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
ENO1	2023	broad.mit.edu	37	1	8921303	8921303	+	3'UTR	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8921303G>A	uc001apj.1	-	12					ENO1_uc001api.1_3'UTR|ENO1_uc001apk.1_3'UTR|ENO1_uc001apl.1_3'UTR|ENO1_uc009vmi.1_3'UTR|ENO1_uc009vmj.1_3'UTR|ENO1_uc009vmk.1_3'UTR	NM_001428	NP_001419	P06733	ENOA_HUMAN	enolase 1						gluconeogenesis|glycolysis|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|response to virus	phosphopyruvate hydratase complex|plasma membrane|sarcomere	DNA binding|magnesium ion binding|phosphopyruvate hydratase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|kidney(1)|central_nervous_system(1)	4	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.42e-07)|COAD - Colon adenocarcinoma(227;2.78e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		GCGGTGGGGCGCTAACTAGCA	0.602													4	17	---	---	---	---	PASS
WASF2	10163	broad.mit.edu	37	1	27755320	27755320	+	Silent	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27755320G>A	uc001bof.1	-	2	297	c.81C>T	c.(79-81)TGC>TGT	p.C27C	WASF2_uc010ofl.1_Silent_p.C27C	NM_006990	NP_008921	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	27					actin cytoskeleton organization|G-protein signaling, coupled to cAMP nucleotide second messenger	actin cytoskeleton|lamellipodium	actin binding			skin(2)|ovary(1)	3		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		TGTTGGTCACGCATTCCAGCT	0.577													4	140	---	---	---	---	PASS
GBP2	2634	broad.mit.edu	37	1	89587611	89587611	+	Silent	SNP	G	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89587611G>C	uc001dmz.1	-	2	310	c.39C>G	c.(37-39)CTC>CTG	p.L13L	GBP2_uc001dmy.1_RNA	NM_004120	NP_004111	P32456	GBP2_HUMAN	guanylate binding protein 2,	13					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)		TGTTATCAATGAGGCTCATTG	0.498													5	252	---	---	---	---	PASS
GSTM5	2949	broad.mit.edu	37	1	110256100	110256100	+	Intron	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110256100A>G	uc001dyn.2	+						GSTM5_uc010ovu.1_Missense_Mutation_p.I17V	NM_000851	NP_000842	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5						xenobiotic metabolic process	endoplasmic reticulum membrane	glutathione transferase activity			central_nervous_system(6)	6		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	TTTCCCATCTATCCAGCTGCC	0.592													84	186	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	120076496	120076496	+	RNA	SNP	A	G	G	rs10754405	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120076496A>G	uc001ehx.1	-	1		c.441T>C								full-length cDNA clone CS0DK008YI13 of HeLa cells Cot 25-normalized of Homo sapiens (human).																		TCCCAGGATCAAAGGTGGAAG	0.493													4	3	---	---	---	---	PASS
TXNIP	10628	broad.mit.edu	37	1	145440347	145440347	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145440347G>T	uc001enn.3	+	5	994	c.653G>T	c.(652-654)CGC>CTC	p.R218L	NBPF10_uc001emp.3_Intron|TXNIP_uc001enm.1_Intron|TXNIP_uc010oys.1_Missense_Mutation_p.R163L	NM_006472	NP_006463	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	218					cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding			ovary(2)	2	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ATTGTGGCCCGCCACACTTAC	0.478													21	118	---	---	---	---	PASS
ASH1L	55870	broad.mit.edu	37	1	155449745	155449745	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155449745C>A	uc009wqq.2	-	3	3396	c.2916G>T	c.(2914-2916)AAG>AAT	p.K972N	ASH1L_uc001fkt.2_Missense_Mutation_p.K972N|ASH1L_uc009wqr.1_Missense_Mutation_p.K972N	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	972					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CATTGTTTCTCTTGGTAATTT	0.343													4	240	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158612201	158612201	+	Silent	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158612201C>T	uc001fst.1	-	33	4936	c.4737G>A	c.(4735-4737)AAG>AAA	p.K1579K		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1579	Spectrin 15.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					TGAGCTTTACCTTCATGGCCT	0.388													9	269	---	---	---	---	PASS
GPR161	23432	broad.mit.edu	37	1	168054595	168054595	+	3'UTR	SNP	T	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168054595T>C	uc001gfc.2	-	8					GPR161_uc001gfb.2_3'UTR|GPR161_uc010pll.1_3'UTR|GPR161_uc010plm.1_3'UTR|GPR161_uc009wvo.2_3'UTR|GPR161_uc001gfd.2_3'UTR|GPR161_uc010pln.1_3'UTR	NM_153832	NP_722561	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161 isoform 2						multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)					AGCTGTGGACTGTAGACATTA	0.473											OREG0013978	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	10	---	---	---	---	PASS
C1orf9	51430	broad.mit.edu	37	1	172501831	172501831	+	5'Flank	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172501831C>T	uc001giq.3	+						C1orf9_uc010pmm.1_5'Flank|C1orf9_uc009wwd.2_5'Flank|C1orf9_uc010pmn.1_5'Flank|C1orf9_uc010pmo.1_5'Flank	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein						multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)		ACTTCTCTAACAAAACCATGG	0.498													6	78	---	---	---	---	PASS
ARID4B	51742	broad.mit.edu	37	1	235345029	235345029	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235345029T>C	uc001hwq.2	-	20	3703	c.3205A>G	c.(3205-3207)ATT>GTT	p.I1069V	ARID4B_uc001hwr.2_Missense_Mutation_p.I983V|ARID4B_uc001hws.3_Missense_Mutation_p.I983V|ARID4B_uc001hwp.2_RNA|ARID4B_uc001hwt.3_Missense_Mutation_p.I750V	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	1069					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TCCACCTCAATTGTGCTATCA	0.493													32	54	---	---	---	---	PASS
SFRS7	6432	broad.mit.edu	37	2	38976716	38976716	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38976716T>A	uc002rqz.2	-	3	579	c.341A>T	c.(340-342)CAT>CTT	p.H114L	SFRS7_uc002rra.2_RNA|SFRS7_uc010ynp.1_Missense_Mutation_p.H114L|GEMIN6_uc002rrb.2_5'Flank	NM_001031684	NP_001026854	Q16629	SRSF7_HUMAN	splicing factor, arginine/serine-rich 7	114	CCHC-type.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding|zinc ion binding				0		all_hematologic(82;0.248)				ATAAGCATAATGTCCCTTTTC	0.413													27	279	---	---	---	---	PASS
SPTBN1	6711	broad.mit.edu	37	2	54785805	54785805	+	Intron	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54785805C>A	uc002rxu.2	+						SPTBN1_uc002rxv.1_Intron|SPTBN1_uc002rxx.2_5'UTR	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			CGGAATGGGGCTCGCCTAAGG	0.622													6	24	---	---	---	---	PASS
CCDC85A	114800	broad.mit.edu	37	2	56603059	56603059	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56603059C>A	uc002rzn.2	+	5	2063	c.1561C>A	c.(1561-1563)CAT>AAT	p.H521N		NM_001080433	NP_001073902	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	521										breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ACCTGTGGTACATTCTCTTAA	0.498													32	60	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	95539132	95539132	+	Splice_Site	SNP	A	G	G	rs74376788	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95539132A>G	uc002stv.1	-	9		c.1317_splice	c.e9+1		TEKT4_uc002stw.1_Intron|TEKT4_uc010fhr.1_RNA					Homo sapiens cDNA FLJ44118 fis, clone TESTI4047069.																		AGCAGAACTTACACAGTCAGA	0.567													2	11	---	---	---	---	PASS
CCDC115	84317	broad.mit.edu	37	2	131096732	131096732	+	Silent	SNP	G	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131096732G>C	uc002tqy.1	-	5	728	c.504C>G	c.(502-504)CTC>CTG	p.L168L	CCDC115_uc002tqw.1_3'UTR|CCDC115_uc010zaf.1_3'UTR|CCDC115_uc002tqx.2_Silent_p.L163L|CCDC115_uc002tqz.1_3'UTR	NM_032357	NP_115733	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115	168	Potential.					endosome|lysosome					0	Colorectal(110;0.1)					GTTTCTCTTGGAGTCCCCGGA	0.612													7	62	---	---	---	---	PASS
TLK1	9874	broad.mit.edu	37	2	171862701	171862701	+	Silent	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171862701A>G	uc002ugn.2	-	18	2332	c.1860T>C	c.(1858-1860)GGT>GGC	p.G620G	TLK1_uc002ugo.2_Silent_p.G641G|TLK1_uc002ugp.2_Silent_p.G572G|TLK1_uc002ugq.2_RNA|TLK1_uc010zdn.1_Silent_p.G524G	NM_012290	NP_036422	Q9UKI8	TLK1_HUMAN	tousled-like kinase 1 isoform 1	620	Protein kinase.				cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1						TTCCATCTACACCATAGCTAT	0.398													15	213	---	---	---	---	PASS
CALCRL	10203	broad.mit.edu	37	2	188210853	188210853	+	3'UTR	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188210853G>A	uc002upv.3	-	15					CALCRL_uc010frt.2_3'UTR	NM_005795	NP_005786	Q16602	CALRL_HUMAN	calcitonin receptor-like precursor							integral to plasma membrane				lung(3)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			CAGAGTCATGGGTCCAAGTCC	0.289													6	14	---	---	---	---	PASS
SGOL2	151246	broad.mit.edu	37	2	201436396	201436396	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201436396A>G	uc002uvw.2	+	7	1440	c.1327A>G	c.(1327-1329)AGG>GGG	p.R443G	SGOL2_uc010zhd.1_Missense_Mutation_p.R443G|SGOL2_uc010zhe.1_Missense_Mutation_p.R443G	NM_152524	NP_689737	Q562F6	SGOL2_HUMAN	shugoshin-like 2 isoform 1	443					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding			ovary(2)|skin(2)	4						GGATGGCAAAAGGGGTGCAGA	0.398													3	263	---	---	---	---	PASS
RNF25	64320	broad.mit.edu	37	2	219533304	219533304	+	Intron	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219533304G>A	uc002vit.2	-						RNF25_uc010fvw.2_5'UTR	NM_022453	NP_071898	Q96BH1	RNF25_HUMAN	ring finger protein 25						positive regulation of NF-kappaB transcription factor activity	cytosol|nucleus	NF-kappaB binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGGGACTCCTGCCCACCACTG	0.423													11	317	---	---	---	---	PASS
PRR21	643905	broad.mit.edu	37	2	240982108	240982108	+	Missense_Mutation	SNP	C	T	T	rs112152720	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240982108C>T	uc010zod.1	-	1	292	c.292G>A	c.(292-294)GTC>ATC	p.V98I		NM_001080835	NP_001074304	Q8WXC7	PRR21_HUMAN	proline rich 21	98	Pro-rich.									ovary(1)|skin(1)	2						GAGGCATGGACGAAGGGCCGT	0.612													9	70	---	---	---	---	PASS
