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
DFFB	1677	broad.mit.edu	37	1	3800177	3800177	+	Nonsense_Mutation	SNP	G	T	T	rs59649948		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3800177G>T	uc001alc.2	+	7	1212	c.889G>T	c.(889-891)GAG>TAG	p.E297*	DFFB_uc001ale.2_RNA|DFFB_uc009vlp.2_RNA|DFFB_uc001alb.2_RNA|DFFB_uc010nzn.1_Nonsense_Mutation_p.E321*|DFFB_uc009vlq.2_RNA|DFFB_uc009vlr.2_Nonsense_Mutation_p.E248*|DFFB_uc001ald.2_Nonsense_Mutation_p.E233*	NM_004402	NP_004393	O76075	DFFB_HUMAN	DNA fragmentation factor, 40 kD, beta	297					apoptotic chromosome condensation|DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction	cytosol|nucleoplasm	deoxyribonuclease activity|enzyme binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		TTTTACCTCAGAGAACCTAAA	0.443													5	93	---	---	---	---	PASS
ANGPTL7	10218	broad.mit.edu	37	1	11249665	11249665	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11249665C>A	uc001ase.2	+	1	268	c.29C>A	c.(28-30)ACC>AAC	p.T10N	MTOR_uc001asd.2_Intron	NM_021146	NP_066969	O43827	ANGL7_HUMAN	angiopoietin-like 7 precursor	10					response to oxidative stress|signal transduction	extracellular region	receptor binding				0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.39e-06)|COAD - Colon adenocarcinoma(227;0.000244)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0487)		TCAGCTGTGACCTGGCTCTGC	0.557													49	44	---	---	---	---	PASS
MTHFR	4524	broad.mit.edu	37	1	11861293	11861293	+	Missense_Mutation	SNP	G	A	A	rs45550133		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11861293G>A	uc001atc.1	-	3	584	c.400C>T	c.(400-402)CGC>TGC	p.R134C	MTHFR_uc001atb.1_Missense_Mutation_p.R157C	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase	134					blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)	TCCTCCAGGCGCTGACGGCAG	0.617													31	8	---	---	---	---	PASS
PHC2	1912	broad.mit.edu	37	1	33790576	33790576	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33790576C>G	uc001bxg.1	-	14	2521	c.2467G>C	c.(2467-2469)GGG>CGG	p.G823R	PHC2_uc001bxh.1_Missense_Mutation_p.G795R|PHC2_uc009vuh.1_Missense_Mutation_p.G824R|PHC2_uc001bxe.1_Missense_Mutation_p.G288R|PHC2_uc001bxf.1_3'UTR	NM_198040	NP_932157	Q8IXK0	PHC2_HUMAN	polyhomeotic-like 2 isoform a	823	SAM.				multicellular organismal development	PcG protein complex	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				AGGGCTTGCCCGTCGATTTCC	0.592													6	5	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39797468	39797468	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39797468G>T	uc010oiu.1	+	1	659	c.528G>T	c.(526-528)GGG>GGT	p.G176G	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	1741					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TGGCAGGGGGGATGGTGAGCT	0.493													22	11	---	---	---	---	PASS
PTPRF	5792	broad.mit.edu	37	1	44071241	44071241	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44071241G>T	uc001cjr.2	+	19	3771	c.3431G>T	c.(3430-3432)GGG>GTG	p.G1144V	PTPRF_uc001cjs.2_Missense_Mutation_p.G1135V|PTPRF_uc001cju.2_Missense_Mutation_p.G522V|PTPRF_uc009vwt.2_Missense_Mutation_p.G704V|PTPRF_uc001cjv.2_Missense_Mutation_p.G604V|PTPRF_uc001cjw.2_Missense_Mutation_p.G370V	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1144	Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CGTGTGGGCGGGAGCATGCTG	0.627													14	9	---	---	---	---	PASS
