1	-						PSD_uc001kve.1_Intron|PSD_uc001kvf.1_Intron|PSD_uc001kvh.1_Intron|PSD_uc009xxd.1_Intron	NM_002779	NP_002770	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing						regulation of ARF protein signal transduction	cytoplasm|plasma membrane|ruffle	ARF guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|urinary_tract(1)	3				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		aaaaaaaaagatgccccttcct	0.000													4	3	---	---	---	---	
FAM180B	399888	broad.mit.edu	37	11	47606232	47606232	+	5'Flank	DEL	T	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47606232delT	uc001ngb.1	+									Q6P0A1	F180B_HUMAN	RecName: Full=Protein FAM180B;							integral to membrane					0						CTTTGATGGGttttttttttt	0.269													5	3	---	---	---	---	
RBM4	5936	broad.mit.edu	37	11	66410772	66410772	+	Intron	DEL	T	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66410772delT	uc009yrj.2	+						RBM4_uc009yrk.2_Intron|RBM4_uc001oiw.1_Intron|RBM4_uc001oix.1_Intron|RBM4_uc010rpj.1_Intron|RBM4_uc001oiy.1_Intron|RBM4_uc001oiz.1_Intron	NM_002896	NP_002887	Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4						circadian regulation of gene expression|entrainment of circadian clock by photoperiod|mRNA processing|negative regulation of translation in response to stress|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|positive regulation of muscle cell differentiation|regulation of alternative nuclear mRNA splicing, via spliceosome|regulation of nucleocytoplasmic transport|RNA splicing|stress-activated MAPK cascade	nuclear speck|nucleolus|stress granule	miRNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|zinc ion binding			ovary(1)	1				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		ATGTTGAGTCTTTTTTTTTTT	0.343													10	6	---	---	---	---	
ARHGEF12	23365	broad.mit.edu	37	11	120352470	120352470	+	Intron	DEL	T	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120352470delT	uc001pxl.1	+						ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		tctttctttcttttttttttt	0.144			T	MLL	AML								3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128060134	128060137	+	IGR	DEL	TGCA	-	-	rs72064229		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128060134_128060137delTGCA								None (None upstream) : ETS1 (268519 downstream)																							CACGTGCGTGTGCACGCGTGcaca	0.363													4	2	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	66935963	66935964	+	Intron	INS	-	AATA	AATA	rs146848650	by1000genomes	TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66935963_66935964insAATA	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stl.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TCCAGGTTGACAATAGTCCAAA	0.381													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77054687	77054687	+	IGR	DEL	T	-	-	rs2369296	by1000genomes	TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77054687delT								OSBPL8 (101098 upstream) : ZDHHC17 (103167 downstream)																							aaaaaaaaaataaataaaGGA	0.358													6	4	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	117965152	117965153	+	Intron	DEL	AG	-	-	rs10545784		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117965152_117965153delAG	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					acacacacacagacacacacac	0.238													4	2	---	---	---	---	
PLA2G1B	5319	broad.mit.edu	37	12	120763035	120763036	+	Intron	INS	-	T	T			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120763035_120763036insT	uc001tyd.2	-						PLA2G1B_uc009zwx.2_Intron	NM_000928	NP_000919	P04054	PA21B_HUMAN	phospholipase A2 group IB precursor						actin filament organization|activation of MAPK activity|activation of phospholipase A2 activity|arachidonic acid secretion|cellular response to insulin stimulus|glucose transport|interleukin-8 production|leukotriene biosynthetic process|multicellular organismal lipid catabolic process|neutrophil chemotaxis|neutrophil mediated immunity|phosphatidylcholine metabolic process|positive regulation of calcium ion transport into cytosol|positive regulation of DNA replication|positive regulation of immune response|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein secretion|positive regulation of transcription from RNA polymerase II promoter	extracellular space	bile acid binding|calcium ion binding|calcium-dependent phospholipase A2 activity|cell surface binding|receptor binding			skin(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TATTGAAAGCAttttttttttt	0.188											OREG0022189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75588839	75588840	+	IGR	INS	-	CTTCCTTC	CTTCCTTC	rs9543833		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75588839_75588840insCTTCCTTC								KLF12 (880445 upstream) : LOC647288 (223050 downstream)																							tttctttctttcttccttcctt	0.139													5	3	---	---	---	---	
MTA1	9112	broad.mit.edu	37	14	105905492	105905493	+	Intron	INS	-	T	T	rs140601392	by1000genomes	TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105905492_105905493insT	uc001yqx.2	+						MTA1_uc001yqy.2_Intron|MTA1_uc001yqz.1_Intron|MTA1_uc001yra.1_Intron	NM_004689	NP_004680	Q13330	MTA1_HUMAN	metastasis associated protein						signal transduction	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		GAGCTCTGCCCCCACCCCTGAG	0.644													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84957462	84957472	+	IGR	DEL	GTGGCATCTGT	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84957462_84957472delGTGGCATCTGT								LOC388152 (58542 upstream) : GOLGA6L5 (90266 downstream)																							CACTTGTAGGGTGGCATCTGTGTGCACTGGC	0.578													5	4	---	---	---	---	