TTLL3	26140	broad.mit.edu	37	3	9870957	9870957	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9870957C>A	uc003btg.2	+	10	1648	c.1432C>A	c.(1432-1434)CCC>ACC	p.P478T	ARPC4_uc003btc.1_Missense_Mutation_p.P122T|TTLL3_uc003btd.3_Missense_Mutation_p.P445T|TTLL3_uc003btf.3_Missense_Mutation_p.P210T|TTLL3_uc010hco.1_Missense_Mutation_p.P414T|TTLL3_uc003bth.3_Missense_Mutation_p.P266T|TTLL3_uc011atj.1_Missense_Mutation_p.P414T|TTLL3_uc003btj.3_Missense_Mutation_p.P266T|TTLL3_uc003bti.3_Missense_Mutation_p.P266T	NM_001025930	NP_001021100	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	478	TTL.				axoneme assembly|cilium assembly|protein polyglycylation	cilium axoneme|cytoplasm|microtubule	protein-glycine ligase activity, initiating|tubulin-tyrosine ligase activity			large_intestine(2)	2	Medulloblastoma(99;0.227)					CACGATGGCACCCTCCACAGC	0.622													59	91	---	---	---	---	PASS
IRAK2	3656	broad.mit.edu	37	3	10283918	10283918	+	3'UTR	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10283918G>A	uc003bve.1	+	13						NM_001570	NP_001561	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2						activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|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	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			lung(5)|breast(3)	8						CCTGATGACCGGAACACAGCT	0.453													3	113	---	---	---	---	PASS
CTNNB1	1499	broad.mit.edu	37	3	41266136	41266136	+	Missense_Mutation	SNP	T	C	C	rs121913407		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41266136T>C	uc010hia.1	+	4	289	c.133T>C	c.(133-135)TCT>CCT	p.S45P	CTNNB1_uc003ckp.2_Missense_Mutation_p.S45P|CTNNB1_uc003ckq.2_Missense_Mutation_p.S45P|CTNNB1_uc003ckr.2_Missense_Mutation_p.S45P|CTNNB1_uc011azf.1_Missense_Mutation_p.S38P|CTNNB1_uc011azg.1_Intron|uc010hib.1_RNA	NM_001904	NP_001895	P35222	CTNB1_HUMAN	beta-catenin	45			Missing (in colorectal cancer).|S -> P (in hepatocellular carcinoma).|S -> F (in hepatocellular carcinoma).		adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens	alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding	p.S45F(396)|p.S45P(163)|p.S45del(79)|p.A5_A80del(63)|p.S45Y(21)|p.S45C(18)|p.S45A(10)|p.H24_S47del(9)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.W25_I140del(4)|p.V22_L139>V(2)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.?(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q72del(1)|p.A20_Q143del(1)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.A43_E54del(1)|p.V22_A80del(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.A5_G80>(1)|p.Q28_Q61del(1)|p.A43_E53del(1)|p.M8_G50del(1)|p.M1_A87del(1)|p.S45_S47>C(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.A5_D144>D(1)|p.P44_N51del(1)|p.P44_S45>AP(1)|p.V22_G80>NNNNN(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.D6_K133del(1)|p.T40_L46del(1)|p.S45fs*2(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.W25_A80del(1)|p.A5_R90del(1)|p.H24_M131del(1)|p.S45E(1)|p.A20_R151del(1)|p.D17_A126del(1)|p.M8_A80del(1)|p.P44_S45insGATTTAP(1)|p.K19_Y142>V(1)|p.A5_E54del(1)|p.L7_I140del(1)|p.S45T(1)|p.A21_A80del(1)|p.E9_I140del(1)|p.S45S(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.G38_S45del(1)|p.E9_A80del(1)|p.D6_I140del(1)|p.S23_I140del(1)|p.A20_L148del(1)|p.Q28_I140del(1)|p.S45_E54del(1)|p.A20_Q72del(1)|p.D17_P128del(1)|p.A20_S111del(1)|p.E9_S47del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	liver(806)|soft_tissue(609)|large_intestine(243)|endometrium(222)|kidney(172)|stomach(157)|central_nervous_system(139)|ovary(104)|skin(97)|pancreas(91)|adrenal_gland(85)|pituitary(81)|salivary_gland(62)|haematopoietic_and_lymphoid_tissue(57)|thyroid(55)|biliary_tract(41)|lung(38)|prostate(24)|bone(20)|small_intestine(17)|cervix(9)|parathyroid(9)|urinary_tract(8)|breast(7)|oesophagus(5)|NS(3)|pleura(2)|upper_aerodigestive_tract(2)|eye(1)	3166				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)	Lithium(DB01356)	CACAGCTCCTTCTCTGAGTGG	0.502		15	H|Mis|T	PLAG1	colorectal|cvarian| hepatoblastoma|others|pleomorphic salivary adenoma				Pilomatrixoma_Familial_Clustering_of				5	105	---	---	---	---	PASS
ZNF167	55888	broad.mit.edu	37	3	44612332	44612332	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44612332A>G	uc010hin.2	+	6	2118	c.1730A>G	c.(1729-1731)AAG>AGG	p.K577R	ZNF167_uc003cni.2_Intron|ZNF167_uc010hio.2_Intron|ZNF167_uc003cnj.2_Missense_Mutation_p.K577R|ZNF167_uc003cnk.2_Intron	NM_018651	NP_061121	Q9P0L1	ZN167_HUMAN	zinc finger protein 167 isoform 1	577					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(197;0.0486)|Kidney(197;0.0609)		ACTGGGGAAAAGCCATACAAA	0.433													3	254	---	---	---	---	PASS
SACM1L	22908	broad.mit.edu	37	3	45761023	45761023	+	Silent	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45761023A>G	uc003cos.2	+	8	813	c.609A>G	c.(607-609)GGA>GGG	p.G203G	SACM1L_uc011bag.1_Silent_p.G100G|SACM1L_uc011bah.1_Silent_p.G137G	NM_014016	NP_054735	Q9NTJ5	SAC1_HUMAN	suppressor of actin 1	203	SAC.					Golgi apparatus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		CTATTAATGGAAAATACTTTG	0.338													6	77	---	---	---	---	PASS
USP19	10869	broad.mit.edu	37	3	49147711	49147711	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49147711C>A	uc003cwd.1	-	25	3796	c.3635G>T	c.(3634-3636)CGC>CTC	p.R1212L	USP19_uc003cwa.2_Missense_Mutation_p.R1020L|USP19_uc003cvz.3_Missense_Mutation_p.R1315L|USP19_uc011bcg.1_Missense_Mutation_p.R1303L|USP19_uc003cwb.2_Silent_p.P670P|USP19_uc003cwc.1_Missense_Mutation_p.R970L|USP19_uc011bch.1_Missense_Mutation_p.R1313L	NM_006677	NP_006668	O94966	UBP19_HUMAN	ubiquitin thioesterase 19	1212	Cytoplasmic (Potential).				ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(4)|breast(2)|lung(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GTTCCGCCGGCGGTAGAAGAG	0.617													3	103	---	---	---	---	PASS
IL17RB	55540	broad.mit.edu	37	3	53883702	53883702	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53883702C>G	uc003dha.2	+	3	145	c.106C>G	c.(106-108)CTA>GTA	p.L36V		NM_018725	NP_061195	Q9NRM6	I17RB_HUMAN	interleukin 17B receptor precursor	36	Extracellular (Potential).				defense response|regulation of cell growth	extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		AGAGTGGATGCTACAACATGA	0.483													7	116	---	---	---	---	PASS
ATP6V1A	523	broad.mit.edu	37	3	113508598	113508598	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113508598G>T	uc003eao.2	+	8	965	c.899G>T	c.(898-900)GGT>GTT	p.G300V	ATP6V1A_uc011bik.1_Missense_Mutation_p.G267V	NM_001690	NP_001681	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal V1 subunit A	300					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|integral to plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			ovary(2)|skin(1)	3						GAGGTTGATGGTAAGGTAGAG	0.353													51	103	---	---	---	---	PASS
COL29A1	256076	broad.mit.edu	37	3	130159274	130159274	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130159274A>T	uc010htj.1	+	35	6586	c.6092A>T	c.(6091-6093)GAT>GTT	p.D2031V	COL29A1_uc010hti.1_RNA|COL29A1_uc010htk.1_Missense_Mutation_p.D70V	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1	2031	VWFA 9.|Nonhelical region.				axon guidance|cell adhesion	collagen					0						ACAGAGTTTGATTTCATCACT	0.423													45	100	---	---	---	---	PASS
TBL1XR1	79718	broad.mit.edu	37	3	176755961	176755961	+	Splice_Site	SNP	C	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176755961C>G	uc003fiw.3	-	12	1308	c.1048_splice	c.e12-1	p.N350_splice	TBL1XR1_uc003fix.3_Splice_Site_p.N350_splice|TBL1XR1_uc011bpz.1_Splice_Site_p.N22_splice	NM_024665	NP_078941	Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TTACTTCATTCTAAAAATAAT	0.323													4	57	---	---	---	---	PASS
EHHADH	1962	broad.mit.edu	37	3	184910384	184910384	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184910384G>A	uc003fpf.2	-	7	1829	c.1802C>T	c.(1801-1803)TCA>TTA	p.S601L	EHHADH_uc011brs.1_Missense_Mutation_p.S505L	NM_001966	NP_001957	Q08426	ECHP_HUMAN	enoyl-Coenzyme A, hydratase/3-hydroxyacyl	601						peroxisome	3-hydroxyacyl-CoA dehydrogenase activity|coenzyme binding|dodecenoyl-CoA delta-isomerase activity|enoyl-CoA hydratase activity			ovary(3)	3	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)		NADH(DB00157)	TCTATACCGTGATAGGAATTT	0.428													34	227	---	---	---	---	PASS
CRMP1	1400	broad.mit.edu	37	4	5837779	5837779	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5837779C>T	uc003gip.2	-	12	1245	c.1144G>A	c.(1144-1146)GCT>ACT	p.A382T	CRMP1_uc003gin.1_Missense_Mutation_p.A294T|CRMP1_uc003giq.2_Missense_Mutation_p.A382T|CRMP1_uc003gir.2_Missense_Mutation_p.A377T|CRMP1_uc003gis.2_Missense_Mutation_p.A496T	NM_001313	NP_001304	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1 isoform 2	382					axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)		CTGGTGACAGCGACAAACTGG	0.567													77	143	---	---	---	---	PASS
USP38	84640	broad.mit.edu	37	4	144133502	144133502	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144133502A>G	uc003ijb.2	+	8	2063	c.1529A>G	c.(1528-1530)GAG>GGG	p.E510G	USP38_uc003ija.3_Missense_Mutation_p.E510G|USP38_uc003ijc.2_RNA	NM_032557	NP_115946	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	510					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_hematologic(180;0.158)					ATATTCTTTGAGGCTTCCAGA	0.383													3	232	---	---	---	---	PASS
FRG1	2483	broad.mit.edu	37	4	190864371	190864371	+	Missense_Mutation	SNP	G	A	A	rs73024915	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190864371G>A	uc003izs.2	+	2	268	c.77G>A	c.(76-78)AGC>AAC	p.S26N		NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1	26	Lys-rich.|Nuclear localization signal (Potential).				rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		aagaaaaagagcaaagataag	0.219													8	171	---	---	---	---	PASS
TAS2R1	50834	broad.mit.edu	37	5	9629679	9629679	+	Silent	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9629679G>A	uc003jem.1	-	1	785	c.466C>T	c.(466-468)CTA>TTA	p.L156L		NM_019599	NP_062545	Q9NYW7	TA2R1_HUMAN	taste receptor T2R1	156	Extracellular (Potential).				chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity			ovary(3)	3						AATTTCCTTAGGAAGTATGGG	0.393													8	151	---	---	---	---	PASS