TAL1	6886	broad.mit.edu	37	1	47685806	47685806	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47685806G>T	uc001cqx.2	-	4	1159	c.582C>A	c.(580-582)AGC>AGA	p.S194R	TAL1_uc009vyq.2_5'UTR|TAL1_uc001cqy.2_Missense_Mutation_p.S194R	NM_003189	NP_003180	P17542	TAL1_HUMAN	T-cell acute lymphocytic leukemia 1	194	Basic motif.				basophil differentiation|cell fate commitment|cell proliferation|embryonic hemopoiesis|erythrocyte differentiation|megakaryocyte differentiation|positive regulation of cell division|positive regulation of chromatin assembly or disassembly|positive regulation of erythrocyte differentiation|positive regulation of mitotic cell cycle|positive regulation of protein complex assembly|positive regulation of transcription from RNA polymerase II promoter	nuclear chromatin	E-box binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity			lung(1)	1						ATCGCTCCCGGCTGTTGGTGA	0.562			T	TRD@|SIL	lymphoblastic leukemia/biphasic								21	7	---	---	---	---	PASS
EPS8L3	79574	broad.mit.edu	37	1	110302413	110302413	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110302413C>A	uc001dyr.1	-	4	287	c.142G>T	c.(142-144)GAG>TAG	p.E48*	EPS8L3_uc001dys.1_Nonsense_Mutation_p.E48*|EPS8L3_uc001dyq.1_Nonsense_Mutation_p.E48*|EPS8L3_uc009wfm.1_Nonsense_Mutation_p.E14*|EPS8L3_uc009wfn.1_Nonsense_Mutation_p.E14*|EPS8L3_uc009wfo.1_Intron	NM_133181	NP_573444	Q8TE67	ES8L3_HUMAN	epidermal growth factor receptor pathway	48						cytoplasm	protein binding			ovary(2)|skin(1)	3		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		AAGGCATCCTCGGGCCCCTGG	0.612													4	32	---	---	---	---	PASS
OVGP1	5016	broad.mit.edu	37	1	111963989	111963989	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111963989T>A	uc001eba.2	-	8	868	c.812A>T	c.(811-813)AAA>ATA	p.K271I	OVGP1_uc001eaz.2_Missense_Mutation_p.K233I|OVGP1_uc010owb.1_Intron	NM_002557	NP_002548	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1 precursor	271					chitin catabolic process|female pregnancy|single fertilization	transport vesicle	cation binding|chitinase activity	p.K271fs*4(1)		ovary(4)|large_intestine(1)	5		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		CTTAGAGGCTTTGAGGAGGCG	0.517													36	19	---	---	---	---	PASS
SYCP1	6847	broad.mit.edu	37	1	115524061	115524061	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115524061T>A	uc001efr.2	+	29	2696	c.2487T>A	c.(2485-2487)CAT>CAA	p.H829Q	SYCP1_uc010owt.1_RNA|SYCP1_uc001efq.2_Missense_Mutation_p.H829Q|SYCP1_uc009wgw.2_Missense_Mutation_p.H804Q	NM_003176	NP_003167	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	829					cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAGTTGATCATGGCATATCCA	0.333													27	7	---	---	---	---	PASS
ITGA10	8515	broad.mit.edu	37	1	145534248	145534248	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145534248C>A	uc001eoa.2	+	14	1829	c.1753C>A	c.(1753-1755)CAT>AAT	p.H585N	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Missense_Mutation_p.H454N|ITGA10_uc009wiw.2_Missense_Mutation_p.H442N|ITGA10_uc010oyw.1_Missense_Mutation_p.H530N	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	585	Extracellular (Potential).|FG-GAP 6.				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GTACCTGTACCATGGAACCCA	0.567													5	95	---	---	---	---	PASS
CD160	11126	broad.mit.edu	37	1	145706688	145706688	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145706688C>G	uc001eol.1	-	3	289	c.71G>C	c.(70-72)GGT>GCT	p.G24A	NBPF10_uc001emp.3_Intron|CD160_uc001eom.1_Missense_Mutation_p.G24A|CD160_uc010oyz.1_RNA	NM_007053	NP_008984	O95971	BY55_HUMAN	CD160 antigen precursor	24					cell proliferation|cell surface receptor linked signaling pathway|cellular defense response|regulation of immune response	anchored to plasma membrane	MHC class I receptor activity|receptor binding				0	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			ATCCTCACCACCAGACTGGAT	0.587													16	49	---	---	---	---	PASS
TCHHL1	126637	broad.mit.edu	37	1	152059147	152059147	+	Silent	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152059147T>C	uc001ezo.1	-	3	1076	c.1011A>G	c.(1009-1011)GGA>GGG	p.G337G		NM_001008536	NP_001008536	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	337							calcium ion binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			CAGCATCCTTTCCTGGTTCTT	0.448													49	163	---	---	---	---	PASS