CORO7	79585	broad.mit.edu	37	16	4407357	4407357	+	Intron	DEL	T	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4407357delT	uc002cwh.3	-						CORO7_uc002cwe.2_Intron|CORO7_uc002cwf.2_Intron|CORO7_uc002cwg.3_Intron|CORO7_uc010uxh.1_Intron|CORO7_uc010uxi.1_Intron	NM_024535	NP_078811	P57737	CORO7_HUMAN	coronin 7							cytoplasmic membrane-bounded vesicle|cytosol|Golgi membrane|integral to membrane of membrane fraction|soluble fraction					0						tctttctttcttttttttttt	0.239													4	2	---	---	---	---	
PMFBP1	83449	broad.mit.edu	37	16	72163921	72163921	+	Intron	DEL	T	-	-	rs67023960		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72163921delT	uc002fcc.3	-						PMFBP1_uc002fcd.2_Intron|PMFBP1_uc002fce.2_Intron|PMFBP1_uc002fcf.2_Intron|PMFBP1_uc010cgo.1_5'Flank	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1											ovary(2)	2		Ovarian(137;0.179)				aatgtttgtattttttttttt	0.000													5	3	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21217018	21217020	+	Intron	DEL	CCT	-	-	rs72412380		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21217018_21217020delCCT	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		TACCTGGCTCCCTCCTCCCTCCT	0.389													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	29103592	29103592	+	IGR	DEL	T	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29103592delT								SUZ12P (6525 upstream) : CRLF3 (6111 downstream)																							GTATCATTCCttttttttttt	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	62932555	62932556	+	IGR	DEL	GT	-	-	rs35142297		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62932555_62932556delGT								LRRC37A3 (16969 upstream) : AMZ2P1 (30112 downstream)																							gtgtgtgttcgtgtgtgtgtgt	0.238													7	5	---	---	---	---	
HELZ	9931	broad.mit.edu	37	17	65146246	65146247	+	Intron	INS	-	TT	TT	rs11372378		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65146246_65146247insTT	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TATTttctttcttttttttttt	0.124													9	5	---	---	---	---	
MAP2K2	5605	broad.mit.edu	37	19	4097203	4097204	+	Intron	INS	-	A	A	rs11449985		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4097203_4097204insA	uc002lzk.2	-						MAP2K2_uc002lzj.2_Intron	NM_030662	NP_109587	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2						activation of MAPK activity|activation of MAPKK activity|axon guidance|epidermal growth factor receptor signaling pathway|ERK1 and ERK2 cascade|innate immune response|insulin receptor signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|extracellular region	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		agactctgcctaaaaaaaaaaa	0.139									Cardiofaciocutaneous_syndrome				11	5	---	---	---	---	
CLEC17A	388512	broad.mit.edu	37	19	14693778	14693779	+	5'Flank	DEL	TG	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14693778_14693779delTG	uc010dzn.1	+						CLEC17A_uc002mzh.1_5'Flank|CLEC17A_uc010xnt.1_5'Flank|CLEC17A_uc010xnu.1_5'Flank|CLEC17A_uc010dzo.1_5'Flank			Q6ZS10	CL17A_HUMAN	SubName: Full=CLEC17A protein;							cell surface|integral to membrane	fucose binding|mannose binding|metal ion binding|receptor activity				0						TCtgtgtgtatgtgtgtgtgtg	0.262													4	4	---	---	---	---	
ATP5SL	55101	broad.mit.edu	37	19	41938474	41938475	+	Intron	DEL	GT	-	-			TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41938474_41938475delGT	uc002oqw.1	-						CYP2F1_uc010xvw.1_Intron|ATP5SL_uc002oqu.1_Intron|ATP5SL_uc002oqv.2_Intron|ATP5SL_uc010xwa.1_Intron|ATP5SL_uc002oqx.1_Intron|ATP5SL_uc002oqy.1_Intron|ATP5SL_uc002oqz.1_Intron|ATP5SL_uc002ora.1_3'UTR|ATP5SL_uc010xwb.1_3'UTR	NM_018035	NP_060505	Q9NW81	AT5SL_HUMAN	ATP5S-like											large_intestine(1)|breast(1)	2						CAgtgtgtgcgtgtgtgtgtgt	0.411													6	3	---	---	---	---	
VSTM2L	128434	broad.mit.edu	37	20	36572311	36572311	+	Intron	DEL	C	-	-	rs33961791		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36572311delC	uc002xhk.3	+							NM_080607	NP_542174	Q96N03	VTM2L_HUMAN	V-set and transmembrane domain containing 2 like											ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)				GATCTTGGGACCCCCCCCCCC	0.418													10	5	---	---	---	---	
KRTAP10-9	386676	broad.mit.edu	37	21	46048132	46048132	+	3'UTR	DEL	C	-	-	rs67739305		TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46048132delC	uc002zfp.3	+	1					C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198690	NP_941963	P60411	KR109_HUMAN	keratin associated protein 10-9							keratin filament					0						TCCCTGACCTCCCCCCCGGGC	0.697													4	3	---	---	---	---	
CYP2D7P1	1564	broad.mit.edu	37	22	42537119	42537120	+	Intron	INS	-	A	A	rs142656198	by1000genomes	TCGA-66-2778-01A-02D-1522-08	TCGA-66-2778-11A-01D-1522-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42537119_42537120insA	uc003bci.2	-						CYP2D7P1_uc003bcg.2_Intron|CYP2D7P1_uc003bch.2_Intron|CYP2D7P1_uc010gyv.2_Intron|CYP2D7P1_uc010gyw.2_Intron	NR_002570				SubName: Full=Cytochrome P450 2D6;          EC=1.14.14.1;												0						GGGCTACCACCGGGGCTGATGC	0.614													6	4	---	---	---	---	