MSH3	4437	broad.mit.edu	37	5	79961132	79961132	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79961132G>A	uc003kgz.2	+	3	782	c.529G>A	c.(529-531)GCA>ACA	p.A177T		NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3	177	Interaction with EXO1.				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		TCTTCTACACGCAAAGAATGC	0.388								MMR					45	67	---	---	---	---	PASS
PCDHB16	57717	broad.mit.edu	37	5	140564009	140564009	+	Silent	SNP	C	T	T	rs61743312		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140564009C>T	uc003liv.2	+	1	3030	c.1875C>T	c.(1873-1875)CGC>CGT	p.R625R	PCDHB9_uc003liw.1_5'Flank	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	625	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCGAGGTGCGCACCGCCAGGC	0.697													5	52	---	---	---	---	PASS
PCDHB9	56127	broad.mit.edu	37	5	140568869	140568869	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140568869G>T	uc003liw.1	+	3	1978	c.1978G>T	c.(1978-1980)GTG>TTG	p.V660L		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	660	Extracellular (Potential).|Cadherin 6.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CACGCTGCACGTGCTCCTGGT	0.706													21	56	---	---	---	---	PASS
TMED9	54732	broad.mit.edu	37	5	177022271	177022271	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177022271C>T	uc003mhx.2	+	5	565	c.562C>T	c.(562-564)CGA>TGA	p.R188*	TMED9_uc010jko.2_RNA	NM_017510	NP_059980	Q9BVK6	TMED9_HUMAN	transmembrane emp24 protein transport domain	188	Lumenal (Potential).				transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|integral to membrane					0	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCTGCAGTGGCGAGAGGAGCG	0.602													29	62	---	---	---	---	PASS
C6orf218	221718	broad.mit.edu	37	6	10430364	10430364	+	RNA	SNP	T	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10430364T>C	uc003myz.2	-	3		c.672A>G				NR_027793				Homo sapiens chromosome 6 open reading frame 218, mRNA (cDNA clone IMAGE:3917693).												0	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.124)				atttggtcactctCATTGAGG	0.303													3	178	---	---	---	---	PASS
TRAM2	9697	broad.mit.edu	37	6	52400646	52400646	+	Splice_Site	SNP	T	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52400646T>A	uc003paq.2	-	2	270	c.121_splice	c.e2-1	p.V41_splice		NM_012288	NP_036420	Q15035	TRAM2_HUMAN	translocation-associated membrane protein 2						collagen biosynthetic process|protein transport|transmembrane transport	integral to membrane	protein binding				0	Lung NSC(77;0.109)					GGCTGTGACCTGTAAAACAAA	0.438													3	88	---	---	---	---	PASS
EEF1A1	1915	broad.mit.edu	37	6	74228474	74228474	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74228474C>T	uc003phi.2	-	4	756	c.719G>A	c.(718-720)CGT>CAT	p.R240H	EEF1A1_uc003phd.2_5'Flank|EEF1A1_uc003phe.2_Missense_Mutation_p.R230H|EEF1A1_uc003phf.2_Missense_Mutation_p.R240H|EEF1A1_uc003phg.2_Missense_Mutation_p.R240H|EEF1A1_uc003phh.2_Missense_Mutation_p.R86H|EEF1A1_uc003phj.2_Missense_Mutation_p.R240H|EEF1A1_uc003phk.2_Missense_Mutation_p.R240H|EEF1A1_uc003phl.2_Intron|EEF1A1_uc003phm.1_Intron	NM_001402	NP_001393	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha	240						cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0						GTCAGTTGGACGAGTTGGTGG	0.498											OREG0003895|OREG0003891	type=REGULATORY REGION|Gene=EEF1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	4	78	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129601260	129601260	+	Silent	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129601260C>T	uc003qbn.2	+	18	2610	c.2505C>T	c.(2503-2505)TGC>TGT	p.C835C	LAMA2_uc003qbo.2_Silent_p.C835C	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	835	Laminin EGF-like 7.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GTGATGGATGCCCTGTCGGGT	0.453													4	77	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	65222986	65222986	+	Intron	SNP	G	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65222986G>T	uc003tud.1	-						CCT6P1_uc003tug.2_RNA|CCT6P1_uc003tuh.2_RNA|CCT6P1_uc003tui.2_RNA|uc003tuk.1_5'Flank					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																		GAATTCTGGCGTTTTTTACAA	0.289													4	28	---	---	---	---	PASS
CROT	54677	broad.mit.edu	37	7	86990868	86990868	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86990868T>A	uc003uit.2	+	5	648	c.403T>A	c.(403-405)TAC>AAC	p.Y135N	CROT_uc003uiu.2_Missense_Mutation_p.Y163N	NM_021151	NP_066974	Q9UKG9	OCTC_HUMAN	peroxisomal carnitine O-octanoyltransferase	135					fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|transport	peroxisomal matrix	carnitine O-octanoyltransferase activity			ovary(2)|lung(1)	3	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	TAACTTGAACTACTGGCAGCT	0.398													6	178	---	---	---	---	PASS
ABCB4	5244	broad.mit.edu	37	7	87082328	87082328	+	Silent	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87082328A>G	uc003uiv.1	-	6	544	c.468T>C	c.(466-468)GCT>GCC	p.A156A	ABCB4_uc003uiw.1_Silent_p.A156A|ABCB4_uc003uix.1_Silent_p.A156A|ABCB4_uc003uiy.2_Silent_p.A156A	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	156	ABC transmembrane type-1 1.|Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					GTCGTAGAATAGCATGAAAAA	0.413													3	189	---	---	---	---	PASS
ADAM22	53616	broad.mit.edu	37	7	87760838	87760838	+	Intron	SNP	A	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87760838A>T	uc003ujn.2	+						ADAM22_uc003ujj.1_3'UTR|ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			TCTGCTACATAACACAATTAG	0.294													11	28	---	---	---	---	PASS
AZGP1	563	broad.mit.edu	37	7	99573680	99573680	+	5'UTR	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99573680A>G	uc003ush.2	-	1						NM_001185	NP_001176	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc						antigen processing and presentation|cell adhesion|immune response|lipid catabolic process|negative regulation of cell proliferation	extracellular region|MHC class I protein complex	fatty acid binding|protein transmembrane transporter activity|ribonuclease activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GGAGGCACAGATATTATCCTG	0.567													4	217	---	---	---	---	PASS
IRF5	3663	broad.mit.edu	37	7	128582163	128582163	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128582163A>C	uc003vog.2	+	2	149	c.28A>C	c.(28-30)ACC>CCC	p.T10P	IRF5_uc010llr.1_Missense_Mutation_p.T10P|IRF5_uc011kot.1_Missense_Mutation_p.T10P|IRF5_uc011kou.1_Missense_Mutation_p.T10P|IRF5_uc010lls.1_Missense_Mutation_p.T10P|IRF5_uc003voh.2_Missense_Mutation_p.T10P|IRF5_uc010llt.2_Missense_Mutation_p.T10P|IRF5_uc003voi.2_Missense_Mutation_p.T10P|IRF5_uc010llu.1_Missense_Mutation_p.T10P|IRF5_uc003vok.2_Missense_Mutation_p.T10P|IRF5_uc003voj.3_Missense_Mutation_p.T10P|IRF5_uc010llv.1_Missense_Mutation_p.T10P|IRF5_uc010llw.1_Missense_Mutation_p.T10P	NM_002200	NP_002191	Q13568	IRF5_HUMAN	interferon regulatory factor 5 isoform a	10					interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0						AGTGGCTCCCACCCCACCCCG	0.622													13	44	---	---	---	---	PASS
GALNT11	63917	broad.mit.edu	37	7	151814291	151814291	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151814291A>G	uc010lqg.1	+	9	1513	c.1283A>G	c.(1282-1284)AAT>AGT	p.N428S	GALNT11_uc011kvm.1_Missense_Mutation_p.N347S|GALNT11_uc003wku.2_Missense_Mutation_p.N428S|GALNT11_uc003wkw.1_Missense_Mutation_p.N176S	NM_022087	NP_071370	Q8NCW6	GLT11_HUMAN	N-acetylgalactosaminyltransferase 11	428	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		AGCTATGGCAATATCAGTGAG	0.348													104	238	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151845758	151845758	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151845758C>A	uc003wla.2	-	52	13473	c.13254G>T	c.(13252-13254)AGG>AGT	p.R4418S	MLL3_uc003wkz.2_Missense_Mutation_p.R3536S|MLL3_uc003wkx.2_Missense_Mutation_p.R576S|MLL3_uc003wky.2_Missense_Mutation_p.R1982S	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	4418					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)		GGTTGAGTAGCCTTGCTGGTC	0.488			N		medulloblastoma								5	172	---	---	---	---	PASS
ST18	9705	broad.mit.edu	37	8	53045685	53045685	+	Silent	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53045685G>A	uc003xqz.2	-	16	2532	c.2376C>T	c.(2374-2376)TGC>TGT	p.C792C	ST18_uc011ldq.1_Silent_p.C439C|ST18_uc011ldr.1_Silent_p.C757C|ST18_uc011lds.1_Silent_p.C697C|ST18_uc003xra.2_Silent_p.C792C	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	792	C2HC-type 4.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TTGCACGAGGGCATCCGGACA	0.468													4	233	---	---	---	---	PASS
CPA6	57094	broad.mit.edu	37	8	68658418	68658418	+	5'UTR	SNP	G	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68658418G>T	uc003xxq.3	-	1					CPA6_uc003xxr.3_5'UTR|CPA6_uc003xxs.2_5'UTR	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			CGAGGCTGGAGGTGGCTCACA	0.567													3	24	---	---	---	---	PASS
SLCO5A1	81796	broad.mit.edu	37	8	70744856	70744856	+	Missense_Mutation	SNP	G	T	T	rs61730155	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70744856G>T	uc003xyl.2	-	2	760	c.53C>A	c.(52-54)CCG>CAG	p.P18Q	SLCO5A1_uc010lzb.2_Missense_Mutation_p.P18Q|SLCO5A1_uc011lfa.1_RNA|SLCO5A1_uc003xyk.2_Missense_Mutation_p.P18Q|SLCO5A1_uc010lzc.2_Missense_Mutation_p.P18Q	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	18	Cytoplasmic (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			TGCAGTGGCCGGCGCCTCCAG	0.627											OREG0018815	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	27	84	---	---	---	---	PASS
NBN	4683	broad.mit.edu	37	8	90955524	90955524	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90955524C>A	uc003yej.1	-	14	2251	c.2141G>T	c.(2140-2142)CGA>CTA	p.R714L	NBN_uc003yei.1_Missense_Mutation_p.R632L|NBN_uc011lgb.1_Missense_Mutation_p.R714L	NM_002485	NP_002476	O60934	NBN_HUMAN	nibrin	714					cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance	Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm	protein N-terminus binding|transcription factor binding			central_nervous_system(3)|kidney(3)|lung(1)	7			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TGTATTCTTTCGAGCATGATG	0.398								Direct_reversal_of_damage|Homologous_recombination	Nijmegen_Breakage_syndrome				4	255	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113236841	113236841	+	3'UTR	SNP	G	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113236841G>T	uc003ynu.2	-	71					CSMD3_uc003yns.2_3'UTR|CSMD3_uc003ynt.2_3'UTR|CSMD3_uc011lhx.1_3'UTR	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							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						GAAGAATTATGGTCCAGTTTA	0.353										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			9	13	---	---	---	---	PASS