NPR1	4881	broad.mit.edu	37	1	153661578	153661578	+	Intron	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153661578G>A	uc001fcs.3	+						NPR1_uc010pdz.1_Intron|NPR1_uc010pea.1_Intron	NM_000906	NP_000897	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1 precursor						body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation		ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity			ovary(3)|lung(2)|stomach(1)|breast(1)	7	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CTGCCTCAGTGAGTGCCTGAG	0.622													21	47	---	---	---	---	PASS
FCRL4	83417	broad.mit.edu	37	1	157548310	157548310	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157548310C>T	uc001fqw.2	-	10	1519	c.1383G>A	c.(1381-1383)TTG>TTA	p.L461L	FCRL4_uc010phy.1_RNA	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor	461	Cytoplasmic (Potential).|ITIM motif 2.					integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)|skin(1)	4	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				CAGAGTATACCAAATCTCCCT	0.393													7	46	---	---	---	---	PASS
OR10J1	26476	broad.mit.edu	37	1	159409849	159409849	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159409849C>T	uc010piv.1	+	1	301	c.301C>T	c.(301-303)CAG>TAG	p.Q101*	uc001fts.3_Intron	NM_012351	NP_036483	P30954	O10J1_HUMAN	olfactory receptor, family 10, subfamily J,	101	Extracellular (Potential).				sensory perception of smell|single fertilization	integral to plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0429)					AGGTATGAGCCAGCCCATATC	0.478													13	47	---	---	---	---	PASS
KCNJ10	3766	broad.mit.edu	37	1	160012156	160012156	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160012156C>T	uc001fuw.1	-	2	317	c.167G>A	c.(166-168)TGG>TAG	p.W56*		NM_002241	NP_002232	P78508	IRK10_HUMAN	potassium inwardly-rectifying channel, subfamily	56	Cytoplasmic (By similarity).					integral to plasma membrane	ATP binding|ATP-activated inward rectifier potassium channel activity			ovary(1)	1	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GAAGGTTGTCCACAGGTCCTT	0.542													26	107	---	---	---	---	PASS
B4GALT3	8703	broad.mit.edu	37	1	161143746	161143746	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161143746C>T	uc001fyq.1	-	5	845	c.583G>A	c.(583-585)GAT>AAT	p.D195N	PPOX_uc010pkh.1_Intron|PPOX_uc001fyi.2_Intron|B4GALT3_uc001fyo.1_5'UTR|B4GALT3_uc001fyp.1_RNA|B4GALT3_uc001fyr.1_Missense_Mutation_p.D195N|B4GALT3_uc001fys.1_Missense_Mutation_p.D195N|B4GALT3_uc009wud.1_Missense_Mutation_p.D195N	NM_003779	NP_003770	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	195	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|metal ion binding|N-acetyllactosamine synthase activity				0	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	AGGTCCACATCGTGCAAGAAC	0.522													17	43	---	---	---	---	PASS
TADA1	117143	broad.mit.edu	37	1	166829516	166829516	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166829516C>T	uc001gdw.2	-	6	783	c.599G>A	c.(598-600)CGA>CAA	p.R200Q	TADA1_uc001gdv.2_Missense_Mutation_p.R58Q	NM_053053	NP_444281	Q96BN2	TADA1_HUMAN	transcriptional adaptor 1-like	200					histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(1)	1						ATGACCATCTCGTAACCGATA	0.363													17	30	---	---	---	---	PASS
SLC19A2	10560	broad.mit.edu	37	1	169439384	169439384	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169439384C>A	uc001gge.3	-	3	1052	c.848G>T	c.(847-849)TGG>TTG	p.W283L	SLC19A2_uc001ggf.3_Missense_Mutation_p.W82L	NM_006996	NP_008927	O60779	S19A2_HUMAN	solute carrier family 19, member 2	283	Cytoplasmic (Potential).				thiamine-containing compound metabolic process	integral to membrane|plasma membrane	folic acid binding|folic acid transporter activity|reduced folate carrier activity|thiamine uptake transmembrane transporter activity				0	all_hematologic(923;0.208)					GAAATCATTCCATAGTACTTT	0.448													5	56	---	---	---	---	PASS