DENND3	22898	broad.mit.edu	37	8	142161764	142161764	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142161764C>A	uc003yvy.2	+	7	940	c.662C>A	c.(661-663)TCG>TAG	p.S221*	DENND3_uc010mep.2_Nonsense_Mutation_p.S234*	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	221	DENN.									ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TTCTTCTCCTCGGACTGGGCT	0.542													3	169	---	---	---	---	PASS
FAM75A6	389730	broad.mit.edu	37	9	43627187	43627187	+	Silent	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43627187C>T	uc011lrb.1	-	4	1529	c.1500G>A	c.(1498-1500)CAG>CAA	p.Q500Q		NM_001145196	NP_001138668	Q5VVP1	F75A6_HUMAN	hypothetical protein LOC389730	500						integral to membrane					0						GGAAAGAAGACTGAAGATGGG	0.547													6	526	---	---	---	---	PASS
TRPM6	140803	broad.mit.edu	37	9	77448983	77448983	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77448983T>G	uc004ajl.1	-	6	838	c.600A>C	c.(598-600)AGA>AGC	p.R200S	TRPM6_uc004ajk.1_Missense_Mutation_p.R195S|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Missense_Mutation_p.R200S|TRPM6_uc010mpd.1_Missense_Mutation_p.R200S|TRPM6_uc010mpe.1_Missense_Mutation_p.R200S|TRPM6_uc004ajn.1_Missense_Mutation_p.R200S	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	200	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						TCCAGATTTTTCTCAAGGAAT	0.403													12	186	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	17032435	17032435	+	Silent	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17032435C>T	uc001ioo.2	-	29	4300	c.4248G>A	c.(4246-4248)GAG>GAA	p.E1416E		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1416	CUB 9.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACCAGATACACTCCTTGTTTG	0.517													13	147	---	---	---	---	PASS
EGR2	1959	broad.mit.edu	37	10	64573635	64573635	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64573635T>G	uc010qim.1	-	3	917	c.763A>C	c.(763-765)ACC>CCC	p.T255P	EGR2_uc010qin.1_Missense_Mutation_p.T205P|EGR2_uc001jmi.2_Missense_Mutation_p.T255P|EGR2_uc010qio.1_Missense_Mutation_p.T268P|EGR2_uc009xph.2_Missense_Mutation_p.T255P	NM_001136177	NP_001129649	P11161	EGR2_HUMAN	early growth response 2 protein isoform a	255					fat cell differentiation|protein export from nucleus|transcription from RNA polymerase II promoter	cytoplasm|nucleus	chromatin binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding			ovary(2)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					ACCCGCAGGGTGTCCAGTGGG	0.602													7	63	---	---	---	---	PASS
NRG3	10718	broad.mit.edu	37	10	84745233	84745233	+	Missense_Mutation	SNP	G	A	A	rs143042604	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84745233G>A	uc001kco.2	+	9	1990	c.1963G>A	c.(1963-1965)GTA>ATA	p.V655I	NRG3_uc010qlz.1_Missense_Mutation_p.V654I|NRG3_uc001kcp.2_Missense_Mutation_p.V458I|NRG3_uc001kcq.2_Missense_Mutation_p.V305I|NRG3_uc001kcr.2_Missense_Mutation_p.V329I	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	679	Cytoplasmic (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		ACTGGCCAGCGTAGAAACCGA	0.473													45	52	---	---	---	---	PASS
ZNF518A	9849	broad.mit.edu	37	10	97916435	97916435	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97916435T>G	uc001klp.2	+	6	1213	c.356T>G	c.(355-357)TTC>TGC	p.F119C	ZNF518A_uc001klo.1_Intron|ZNF518A_uc001klq.2_Missense_Mutation_p.F119C|ZNF518A_uc001klr.2_Missense_Mutation_p.F119C	NM_014803	NP_055618	Q6AHZ1	Z518A_HUMAN	zinc finger protein 518	119					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		ATACTCAATTTCAGCTGTTTA	0.388													13	277	---	---	---	---	PASS
OR5AK2	390181	broad.mit.edu	37	11	56756565	56756565	+	Silent	SNP	G	A	A	rs62001001	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56756565G>A	uc010rjp.1	+	1	177	c.177G>A	c.(175-177)ACG>ACA	p.T59T		NM_001005323	NP_001005323	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK,	59	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3						AAACACTCACGTACTTTTTTC	0.363													105	133	---	---	---	---	PASS
DAK	26007	broad.mit.edu	37	11	61111398	61111398	+	Silent	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61111398G>A	uc001nre.2	+	12	1310	c.1053G>A	c.(1051-1053)CGG>CGA	p.R351R	DDB1_uc010rlf.1_5'Flank|DAK_uc009ynm.1_Silent_p.R281R	NM_015533	NP_056348	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2	351					glycerol metabolic process	cytosol	ATP binding|FAD-AMP lyase (cyclizing) activity|glycerone kinase activity|metal ion binding				0						AGCGGAGCCGGGTAGCCCCTG	0.602													6	85	---	---	---	---	PASS
GAL3ST3	89792	broad.mit.edu	37	11	65812899	65812899	+	5'UTR	SNP	A	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65812899A>C	uc001ogv.2	-	1					GAL3ST3_uc001ogw.2_5'UTR	NM_033036	NP_149025	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3						monosaccharide metabolic process|oligosaccharide metabolic process|poly-N-acetyllactosamine metabolic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi cisterna membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|carbohydrate binding|galactosylceramide sulfotransferase activity|proteoglycan sulfotransferase activity			ovary(1)	1						CGGAGTACCCACCCCTGGACC	0.647											OREG0021093	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	25	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92568131	92568131	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92568131G>A	uc001pdj.3	+	14	9984	c.9967G>A	c.(9967-9969)GCT>ACT	p.A3323T		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	3323	Cadherin 30.|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)				AGCTCTCAGCGCTGTGGCCAC	0.498										TCGA Ovarian(4;0.039)			17	17	---	---	---	---	PASS
DDX6	1656	broad.mit.edu	37	11	118657025	118657025	+	5'UTR	SNP	T	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118657025T>A	uc001pub.2	-	2					DDX6_uc001puc.2_5'UTR	NM_004397	NP_004388	P26196	DDX6_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|RNA-induced silencing complex|stress granule	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|RNA helicase activity			ovary(1)	1	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)		GAAACTGTAATAACAGTTTAT	0.363			T	IGH@	B-NHL								12	31	---	---	---	---	PASS
VSIG2	23584	broad.mit.edu	37	11	124618255	124618255	+	Intron	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124618255C>T	uc001qas.2	-						VSIG2_uc001qat.2_3'UTR	NM_014312	NP_055127	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2							integral to plasma membrane|membrane fraction				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.215)	Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0215)		TTTCCTCCCTCCTTGCGCCAC	0.572													35	54	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49420423	49420423	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49420423C>A	uc001rta.3	-	48	15326	c.15326G>T	c.(15325-15327)TGC>TTC	p.C5109F		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	5109	RING-type 4; degenerate.		C -> F (in KABS).		chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						GACATTGGGGCAACGCATGCG	0.547			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			33	71	---	---	---	---	PASS
C12orf26	84190	broad.mit.edu	37	12	82792603	82792603	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82792603C>A	uc001szq.2	+	4	582	c.561C>A	c.(559-561)TAC>TAA	p.Y187*		NM_032230	NP_115606	Q8N6Q8	CL026_HUMAN	hypothetical protein LOC84190	187											0						GTAAAGGCTACCTAAGCTCTT	0.318													6	103	---	---	---	---	PASS
LHX5	64211	broad.mit.edu	37	12	113909233	113909233	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113909233G>A	uc001tvj.1	-	1	645	c.71C>T	c.(70-72)GCG>GTG	p.A24V		NM_022363	NP_071758	Q9H2C1	LHX5_HUMAN	LIM homeobox protein 5	24	LIM zinc-binding 1.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GATGTGCCACGCGCGGTCCAG	0.612													3	16	---	---	---	---	PASS
SCARB1	949	broad.mit.edu	37	12	125348169	125348169	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125348169G>C	uc001ugo.3	-	1	351	c.98C>G	c.(97-99)CCG>CGG	p.P33R	SCARB1_uc001ugn.3_Missense_Mutation_p.P33R|SCARB1_uc001ugm.3_Missense_Mutation_p.P33R|SCARB1_uc010tbd.1_Missense_Mutation_p.P33R|SCARB1_uc001ugp.3_Missense_Mutation_p.P33R	NM_005505	NP_005496	Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1 isoform 1	33	Extracellular (Potential).				adhesion to symbiont|cell adhesion|cholesterol efflux|cholesterol homeostasis|cholesterol import|detection of lipopolysaccharide|high-density lipoprotein particle clearance|high-density lipoprotein particle remodeling|lipopolysaccharide transport|lipoprotein metabolic process|positive regulation of cholesterol storage|positive regulation of endothelial cell migration|positive regulation of nitric-oxide synthase activity|recognition of apoptotic cell|reverse cholesterol transport|triglyceride homeostasis|wound healing	caveola	1-phosphatidylinositol binding|apolipoprotein A-I binding|high-density lipoprotein particle receptor activity|lipopolysaccharide receptor activity|low-density lipoprotein particle binding|phosphatidylserine binding|transporter activity			kidney(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	GATGAGCGACGGCACCATCAC	0.716													3	15	---	---	---	---	PASS
TPTE2	93492	broad.mit.edu	37	13	20024290	20024290	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20024290A>G	uc001umd.2	-	14	1110	c.899T>C	c.(898-900)TTC>TCC	p.F300S	TPTE2_uc009zzk.2_RNA|TPTE2_uc009zzl.2_Missense_Mutation_p.F189S|TPTE2_uc001ume.2_Missense_Mutation_p.F223S|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_RNA	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	300	Phosphatase tensin-type.					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TTCCTTGGTGAAAACCACCAT	0.323													11	185	---	---	---	---	PASS
USP12	219333	broad.mit.edu	37	13	27649444	27649444	+	Silent	SNP	T	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27649444T>A	uc001uqy.2	-	7	1069	c.816A>T	c.(814-816)ACA>ACT	p.T272T		NM_182488	NP_872294	O75317	UBP12_HUMAN	ubiquitin thiolesterase 12	272					protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)	1		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		AAGAGAGTTTTGTATATCGAT	0.358													42	61	---	---	---	---	PASS
C14orf135	64430	broad.mit.edu	37	14	60591549	60591549	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60591549A>G	uc001xer.3	+	8	2480	c.1958A>G	c.(1957-1959)GAC>GGC	p.D653G	C14orf135_uc001xeq.2_Missense_Mutation_p.D653G|C14orf135_uc010apm.2_RNA	NM_022495	NP_071940	Q63HM2	CN135_HUMAN	hepatitis C virus F protein-binding protein 2	887						integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)		CCTGCTGTTGACAAAGGAAAA	0.438													13	384	---	---	---	---	PASS
VIPAR	63894	broad.mit.edu	37	14	77896064	77896064	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77896064C>T	uc001xtt.1	-	18	1564	c.1226G>A	c.(1225-1227)CGG>CAG	p.R409Q	VIPAR_uc001xtu.1_Missense_Mutation_p.R409Q|VIPAR_uc010tvj.1_Missense_Mutation_p.R360Q|VIPAR_uc001xtv.1_Missense_Mutation_p.R409Q	NM_022067	NP_071350	Q9H9C1	VIPAR_HUMAN	hypothetical protein LOC63894	409					endosome to lysosome transport|intracellular protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	early endosome|late endosome|recycling endosome	protein binding			central_nervous_system(1)	1						TTCGACAACCCGATGGAAGCC	0.502													25	414	---	---	---	---	PASS
TECPR2	9895	broad.mit.edu	37	14	102891314	102891314	+	Splice_Site	SNP	A	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102891314A>T	uc001ylw.1	+	6	787	c.639_splice	c.e6-2	p.S213_splice	TECPR2_uc010txw.1_Intron|TECPR2_uc010awl.2_Splice_Site_p.S213_splice|TECPR2_uc010txx.1_Intron	NM_014844	NP_055659	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2								protein binding			lung(1)|central_nervous_system(1)|skin(1)	3						TTCTAATTTTAGTACTGGGAA	0.383													4	137	---	---	---	---	PASS
MARK3	4140	broad.mit.edu	37	14	103918266	103918266	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103918266G>A	uc001ymz.3	+	5	1024	c.358G>A	c.(358-360)GAA>AAA	p.E120K	MARK3_uc001ymx.3_Missense_Mutation_p.E120K|MARK3_uc001ymw.3_Missense_Mutation_p.E120K|MARK3_uc001yna.3_Missense_Mutation_p.E120K|MARK3_uc001ymy.3_Missense_Mutation_p.E120K|MARK3_uc010awp.2_Missense_Mutation_p.E120K	NM_001128918	NP_001122390	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	120	Protein kinase.						ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)			GAAGTTATTCGAAGTCATTGA	0.353													26	337	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105419145	105419145	+	Silent	SNP	G	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105419145G>C	uc010axc.1	-	7	2763	c.2643C>G	c.(2641-2643)CTC>CTG	p.L881L	AHNAK2_uc001ypx.2_Silent_p.L781L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	881						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCTGAATGCTGAGGTCAGTGG	0.652													5	346	---	---	---	---	PASS
TJP1	7082	broad.mit.edu	37	15	30025006	30025006	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30025006C>A	uc001zcr.2	-	14	2225	c.1750G>T	c.(1750-1752)GCC>TCC	p.A584S	TJP1_uc010azl.2_Missense_Mutation_p.A572S|TJP1_uc001zcq.2_Missense_Mutation_p.A588S|TJP1_uc001zcs.2_Missense_Mutation_p.A584S	NM_003257	NP_003248	Q07157	ZO1_HUMAN	tight junction protein 1 isoform a	584	SH3.				cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TGTACACTGGCTAGCTGCTCA	0.403													40	45	---	---	---	---	PASS
ARHGAP11B	89839	broad.mit.edu	37	15	30925726	30925726	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30925726A>C	uc001zet.1	+	3	379	c.234A>C	c.(232-234)GAA>GAC	p.E78D	ARHGAP11B_uc010azv.1_RNA|ARHGAP11B_uc001zeu.2_RNA	NM_001039841	NP_001034930	Q3KRB8	RHGBB_HUMAN	Rho GTPase activating protein 11B	78	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		CTTTAGAAGAACATATTCATA	0.373													4	186	---	---	---	---	PASS
PML	5371	broad.mit.edu	37	15	74328422	74328422	+	Intron	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74328422C>A	uc002awv.2	+						PML_uc002awm.2_3'UTR|PML_uc002awl.2_3'UTR|PML_uc002awj.1_3'UTR|PML_uc002awk.2_3'UTR|PML_uc002awn.2_3'UTR|PML_uc002awo.2_3'UTR|PML_uc002awp.2_3'UTR|PML_uc002awq.2_Intron|PML_uc002awr.2_Intron|PML_uc002aws.2_Intron|PML_uc002awt.2_Intron|PML_uc002awu.2_Intron|PML_uc010ule.1_Intron|PML_uc002awx.2_3'UTR|PML_uc002awy.2_3'UTR	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1						cell cycle arrest|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 induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5						aggaatgaatCAACGAATGAA	0.373			T	RARA|PAX5	APL|ALL								5	277	---	---	---	---	PASS
DET1	55070	broad.mit.edu	37	15	89074916	89074916	+	Silent	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89074916G>A	uc002bmr.2	-	2	173	c.21C>T	c.(19-21)ACC>ACT	p.T7T	DET1_uc002bmp.3_RNA|DET1_uc010bnk.2_RNA|DET1_uc002bmq.2_Silent_p.T18T	NM_001144074	NP_001137546	Q7L5Y6	DET1_HUMAN	de-etiolated 1 isoform 2	7						nucleus				lung(1)|pancreas(1)	2	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)			GAGGCTTGATGGTAGAAACAT	0.413													3	106	---	---	---	---	PASS
PIGQ	9091	broad.mit.edu	37	16	633353	633353	+	Missense_Mutation	SNP	T	C	C	rs710924	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:633353T>C	uc002cho.2	+	10	2104	c.2002T>C	c.(2002-2004)TGT>CGT	p.C668R	PIGQ_uc010bqw.2_3'UTR|PIGQ_uc002chn.2_3'UTR|PIGQ_uc010uui.1_3'UTR|PIGQ_uc002chp.2_Missense_Mutation_p.C238R|uc010uuj.1_Missense_Mutation_p.T145A	NM_148920	NP_683721	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	668					C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)				GCCCACCCTGTGTACCCAGGT	0.692													3	177	---	---	---	---	PASS
NOMO2	283820	broad.mit.edu	37	16	18555076	18555076	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18555076G>A	uc002dfe.2	-	7	670	c.598C>T	c.(598-600)CGT>TGT	p.R200C	NOMO2_uc002dff.2_Missense_Mutation_p.R200C|NOMO2_uc010bvx.2_Missense_Mutation_p.R33C	NM_001004060	NP_001004060	Q5JPE7	NOMO2_HUMAN	nodal modulator 2 isoform 1	200	Lumenal (Potential).					endoplasmic reticulum membrane|integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			skin(1)	1						ttggttacacgcactgtggtg	0.239													28	81	---	---	---	---	PASS
NOB1	28987	broad.mit.edu	37	16	69776170	69776170	+	3'UTR	SNP	A	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69776170A>G	uc002exs.2	-	9						NM_014062	NP_054781	Q9ULX3	NOB1_HUMAN	nin one binding protein							nucleus	metal ion binding|protein binding				0						ACGGCTGGGGAAATGGGTCAC	0.602													5	24	---	---	---	---	PASS
CRISPLD2	83716	broad.mit.edu	37	16	84906612	84906612	+	Silent	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84906612C>T	uc010voh.1	+	10	1223	c.996C>T	c.(994-996)TGC>TGT	p.C332C	CRISPLD2_uc010vog.1_Intron|CRISPLD2_uc002fio.2_Silent_p.C331C|CRISPLD2_uc002fim.2_Silent_p.C332C|CRISPLD2_uc002fin.3_Silent_p.C332C	NM_031476	NP_113664	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain	332	LCCL 1.					extracellular region|transport vesicle					0						CTAGCATATGCCGCGCCGCCA	0.542													5	184	---	---	---	---	PASS
AMAC1L3	643664	broad.mit.edu	37	17	7386301	7386301	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7386301A>C	uc010cmj.1	+	2	1113	c.998A>C	c.(997-999)GAA>GCA	p.E333A	ZBTB4_uc002ghd.3_Intron|POLR2A_uc002ghe.2_5'Flank|POLR2A_uc002ghf.3_5'Flank	NM_001102614	NP_001096084	P0C7Q6	AMCL3_HUMAN	acyl-malonyl condensing enzyme 1-like 3	333						integral to membrane					0		Prostate(122;0.173)				TGTGAGAGGGAAGGGAAGGTG	0.557													3	77	---	---	---	---	PASS
KRTAP3-3	85293	broad.mit.edu	37	17	39150166	39150166	+	Missense_Mutation	SNP	C	T	T	rs146610892	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39150166C>T	uc002hvr.1	-	1	220	c.184G>A	c.(184-186)GTG>ATG	p.V62M		NM_033185	NP_149441	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	62						keratin filament	structural molecule activity				0		Breast(137;0.00043)				CAGGTGGGCACGCAGGGCTGA	0.632													5	149	---	---	---	---	PASS
DHX40	79665	broad.mit.edu	37	17	57679935	57679935	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57679935G>A	uc002ixn.1	+	15	2006	c.1859G>A	c.(1858-1860)CGA>CAA	p.R620Q	DHX40_uc010woe.1_Missense_Mutation_p.R543Q|DHX40_uc010wof.1_Missense_Mutation_p.R135Q	NM_024612	NP_078888	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	620							ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GAAGTACTACGAAGATGTCTT	0.338													50	109	---	---	---	---	PASS
PITPNC1	26207	broad.mit.edu	37	17	65688807	65688807	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65688807G>A	uc002jgc.2	+	9	1149	c.802G>A	c.(802-804)GTC>ATC	p.V268I	PITPNC1_uc002jgb.2_3'UTR	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein,	268					signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			GCCTTCTTCCGTCCGCAGTGC	0.557													34	153	---	---	---	---	PASS
ENPP7	339221	broad.mit.edu	37	17	77711840	77711840	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77711840G>A	uc002jxa.2	+	5	1392	c.1372G>A	c.(1372-1374)GCA>ACA	p.A458T		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	458					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			central_nervous_system(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GTCTGAGGTCGCATAACGCCC	0.642													4	117	---	---	---	---	PASS
AFG3L2	10939	broad.mit.edu	37	18	12358924	12358924	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12358924C>A	uc002kqz.1	-	8	884	c.771G>T	c.(769-771)ATG>ATT	p.M257I		NM_006796	NP_006787	Q9Y4W6	AFG32_HUMAN	AFG3 ATPase family gene 3-like 2	257	Helical; (Potential).				cell death|protein catabolic process|proteolysis	integral to membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0					Adenosine triphosphate(DB00171)	CCGTAGGCAGCATGCTCAGCA	0.552													3	33	---	---	---	---	PASS