SCYL3	57147	broad.mit.edu	37	1	169823643	169823643	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169823643G>C	uc001ggs.2	-	13	2135	c.1937C>G	c.(1936-1938)CCC>CGC	p.P646R	SCYL3_uc010plw.1_Missense_Mutation_p.P238R|SCYL3_uc001ggt.2_Missense_Mutation_p.P592R|SCYL3_uc001ggu.2_RNA	NM_181093	NP_851607	Q8IZE3	PACE1_HUMAN	SCY1-like 3 isoform 2	646	Interaction with EZR.				cell migration	Golgi apparatus|lamellipodium	ATP binding|protein binding|protein kinase activity			ovary(1)|skin(1)	2	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AACCTTAAGGGGCCTTTCTTG	0.438													18	86	---	---	---	---	PASS
BAT2L2	23215	broad.mit.edu	37	1	171510347	171510347	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171510347A>T	uc010pmg.1	+	16	4002	c.3736A>T	c.(3736-3738)AGT>TGT	p.S1246C	BAT2L2_uc010pmh.1_Missense_Mutation_p.S223C	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	1246							protein C-terminus binding				0						TGAAACACGGAGTGAGAGCTC	0.473													56	45	---	---	---	---	PASS
BAT2L2	23215	broad.mit.edu	37	1	171511306	171511306	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171511306G>T	uc010pmg.1	+	16	4961	c.4695G>T	c.(4693-4695)AGG>AGT	p.R1565S	BAT2L2_uc010pmh.1_Missense_Mutation_p.R542S	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	1565							protein C-terminus binding				0						AATCAGGAAGGAATTTCTCAG	0.428													19	7	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176564385	176564385	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176564385C>A	uc001gkz.2	+	3	2809	c.1645C>A	c.(1645-1647)CTG>ATG	p.L549M	PAPPA2_uc001gky.1_Missense_Mutation_p.L549M|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	549	Metalloprotease.				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						GCAGATTCGTCTGCAGCACGA	0.567													10	42	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176564722	176564722	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176564722C>A	uc001gkz.2	+	3	3146	c.1982C>A	c.(1981-1983)TCA>TAA	p.S661*	PAPPA2_uc001gky.1_Nonsense_Mutation_p.S661*|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	661	Metalloprotease.				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						GACCCTGACTCACCCAAGAGG	0.498													4	29	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176769217	176769217	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176769217G>A	uc001gkz.2	+	21	6315	c.5151G>A	c.(5149-5151)CGG>CGA	p.R1717R	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1717	Sushi 5.				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						GCACTGGCCGGCGTCAATGGC	0.498													34	79	---	---	---	---	PASS
PRG4	10216	broad.mit.edu	37	1	186277488	186277488	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186277488G>A	uc001gru.3	+	7	2688	c.2637G>A	c.(2635-2637)GAG>GAA	p.E879E	PRG4_uc001grt.3_Silent_p.E838E|PRG4_uc009wyl.2_Silent_p.E786E|PRG4_uc009wym.2_Silent_p.E745E|PRG4_uc010poo.1_RNA	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	879					cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						CAACTCCTGAGCTTTCTGCAG	0.488													165	116	---	---	---	---	PASS
CFHR4	10877	broad.mit.edu	37	1	196881962	196881962	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196881962T>A	uc001gto.2	+	3	418	c.349T>A	c.(349-351)TGT>AGT	p.C117S	CFHR4_uc009wyy.2_Missense_Mutation_p.C363S|CFHR4_uc001gtp.2_Missense_Mutation_p.C364S	NM_006684	NP_006675	Q92496	FHR4_HUMAN	complement factor H-related 4 precursor	117	Sushi 2.					extracellular region	lipid transporter activity			ovary(1)|pancreas(1)|skin(1)	3						acaatataaatGTAAACCAGG	0.279													26	54	---	---	---	---	PASS