MED16	10025	broad.mit.edu	37	19	881676	881676	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:881676G>T	uc002lqd.1	-	7	1175	c.1024C>A	c.(1024-1026)CTA>ATA	p.L342I	MED16_uc010drw.1_Missense_Mutation_p.L167I|MED16_uc002lqe.2_Missense_Mutation_p.L331I|MED16_uc002lqf.2_Missense_Mutation_p.L331I|MED16_uc010xfv.1_Intron|MED16_uc010xfw.1_Missense_Mutation_p.L331I|MED16_uc010xfx.1_Missense_Mutation_p.L187I|MED16_uc010xfy.1_Intron	NM_005481	NP_005472	Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	342					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		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)		GTGGCCGATAGGATCCGCCAT	0.577													4	136	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	38976722	38976722	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38976722C>A	uc002oit.2	+	34	5557	c.5427C>A	c.(5425-5427)GAC>GAA	p.D1809E	RYR1_uc002oiu.2_Missense_Mutation_p.D1809E	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	1809	Cytoplasmic.|6 X approximate repeats.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	CCCTGCGGGACAAGGCACTGA	0.711													43	57	---	---	---	---	PASS
CYP2A7	1549	broad.mit.edu	37	19	41530180	41530180	+	Intron	SNP	G	A	A	rs143122474	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41530180G>A	uc002opo.2	-						uc002ops.1_RNA	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCTTGCATGCGGATGAGAAAC	0.582													9	20	---	---	---	---	PASS
ZNF71	58491	broad.mit.edu	37	19	57133835	57133835	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57133835C>A	uc002qnm.3	+	3	1418	c.1180C>A	c.(1180-1182)CGC>AGC	p.R394S		NM_021216	NP_067039	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	394	C2H2-type 10.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		CTTCACGGGGCGCTCGTCCCT	0.627													3	58	---	---	---	---	PASS
A1BG	1	broad.mit.edu	37	19	58863782	58863782	+	Silent	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58863782C>T	uc002qsd.3	-	4	542	c.480G>A	c.(478-480)GAG>GAA	p.E160E	NCRNA00181_uc002qse.2_Intron|A1BG_uc002qsf.1_RNA|NCRNA00181_uc002qsg.2_RNA	NM_130786	NP_570602	P04217	A1BG_HUMAN	alpha 1B-glycoprotein precursor	160	Ig-like V-type 2.					extracellular region					0		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)		CCTCAGGCACCTCCAGAAACT	0.627													12	207	---	---	---	---	PASS
PHF20	51230	broad.mit.edu	37	20	34389529	34389529	+	Splice_Site	SNP	T	G	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34389529T>G	uc002xek.1	+	2	194	c.83_splice	c.e2+2	p.W28_splice	PHF20_uc002xei.1_Splice_Site_p.W28_splice|PHF20_uc010gfo.1_Splice_Site_p.W28_splice|PHF20_uc002xej.1_Splice_Site|PHF20_uc002xeh.2_Splice_Site	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)					AAAAAACTGGTACTTTTACAT	0.413													4	74	---	---	---	---	PASS
C20orf111	51526	broad.mit.edu	37	20	42826279	42826279	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42826279T>C	uc002xlk.2	-	4	429	c.292A>G	c.(292-294)ATA>GTA	p.I98V		NM_016470	NP_057554	Q9NX31	CT111_HUMAN	oxidative stress responsive 1	98											0		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			GAAGACGCTATTGTACTGCAA	0.488													21	159	---	---	---	---	PASS
MATN4	8785	broad.mit.edu	37	20	43926838	43926838	+	Silent	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43926838C>T	uc002xnn.2	-	7	1585	c.1398G>A	c.(1396-1398)TCG>TCA	p.S466S	MATN4_uc002xno.2_Silent_p.S425S|MATN4_uc002xnp.2_Silent_p.S384S|MATN4_uc010zwr.1_Silent_p.S414S|MATN4_uc002xnr.1_Silent_p.S466S	NM_003833	NP_003824	O95460	MATN4_HUMAN	matrilin 4 isoform 1 precursor	507	VWFA 2.					extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)				CTGCCCACACCGAGATGTCAT	0.672													5	73	---	---	---	---	PASS
SRMS	6725	broad.mit.edu	37	20	62178595	62178595	+	Silent	SNP	G	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62178595G>A	uc002yfi.1	-	1	263	c.222C>T	c.(220-222)CGC>CGT	p.R74R		NM_080823	NP_543013	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory	74	SH3.						ATP binding|non-membrane spanning protein tyrosine kinase activity			stomach(1)|lung(1)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			GCCTGTCCCCGCGGCGGACAC	0.701													28	359	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	11014952	11014952	+	RNA	SNP	A	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11014952A>T	uc002yis.1	-	7		c.1494T>A						P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CACATTGTCTACATTGCAGAA	0.333													4	91	---	---	---	---	PASS
C22orf25	128989	broad.mit.edu	37	22	20024388	20024388	+	Intron	SNP	C	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20024388C>A	uc010grw.1	+						C22orf25_uc002zrb.1_Intron|C22orf25_uc002zrc.1_Intron|C22orf25_uc002zrd.1_Intron|C22orf25_uc002zre.2_Intron|C22orf25_uc010grx.2_Intron|C22orf25_uc011ahe.1_Intron|C22orf25_uc011ahf.1_Intron|C22orf25_uc011ahg.1_5'UTR|C22orf25_uc002zrg.2_5'UTR|C22orf25_uc011ahh.1_Intron|C22orf25_uc002zrf.2_Intron|C22orf25_uc011ahi.1_Intron|C22orf25_uc010gry.1_RNA|C22orf25_uc002zrh.1_5'UTR	NM_152906	NP_690870	Q6ICL3	CV025_HUMAN	hypothetical protein LOC128989												0	Colorectal(54;0.0533)					GTAACCCCCTCGCTCTGCATC	0.607													3	111	---	---	---	---	PASS
APOBEC3D	140564	broad.mit.edu	37	22	39421246	39421246	+	Silent	SNP	C	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39421246C>T	uc011aoe.1	+	3	436	c.382C>T	c.(382-384)CTG>TTG	p.L128L	APOBEC3D_uc011aod.1_Silent_p.L128L|APOBEC3D_uc011aof.1_Intron|APOBEC3D_uc003awu.3_Intron|APOBEC3D_uc003awt.3_Silent_p.L128L|APOBEC3D_uc010gxu.2_Intron	NM_152426	NP_689639	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic	128					negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding				0	Melanoma(58;0.04)					CAATGTCACCCTGACCATCTC	0.572													7	103	---	---	---	---	PASS
TCTEX1D1	200132	broad.mit.edu	37	1	67242261	67242262	+	Intron	DEL	TA	-	-	rs60960124		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67242261_67242262delTA	uc001dcv.2	+						TCTEX1D1_uc009wau.2_Intron|TCTEX1D1_uc009wav.2_Intron	NM_152665	NP_689878	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1												0						tgtgtgtgtgtATATACATAAA	0.233													5	5	---	---	---	---	
FAM72B	653820	broad.mit.edu	37	1	120839655	120839657	+	5'UTR	DEL	CTT	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120839655_120839657delCTT	uc009whp.2	+	1					FAM72B_uc001ein.3_5'UTR	NM_001100910	NP_001094380	Q86X60	FA72B_HUMAN	hypothetical protein LOC653820												0	all_neural(166;0.181)	all_lung(203;7.27e-05)|Lung NSC(69;0.000389)|all_epithelial(167;0.068)		Lung(183;0.0327)|LUSC - Lung squamous cell carcinoma(189;0.19)		TCAATAAATACTTCTTCTACTCC	0.429													4	2	---	---	---	---	
RPRD2	23248	broad.mit.edu	37	1	150390386	150390387	+	Intron	INS	-	TCTC	TCTC	rs140431392	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150390386_150390387insTCTC	uc009wlr.2	+						RPRD2_uc010pcc.1_Intron|RPRD2_uc001eup.3_Intron	NM_015203	NP_056018	Q5VT52	RPRD2_HUMAN	Regulation of nuclear pre-mRNA domain containing								protein binding			ovary(1)	1						tcttttctttttctctctctct	0.104													4	2	---	---	---	---	
IFI16	3428	broad.mit.edu	37	1	158990473	158990473	+	Intron	DEL	T	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158990473delT	uc001ftg.2	+						IFI16_uc010pis.1_Intron	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16						cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)					CTTTTTTTAATTTTTTTTTTC	0.274													5	4	---	---	---	---	
BAT2L2	23215	broad.mit.edu	37	1	171483662	171483663	+	Intron	INS	-	T	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171483662_171483663insT	uc010pmg.1	+						BAT2L2_uc001ghq.1_Intron|BAT2L2_uc001ghr.1_Intron	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2								protein C-terminus binding				0						ATGGATTCATATTTTTTTTTAA	0.361													4	2	---	---	---	---	
OR2L13	284521	broad.mit.edu	37	1	248167233	248167233	+	Intron	DEL	A	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248167233delA	uc001ids.2	+							NM_175911	NP_787107	Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			TGTAATCTCCAACAGAGGACA	0.507													159	62	---	---	---	---	
POLR1B	84172	broad.mit.edu	37	2	113310210	113310210	+	Intron	DEL	C	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113310210delC	uc002thw.2	+						POLR1B_uc010fkn.2_Intron|POLR1B_uc002thx.2_Intron|POLR1B_uc010fko.2_Intron|POLR1B_uc010fkp.2_Intron|POLR1B_uc010yxn.1_Intron|POLR1B_uc002thy.2_Intron|POLR1B_uc010yxo.1_Intron	NM_019014	NP_061887	Q9H9Y6	RPA2_HUMAN	RNA polymerase I polypeptide B isoform 1						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(1)	1						TTTTTTTTTTCTGTTTTCACA	0.308													171	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	40418607	40418610	+	IGR	DEL	AGGA	-	-	rs112497421		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40418607_40418610delAGGA								EIF1B (64694 upstream) : ENTPD3 (10063 downstream)																							ggagggagggaggaaggaaggaag	0.000													5	3	---	---	---	---	
PDS5A	23244	broad.mit.edu	37	4	39827205	39827205	+	Intron	DEL	T	-	-	rs72009420		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39827205delT	uc003guv.3	-						PDS5A_uc010ifo.2_Intron	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0						ATCTAAAATCttttttttttt	0.149													9	4	---	---	---	---	
C5orf44	80006	broad.mit.edu	37	5	64948169	64948170	+	Intron	INS	-	TC	TC			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64948169_64948170insTC	uc003jtz.3	+						C5orf44_uc003jua.3_Intron|C5orf44_uc003juc.3_Intron|C5orf44_uc010iwv.2_Intron	NM_024941	NP_079217	A5PLN9	CE044_HUMAN	hypothetical protein LOC80006 isoform 2											ovary(1)	1						ttcttttctttttttttttttt	0.158													2	6	---	---	---	---	
DMGDH	29958	broad.mit.edu	37	5	78326471	78326472	+	Intron	DEL	AA	-	-	rs10540579		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78326471_78326472delAA	uc003kfs.2	-						DMGDH_uc011cte.1_Intron|DMGDH_uc011ctf.1_Intron|DMGDH_uc011ctg.1_Intron	NM_013391	NP_037523	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase precursor						choline metabolic process|glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|dimethylglycine dehydrogenase activity|electron carrier activity			ovary(2)|liver(1)|skin(1)	4		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		tctgtctctcaaaaaaaaaaaa	0.114													3	3	---	---	---	---	