FAM58B	339521	broad.mit.edu	37	1	200183331	200183331	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200183331G>T	uc009wzi.1	+	1	676	c.640G>T	c.(640-642)GAG>TAG	p.E214*		NM_001105517	NP_001098987	P0C7Q3	FA58B_HUMAN	family with sequence similarity 58 member B	214					regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent		protein kinase binding				0	Prostate(682;0.19)					GGTGCCCGCCGAGGTCGAGGC	0.562													4	69	---	---	---	---	PASS
CNTN2	6900	broad.mit.edu	37	1	205034927	205034927	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205034927T>A	uc001hbr.2	+	14	1975	c.1706T>A	c.(1705-1707)ATT>AAT	p.I569N	CNTN2_uc001hbq.1_Missense_Mutation_p.I460N|CNTN2_uc001hbs.2_Missense_Mutation_p.I357N	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor	569	Ig-like C2-type 6.				axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			AAGGAGACCATTGGGGATCTG	0.637													11	36	---	---	---	---	PASS
CR2	1380	broad.mit.edu	37	1	207639950	207639950	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207639950G>A	uc001hfw.2	+	2	232	c.138G>A	c.(136-138)GTG>GTA	p.V46V	CR2_uc001hfv.2_Silent_p.V46V|CR2_uc009xch.2_Silent_p.V46V	NM_001877	NP_001868	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)	46	Sushi 1.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8						TTGGTACCGTGATAAGGTACA	0.433													8	127	---	---	---	---	PASS
EPRS	2058	broad.mit.edu	37	1	220153567	220153567	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220153567C>G	uc001hly.1	-	26	3841	c.3571G>C	c.(3571-3573)GAC>CAC	p.D1191H		NM_004446	NP_004437	P07814	SYEP_HUMAN	glutamyl-prolyl tRNA synthetase	1191	Prolyl-tRNA synthetase.				glutamyl-tRNA aminoacylation|prolyl-tRNA aminoacylation|protein complex assembly	cytosol|soluble fraction	ATP binding|glutamate-tRNA ligase activity|proline-tRNA ligase activity|protein binding|RNA binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0735)	L-Glutamic Acid(DB00142)|L-Proline(DB00172)	GCATATAAGTCAAGTATCTGC	0.328													42	34	---	---	---	---	PASS
DUSP10	11221	broad.mit.edu	37	1	221912353	221912353	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221912353C>A	uc001hmy.1	-	2	916	c.734G>T	c.(733-735)CGA>CTA	p.R245L	DUSP10_uc001hmx.1_5'Flank|DUSP10_uc001hmz.1_Intron	NM_007207	NP_009138	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10 isoform a	245	Rhodanese.				inactivation of MAPK activity|JNK cascade|negative regulation of JNK cascade|negative regulation of JUN kinase activity|negative regulation of stress-activated MAPK cascade	Golgi apparatus|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|lung(1)	2				GBM - Glioblastoma multiforme(131;0.0103)		GGGCATCACTCGGCTTGGTTC	0.468													4	106	---	---	---	---	PASS
HHIPL2	79802	broad.mit.edu	37	1	222717398	222717398	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222717398G>A	uc001hnh.1	-	2	513	c.455C>T	c.(454-456)ACC>ATC	p.T152I		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor	152					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)		GCGGTCATTGGTCAGCAGGGA	0.572													13	91	---	---	---	---	PASS
VN1R5	317705	broad.mit.edu	37	1	247420126	247420126	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247420126T>A	uc010pyu.1	+	2	753	c.753T>A	c.(751-753)AGT>AGA	p.S251R		NM_173858	NP_776257	Q7Z5H4	VN1R5_HUMAN	vomeronasal 1 receptor 5	251	Cytoplasmic (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0	all_cancers(71;5.7e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)	all_cancers(173;0.0314)	OV - Ovarian serous cystadenocarcinoma(106;0.00854)			GCTATCTCAGTGCCTTCACAC	0.468													25	90	---	---	---	---	PASS
OR2T33	391195	broad.mit.edu	37	1	248436684	248436684	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248436684A>G	uc010pzi.1	-	1	433	c.433T>C	c.(433-435)TCG>CCG	p.S145P		NM_001004695	NP_001004695	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T,	145	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			AGCCAACACGACATGGTCATC	0.577													43	116	---	---	---	---	PASS