FAM81B	153643	broad.mit.edu	37	5	94755802	94755805	+	Intron	DEL	CAAA	-	-	rs145960524		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94755802_94755805delCAAA	uc003kla.1	+						FAM81B_uc010jbe.1_Intron	NM_152548	NP_689761	Q96LP2	FA81B_HUMAN	hypothetical protein LOC153643											ovary(1)|skin(1)	2		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		cacctagaatcaaaccactgctgc	0.157													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	834408	834411	+	IGR	DEL	CCTA	-	-	rs72349013		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:834408_834411delCCTA								EXOC2 (141299 upstream) : LOC285768 (126831 downstream)																							ttccttccttcctaccttccttcc	0.123													6	8	---	---	---	---	
COL19A1	1310	broad.mit.edu	37	6	70866387	70866388	+	Intron	DEL	GA	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70866387_70866388delGA	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						tatgtatatGgagagagagaga	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92356678	92356679	+	Intron	DEL	AA	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92356678_92356679delAA	uc003pod.2	-											Homo sapiens cDNA clone IMAGE:5284581.																		aattttagccAAAAAAAAAAAA	0.045													6	5	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151853293	151853293	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151853293delC	uc003wla.2	-	45	12028	c.11809delG	c.(11809-11811)GAAfs	p.E3937fs	MLL3_uc003wkz.2_Frame_Shift_Del_p.E3055fs|MLL3_uc003wkx.2_Frame_Shift_Del_p.E95fs|MLL3_uc003wky.2_Frame_Shift_Del_p.E1501fs	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	3937					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)		ATCATACCTTCATGGCTCACT	0.438			N		medulloblastoma								271	22	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151859486	151859487	+	Frame_Shift_Ins	INS	-	TT	TT			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151859486_151859487insTT	uc003wla.2	-	43	11394_11395	c.11175_11176insAA	c.(11173-11178)ACAGAGfs	p.T3725fs	MLL3_uc003wkz.2_Frame_Shift_Ins_p.T2786fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.T1234fs	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	3725_3726					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)		GGGCAGGACTCTGTCTCAGCCT	0.480			N		medulloblastoma								455	196	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151873437	151873437	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151873437delG	uc003wla.2	-	38	9320	c.9101delC	c.(9100-9102)CCTfs	p.P3034fs	MLL3_uc003wkz.2_Frame_Shift_Del_p.P2095fs|MLL3_uc003wky.2_Frame_Shift_Del_p.P543fs	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	3034	Gln-rich.				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)		TAATGTTTGAGGAATCATTAG	0.473			N		medulloblastoma								145	61	---	---	---	---	
DDHD2	23259	broad.mit.edu	37	8	38090389	38090391	+	Intron	DEL	TTG	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38090389_38090391delTTG	uc003xlb.2	+						DDHD2_uc003xla.2_Intron|DDHD2_uc003xlc.2_Intron|DDHD2_uc011lbl.1_5'Flank	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1						lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			TATGTAGATTTTGTTGTTGTTGT	0.340													4	2	---	---	---	---	
DSCC1	79075	broad.mit.edu	37	8	120850633	120850638	+	In_Frame_Del	DEL	CACCAG	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120850633_120850638delCACCAG	uc003yov.2	-	8	1069_1074	c.934_939delCTGGTG	c.(934-939)CTGGTGdel	p.LV312del		NM_024094	NP_076999	Q9BVC3	DCC1_HUMAN	defective in sister chromatid cohesion 1	312_313					DNA replication|maintenance of mitotic sister chromatid cohesion|post-translational protein acetylation|regulation of DNA replication	chromatin|chromosome, centromeric region|nucleoplasm	DNA binding|protein binding			pancreas(1)	1	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			AGTGTCTATCCACCAGCGCTAAACCC	0.364													170	47	---	---	---	---	
CYC1	1537	broad.mit.edu	37	8	145151373	145151373	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145151373delA	uc003zaz.3	+	4	630	c.587delA	c.(586-588)GACfs	p.D196fs	CYC1_uc003zay.2_Frame_Shift_Del_p.D137fs	NM_001916	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	196	Cytochrome c.				respiratory electron transport chain|transport	cell junction|integral to membrane|mitochondrial inner membrane|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding				0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TTGCCCCCTGACCTCAGCTAC	0.577											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	145	20	---	---	---	---	
C9orf84	158401	broad.mit.edu	37	9	114489999	114490000	+	Frame_Shift_Ins	INS	-	CCAAA	CCAAA			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114489999_114490000insCCAAA	uc004bfr.2	-	11	1690_1691	c.1555_1556insTTTGG	c.(1555-1557)GACfs	p.D519fs	C9orf84_uc011lwt.1_RNA|C9orf84_uc004bfq.2_Frame_Shift_Ins_p.D480fs|C9orf84_uc010mug.2_Frame_Shift_Ins_p.D465fs	NM_173521	NP_775792	Q5VXU9	CI084_HUMAN	hypothetical protein LOC158401 isoform 1	519										ovary(2)	2						GCTCAAAAGGTCCAAATCATTC	0.332													327	22	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122796240	122796249	+	IGR	DEL	TGTGTGTGTG	-	-	rs2416748		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122796240_122796249delTGTGTGTGTG								DBC1 (664501 upstream) : MIR147 (211008 downstream)																							ctcacatatttgtgtgtgtgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	123575649	123575650	+	IGR	DEL	GT	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123575649_123575650delGT								LOC402377 (14640 upstream) : PSMD5 (2684 downstream)																							TGGAAAAAAAgtgtgtgtgtgt	0.302													4	2	---	---	---	---	
KCNT1	57582	broad.mit.edu	37	9	138606581	138606582	+	Intron	INS	-	GG	GG	rs141291153	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138606581_138606582insGG	uc011mdq.1	+						KCNT1_uc011mdr.1_Intron|KCNT1_uc010nbf.2_Intron	NM_020822	NP_065873	Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1							membrane	binding|calcium-activated potassium channel activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		GGACCGGGCGCGGGGTGGGGGC	0.614													8	5	---	---	---	---	
HECTD2	143279	broad.mit.edu	37	10	93252270	93252271	+	Intron	DEL	TG	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93252270_93252271delTG	uc001khl.2	+						LOC100188947_uc010qnl.1_Intron|HECTD2_uc010qnm.1_Intron|HECTD2_uc001khm.2_Intron|HECTD2_uc009xty.1_Intron|HECTD2_uc001khn.1_Intron	NM_182765	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing 2 isoform a						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			skin(1)	1						TTTTATAAACTGTGTTTCTTCA	0.302													117	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	126555975	126555975	+	IGR	DEL	G	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126555975delG								FAM175B (30737 upstream) : ZRANB1 (72997 downstream)																							aaaaaaaaaagaaaaagaaaG	0.254													4	2	---	---	---	---	
FAR1	84188	broad.mit.edu	37	11	13722198	13722199	+	Intron	INS	-	TCT	TCT	rs137872059	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13722198_13722199insTCT	uc001mld.2	+						FAR1_uc009ygp.2_Intron	NM_032228	NP_115604	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1						ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2						TAAAAGAATTCTCTTCTTCTTC	0.317													4	3	---	---	---	---	
SAA4	6291	broad.mit.edu	37	11	18253712	18253713	+	Intron	INS	-	AGCCCCTGCACCC	AGCCCCTGCACCC	rs143986842	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18253712_18253713insAGCCCCTGCACCC	uc001mny.2	-							NM_006512	NP_006503	P35542	SAA4_HUMAN	serum amyloid A4, constitutive precursor						acute-phase response	high-density lipoprotein particle					0						ttacaggtgtgagcccctgcac	0.208													3	3	---	---	---	---	
ATL3	25923	broad.mit.edu	37	11	63400292	63400293	+	Intron	INS	-	CAAAA	CAAAA			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63400292_63400293insCAAAA	uc001nxk.1	-						ATL3_uc010rms.1_Intron|ATL3_uc010rmr.1_Intron	NM_015459	NP_056274	Q6DD88	ATLA3_HUMAN	atlastin 3						endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			pancreas(1)	1						TATTTGCTATTcaaaacaaaac	0.257													16	7	---	---	---	---	
ATM	472	broad.mit.edu	37	11	108206869	108206869	+	Intron	DEL	A	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108206869delA	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)		acaaaaagttaaaaaaaaaaa	0.000			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)			3	4	---	---	---	---	
OR10S1	219873	broad.mit.edu	37	11	123848637	123848639	+	5'Flank	DEL	ATT	-	-	rs34866186		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123848637_123848639delATT	uc001pzm.1	-							NM_001004474	NP_001004474	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GACTGTAAGAATTATTTGCAGAA	0.310													1	5	---	---	---	---	
CDKN1B	1027	broad.mit.edu	37	12	12870803	12870803	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12870803delC	uc001rat.2	+	1	502	c.30delC	c.(28-30)AGCfs	p.S10fs		NM_004064	NP_004055	P46527	CDN1B_HUMAN	cyclin-dependent kinase inhibitor 1B	10				S->E: Increased stability in vivo and in vitro.|S->A: Loss of phosphorylation by UHMK1. No translocation to the cytoplasm. Greater cell cycle arrest.|S->D: Exported to the cytoplasm. Inhibits cell cycle arrest.	autophagic cell death|cell cycle arrest|cellular response to lithium ion|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process|S phase of mitotic cell cycle	cytosol|endosome|nucleoplasm	cyclin-dependent protein kinase inhibitor activity|protein phosphatase binding|transforming growth factor beta receptor, cytoplasmic mediator activity			ovary(1)|lung(1)	2		Prostate(47;0.0322)|all_epithelial(100;0.159)		BRCA - Breast invasive adenocarcinoma(232;0.0336)		CTAACGGGAGCCCTAGCCTGG	0.607									Multiple_Endocrine_Neoplasia_type_1|Multiple_Endocrine_Neoplasia_type_4				77	10	---	---	---	---	
PDE3A	5139	broad.mit.edu	37	12	20799402	20799403	+	Intron	DEL	TG	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20799402_20799403delTG	uc001reh.1	+							NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A						lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)	4	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)	AACTGATGACTGTTCCTGTTCA	0.406													122	11	---	---	---	---	
ARID2	196528	broad.mit.edu	37	12	46246234	46246241	+	Frame_Shift_Del	DEL	GTGGTACT	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46246234_46246241delGTGGTACT	uc001ros.1	+	15	4328_4335	c.4328_4335delGTGGTACT	c.(4327-4335)AGTGGTACTfs	p.S1443fs	ARID2_uc001ror.2_Frame_Shift_Del_p.S1443fs|ARID2_uc009zkg.1_Frame_Shift_Del_p.S899fs|ARID2_uc009zkh.1_Frame_Shift_Del_p.S1070fs|ARID2_uc001rou.1_Frame_Shift_Del_p.S777fs	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1443_1445					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CAGCAATTTAGTGGTACTGATTTGCTTA	0.418													315	67	---	---	---	---	
FMNL3	91010	broad.mit.edu	37	12	50055744	50055744	+	Intron	DEL	C	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50055744delC	uc001ruv.1	-						FMNL3_uc001ruw.1_Intron|FMNL3_uc001ruu.1_Intron	NM_175736	NP_783863	Q8IVF7	FMNL3_HUMAN	formin-like 3 isoform 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4						CGGGGTGGTACTCACATGACA	0.483													126	43	---	---	---	---	
CPM	1368	broad.mit.edu	37	12	69252512	69252512	+	Intron	DEL	G	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69252512delG	uc001sup.2	-						CPM_uc001sur.2_Intron|CPM_uc001suq.2_Intron	NM_198320	NP_938079	P14384	CBPM_HUMAN	carboxypeptidase M precursor						anatomical structure morphogenesis|proteolysis	anchored to membrane|cytoplasm|nucleus|plasma membrane	metallocarboxypeptidase activity|zinc ion binding				0	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			GAATTTTTGTGGTTTTTTTTT	0.323													5	3	---	---	---	---	
CCDC60	160777	broad.mit.edu	37	12	119957682	119957683	+	Intron	DEL	TA	-	-	rs71900111	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119957682_119957683delTA	uc001txe.2	+						uc001txf.2_Intron	NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60											ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		tgtgtgtgtgtatacctgtgtg	0.168													6	3	---	---	---	---	
TPTE2	93492	broad.mit.edu	37	13	20000709	20000710	+	Intron	INS	-	TG	TG			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20000709_20000710insTG	uc001umd.2	-						TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_Intron|TPTE2_uc010tcl.1_Intron	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid							endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		AACGATAACAAAAGTTCCTTTT	0.292													63	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	36463290	36463291	+	IGR	INS	-	TCCT	TCCT	rs66569553		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36463290_36463291insTCCT								BRMS1L (122122 upstream) : MBIP (304473 downstream)																							GACCATATTTAtccttccttcc	0.158													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	39680968	39680968	+	IGR	DEL	A	-	-	rs35552069		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39680968delA								PNN (28547 upstream) : MIA2 (22157 downstream)																							actccatctcaaaaaaaaaaa	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	83762841	83762860	+	IGR	DEL	AGAGAAGAGAAGAGAAGAGA	-	-	rs34334130		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83762841_83762860delAGAGAAGAGAAGAGAAGAGA								None (None upstream) : None (None downstream)																							gctgtGAAAGagagaagagaagagaagagaagagaagaga	0.014													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	31085320	31085320	+	IGR	DEL	C	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31085320delC								ARHGAP11B (107511 upstream) : MTMR15 (110735 downstream)																							TTTCTTTTTTCTAGCCATGAT	0.403													4	2	---	---	---	---	
PRSS21	10942	broad.mit.edu	37	16	2867531	2867531	+	Intron	DEL	A	-	-	rs111876704		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2867531delA	uc002crt.2	+						PRSS21_uc002crs.2_Intron|PRSS21_uc002crr.2_Intron	NM_006799	NP_006790	Q9Y6M0	TEST_HUMAN	testisin isoform 1						proteolysis	anchored to membrane|cytoplasm|membrane fraction|plasma membrane	serine-type endopeptidase activity			ovary(1)|skin(1)	2						GAGGGGGTAGAGGGGGGCCTT	0.697													4	3	---	---	---	---	
VPS35	55737	broad.mit.edu	37	16	46694732	46694733	+	Intron	INS	-	AA	AA	rs33973421		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46694732_46694733insAA	uc002eef.3	-						VPS35_uc002eed.2_3'UTR|VPS35_uc002eee.2_Intron	NM_018206	NP_060676	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35						protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				TACTGACTATCAAAAAAAAAAA	0.203													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74419892	74419892	+	Intron	DEL	T	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74419892delT	uc010vmt.1	+											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		cctttctctcttttttttttt	0.169													6	3	---	---	---	---	
SLC47A1	55244	broad.mit.edu	37	17	19461211	19461211	+	Intron	DEL	A	-	-	rs138104299		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19461211delA	uc002gvy.1	+						SLC47A1_uc010vyy.1_Intron|SLC47A1_uc002gvx.2_Intron|SLC47A1_uc010vyz.1_Intron|SLC47A1_uc010cqp.1_Intron|SLC47A1_uc010cqq.1_Intron|SLC47A1_uc010vza.1_Intron|SLC47A1_uc010vzb.1_Intron|SLC47A1_uc010vzc.1_Intron	NM_018242	NP_060712	Q96FL8	S47A1_HUMAN	solute carrier family 47, member 1							integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)					CTTTCCCTCCAAAAAAAAAAA	0.279													6	4	---	---	---	---	
CCDC144NL	339184	broad.mit.edu	37	17	20768756	20768756	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20768756delT	uc002gyf.2	-	4	758	c.638delA	c.(637-639)AAGfs	p.K213fs	uc002gyg.1_5'Flank|uc002gyh.1_5'Flank	NM_001004306	NP_001004306	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family,	213											0						CACATGATTCTTCCCCTTTCT	0.368													162	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25773154	25773157	+	IGR	DEL	AGGC	-	-	rs55913500	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25773154_25773157delAGGC								WSB1 (132509 upstream) : KSR1 (25879 downstream)																							gaaagaAGGAAGGCAAGACAGagg	0.039													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	34295123	34295126	+	IGR	DEL	TCTC	-	-	rs150052095		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34295123_34295126delTCTC								LYZL6 (24452 upstream) : CCL16 (8410 downstream)																							tttctttctttctctctctctctc	0.127													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	65772734	65772734	+	IGR	DEL	A	-	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65772734delA								NOL11 (32468 upstream) : BPTF (49046 downstream)																							actccatctcaaaaaaaaaaa	0.229													4	2	---	---	---	---	
MRPS7	51081	broad.mit.edu	37	17	73259796	73259797	+	Intron	INS	-	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73259796_73259797insA	uc002jnm.3	+						GGA3_uc002jni.1_5'Flank|GGA3_uc002jnj.1_5'Flank|GGA3_uc010wrw.1_5'Flank|GGA3_uc002jnk.1_5'Flank|GGA3_uc010wrx.1_5'Flank|GGA3_uc010wry.1_5'Flank|GGA3_uc010wrz.1_5'Flank|MRPS7_uc002jnl.2_3'UTR|MRPS7_uc002jnn.3_Intron	NM_015971	NP_057055	Q9Y2R9	RT07_HUMAN	mitochondrial ribosomal protein S7 precursor						translation	cytosolic small ribosomal subunit|mitochondrion	protein binding|RNA binding|structural constituent of ribosome			central_nervous_system(1)	1	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)			cccgtctctacaaaaaaaacaa	0.000													4	2	---	---	---	---	
MYO5B	4645	broad.mit.edu	37	18	47501149	47501150	+	Intron	INS	-	CA	CA	rs146410387	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47501149_47501150insCA	uc002leb.2	-						MYO5B_uc002lec.1_Intron	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		GCAGTCTCTCTcacacacacac	0.426													4	3	---	---	---	---	
C19orf6	91304	broad.mit.edu	37	19	1014538	1014547	+	Intron	DEL	CGTGATGGGG	-	-	rs143052245		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1014538_1014547delCGTGATGGGG	uc002lqr.1	-						C19orf6_uc002lqq.1_5'Flank|C19orf6_uc002lqs.1_Intron	NM_001033026	NP_001028198	Q4ZIN3	MBRL_HUMAN	membralin isoform 1							cytoplasm|integral to membrane				pancreas(2)|breast(1)	3		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		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)|GBM - Glioblastoma multiforme(1328;0.0252)|STAD - Stomach adenocarcinoma(1328;0.18)		CAAGGGCCTACGTGATGGGGCGTGATGGGG	0.681													8	5	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9389980	9389981	+	Intron	INS	-	A	A	rs57434661	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9389980_9389981insA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						TGGTGAGAAATAAAAAAAAAAA	0.347													4	2	---	---	---	---	
TP53TG5	27296	broad.mit.edu	37	20	44006413	44006414	+	Intron	INS	-	A	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44006413_44006414insA	uc002xny.2	-						SYS1-DBNDD2_uc002xnx.2_Intron	NM_014477	NP_055292	Q9Y2B4	T53G5_HUMAN	TP53-target gene 5 protein						intracellular signal transduction|negative regulation of cell growth	cytoplasm|nucleus				central_nervous_system(1)	1						ctgactctaccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
NCAM2	4685	broad.mit.edu	37	21	22664219	22664219	+	Intron	DEL	A	-	-	rs71322042		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22664219delA	uc002yld.1	+						NCAM2_uc011acb.1_Intron|NCAM2_uc011acc.1_Intron	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor						neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		TTCTTTTAGGAAAAAAAAAAA	0.284													2	5	---	---	---	---	
CCT8L2	150160	broad.mit.edu	37	22	17075872	17075872	+	5'Flank	DEL	A	-	-	rs148690764		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17075872delA	uc002zlp.1	-							NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1						cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CACAGTAATGAAAAAAAAAAA	0.323													4	2	---	---	---	---	