OR14C36	127066	broad.mit.edu	37	1	248512734	248512734	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248512734T>A	uc010pzl.1	+	1	658	c.658T>A	c.(658-660)TTT>ATT	p.F220I		NM_001001918	NP_001001918	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C,	220	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3						CATTCACATCTTTTCGACCGT	0.498													18	59	---	---	---	---	PASS
OR14I1	401994	broad.mit.edu	37	1	248845378	248845378	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248845378C>A	uc001ieu.1	-	1	228	c.228G>T	c.(226-228)GTG>GTT	p.V76V		NM_001004734	NP_001004734	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I,	76	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TGGATTTAGGCACAGTGACTG	0.473													11	38	---	---	---	---	PASS
SMC6	79677	broad.mit.edu	37	2	17906556	17906556	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17906556T>C	uc002rco.2	-	9	990	c.694A>G	c.(694-696)AGA>GGA	p.R232G	SMC6_uc010exo.2_Missense_Mutation_p.R232G|SMC6_uc002rcn.2_Missense_Mutation_p.R232G|SMC6_uc002rcp.1_Missense_Mutation_p.R258G|SMC6_uc002rcq.2_Missense_Mutation_p.R258G|SMC6_uc002rcr.1_Missense_Mutation_p.R232G	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	232	Potential.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TCCTTTGTTCTTTCTTTCGTT	0.303													26	28	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21232746	21232746	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21232746C>T	uc002red.2	-	26	7122	c.6994G>A	c.(6994-6996)GAG>AAG	p.E2332K		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	2332					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	TTGATTTTCTCAGCTACTTCA	0.343													13	84	---	---	---	---	PASS
DPYSL5	56896	broad.mit.edu	37	2	27121593	27121593	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27121593G>T	uc002rhu.3	+	2	384	c.226G>T	c.(226-228)GCC>TCC	p.A76S	DPYSL5_uc002rhv.3_Missense_Mutation_p.A76S	NM_020134	NP_064519	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	76					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCATGAATGCCACGTGCGT	0.537													14	40	---	---	---	---	PASS
C2orf16	84226	broad.mit.edu	37	2	27800671	27800671	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27800671T>A	uc002rkz.3	+	1	1283	c.1232T>A	c.(1231-1233)CTA>CAA	p.L411Q		NM_032266	NP_115642	Q68DN1	CB016_HUMAN	hypothetical protein LOC84226	411										large_intestine(1)	1	Acute lymphoblastic leukemia(172;0.155)					AAGCAATGGCTACAAATGGAG	0.468													16	68	---	---	---	---	PASS
C2orf16	84226	broad.mit.edu	37	2	27801331	27801331	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27801331G>A	uc002rkz.3	+	1	1943	c.1892G>A	c.(1891-1893)TGT>TAT	p.C631Y		NM_032266	NP_115642	Q68DN1	CB016_HUMAN	hypothetical protein LOC84226	631										large_intestine(1)	1	Acute lymphoblastic leukemia(172;0.155)					GCAATAAATTGTGTGGATTTA	0.408													54	22	---	---	---	---	PASS
GPN1	11321	broad.mit.edu	37	2	27852010	27852010	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27852010G>T	uc010ymc.1	+	1	148	c.127G>T	c.(127-129)GGA>TGA	p.G43*	ZNF512_uc010yly.1_Intron|CCDC121_uc010eze.2_5'Flank|CCDC121_uc002rld.2_5'Flank|CCDC121_uc002rle.2_5'Flank|GPN1_uc010ezf.2_Intron|GPN1_uc010yma.1_Intron|GPN1_uc010ymb.1_Intron|GPN1_uc010ymd.1_5'UTR|GPN1_uc010yme.1_Nonsense_Mutation_p.G43*|GPN1_uc010ezg.1_5'Flank	NM_007266	NP_009197	Q9HCN4	GPN1_HUMAN	GPN-loop GTPase 1 isoform a	29	GTP (Pootential).					cytoplasm	GTP binding|nucleoside-triphosphatase activity|protein binding				0						GGGAATGGCGGGATCCGGGAA	0.622													8	38	---	---	---	---	PASS
SLC4A1AP	22950	broad.mit.edu	37	2	27887973	27887973	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27887973G>T	uc002rlk.3	+	2	1114	c.832G>T	c.(832-834)GAG>TAG	p.E278*	SUPT7L_uc002rlh.1_5'Flank|SUPT7L_uc002rli.1_5'Flank|SUPT7L_uc010ymf.1_5'Flank|SUPT7L_uc002rlj.1_5'Flank|SUPT7L_uc010ezh.1_5'Flank	NM_018158	NP_060628	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger),	278						cytoplasm|nucleus	double-stranded RNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)					TCAGGGACCAGAGGAAGACCG	0.294													7	135	---	---	---	---	PASS
PLEKHH2	130271	broad.mit.edu	37	2	43927638	43927638	+	Missense_Mutation	SNP	A	G	G	rs144437669		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43927638A>G	uc010yny.1	+	8	1624	c.1541A>G	c.(1540-1542)TAT>TGT	p.Y514C	PLEKHH2_uc002rte.3_Missense_Mutation_p.Y514C|PLEKHH2_uc002rtf.3_Missense_Mutation_p.Y513C	NM_172069	NP_742066	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H	514						cytoplasm|cytoskeleton|integral to membrane	binding			skin(2)|central_nervous_system(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TTATTTTCCTATGACTCCTTG	0.448													22	124	---	---	---	---	PASS
MSH6	2956	broad.mit.edu	37	2	48027187	48027187	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48027187T>G	uc002rwd.3	+	4	2217	c.2065T>G	c.(2065-2067)TTC>GTC	p.F689V	MSH6_uc002rwc.2_Missense_Mutation_p.F689V|MSH6_uc010fbj.2_Missense_Mutation_p.F387V|MSH6_uc010yoi.1_Missense_Mutation_p.F559V|MSH6_uc010yoj.1_Missense_Mutation_p.F387V	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	689					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGGTTGTGTCTTCTACCTCAA	0.423			Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				42	152	---	---	---	---	PASS
FANCL	55120	broad.mit.edu	37	2	58392929	58392929	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58392929G>T	uc002rzw.3	-	8	688	c.621C>A	c.(619-621)ATC>ATA	p.I207I	FANCL_uc002rzx.3_Silent_p.I212I|FANCL_uc010fce.2_Silent_p.I207I|FANCL_uc010fcf.1_Silent_p.I148I	NM_018062	NP_060532	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L isoform	207					DNA repair	cytoplasm|nucleoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						TCTTCTCATCGATTTCATCCA	0.408								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				52	25	---	---	---	---	PASS
C2orf86	51057	broad.mit.edu	37	2	63720003	63720003	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63720003G>T	uc002sch.2	-	2	593	c.147C>A	c.(145-147)ACC>ACA	p.T49T	C2orf86_uc002sci.1_Silent_p.T25T	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2	49					cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0						CAATGTGTAAGGTATTCTTCA	0.348													8	235	---	---	---	---	PASS
DYSF	8291	broad.mit.edu	37	2	71883310	71883310	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71883310G>T	uc002sie.2	+	42	4904	c.4528G>T	c.(4528-4530)GAG>TAG	p.E1510*	DYSF_uc010feg.2_Nonsense_Mutation_p.E1541*|DYSF_uc010feh.2_Nonsense_Mutation_p.E1517*|DYSF_uc002sig.3_Nonsense_Mutation_p.E1496*|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_Nonsense_Mutation_p.E1531*|DYSF_uc010fef.2_Nonsense_Mutation_p.E1548*|DYSF_uc010fei.2_Nonsense_Mutation_p.E1527*|DYSF_uc010fek.2_Nonsense_Mutation_p.E1528*|DYSF_uc010fej.2_Nonsense_Mutation_p.E1518*|DYSF_uc010fel.2_Nonsense_Mutation_p.E1497*|DYSF_uc010feo.2_Nonsense_Mutation_p.E1542*|DYSF_uc010fem.2_Nonsense_Mutation_p.E1532*|DYSF_uc010fen.2_Nonsense_Mutation_p.E1549*|DYSF_uc002sif.2_Nonsense_Mutation_p.E1511*|DYSF_uc010yqy.1_Nonsense_Mutation_p.E391*|DYSF_uc010yqz.1_Nonsense_Mutation_p.E271*	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	1510	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						CACACAGCTGGAGAATGTGGA	0.358													7	175	---	---	---	---	PASS
ALMS1	7840	broad.mit.edu	37	2	73762076	73762076	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73762076G>T	uc002sje.1	+	14	10021	c.9910G>T	c.(9910-9912)GGA>TGA	p.G3304*	ALMS1_uc002sjf.1_Nonsense_Mutation_p.G3260*|ALMS1_uc002sjg.2_Nonsense_Mutation_p.G2690*|ALMS1_uc002sjh.1_Nonsense_Mutation_p.G2690*|ALMS1_uc010fev.1_Missense_Mutation_p.D119Y	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3302					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9						CTCCCATTCAGGTATTATGCA	0.358													10	233	---	---	---	---	PASS
LRRTM4	80059	broad.mit.edu	37	2	77746050	77746050	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77746050G>A	uc002snr.2	-	3	1360	c.945C>T	c.(943-945)TGC>TGT	p.C315C	LRRTM4_uc002snq.2_Silent_p.C315C|LRRTM4_uc002sns.2_Silent_p.C315C|LRRTM4_uc002snt.2_Silent_p.C316C	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	315	LRRCT.|Extracellular (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		TGCTCCGACTGCATTCCCACA	0.393													6	19	---	---	---	---	PASS
LRRTM4	80059	broad.mit.edu	37	2	77746622	77746622	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77746622G>C	uc002snr.2	-	3	788	c.373C>G	c.(373-375)CAC>GAC	p.H125D	LRRTM4_uc002snq.2_Missense_Mutation_p.H125D|LRRTM4_uc002sns.2_Missense_Mutation_p.H125D|LRRTM4_uc002snt.2_Missense_Mutation_p.H126D	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	125	LRR 3.|Extracellular (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		GTTTTATTGTGCAGATAAGTA	0.383													15	59	---	---	---	---	PASS
POLR1A	25885	broad.mit.edu	37	2	86292414	86292414	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86292414G>A	uc002sqs.2	-	14	2420	c.2041C>T	c.(2041-2043)CTG>TTG	p.L681L	POLR1A_uc010ytb.1_Silent_p.L47L	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A	681					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						CCTGTCCACAGCGGAAAGGGC	0.493													14	114	---	---	---	---	PASS
RMND5A	64795	broad.mit.edu	37	2	86980655	86980655	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86980655G>T	uc010ytm.1	+	4	872	c.495G>T	c.(493-495)AAG>AAT	p.K165N	RMND5A_uc002srs.3_Intron|RMND5A_uc002srr.2_Missense_Mutation_p.K165N	NM_022780	NP_073617	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog	165	CTLH.									ovary(1)|skin(1)	2						AGGCATTAAAGGTCAGAGTTC	0.368													5	71	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89160397	89160397	+	RNA	SNP	C	A	A	rs141201227	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89160397C>A	uc010ytr.1	-	239		c.9393G>T			uc002sti.1_5'Flank|uc002stj.1_Intron					Parts of antibodies, mostly variable regions.																		AGTGCACTTACGTTTGATCTC	0.423													103	37	---	---	---	---	PASS
FER1L5	90342	broad.mit.edu	37	2	97370014	97370014	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97370014G>T	uc010fia.2	+	51	5972	c.5972G>T	c.(5971-5973)TGG>TTG	p.W1991L	FER1L5_uc002sws.3_Missense_Mutation_p.W700L|FER1L5_uc002swt.3_Missense_Mutation_p.W700L|FER1L5_uc010yus.1_Missense_Mutation_p.W699L	NM_001113382	NP_001106853	A0AVI2	FR1L5_HUMAN	fer-1-like 5 isoform 2	1991						integral to membrane				ovary(1)	1						TATATTTTCTGGAAACGCTAT	0.473													7	147	---	---	---	---	PASS
CNNM4	26504	broad.mit.edu	37	2	97427870	97427870	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97427870C>A	uc002swx.2	+	1	1232	c.1134C>A	c.(1132-1134)ACC>ACA	p.T378T		NM_020184	NP_064569	Q6P4Q7	CNNM4_HUMAN	cyclin M4	378	CBS 1.				biomineral tissue development|ion transport|response to stimulus|visual perception	integral to membrane|plasma membrane				breast(2)|ovary(1)	3						ATATCATGACCCAGCTCCAGG	0.522													5	60	---	---	---	---	PASS
AFF3	3899	broad.mit.edu	37	2	100176910	100176910	+	Intron	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100176910C>A	uc002tag.2	-						AFF3_uc002taf.2_Intron	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						TTAGAAAAAGCGGGGAGGAGG	0.408													36	62	---	---	---	---	PASS
MAP4K4	9448	broad.mit.edu	37	2	102314986	102314986	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102314986G>T	uc002tbg.2	+	2	164	c.109G>T	c.(109-111)GGA>TGA	p.G37*	MAP4K4_uc002tbc.2_Nonsense_Mutation_p.G37*|MAP4K4_uc002tbd.2_Nonsense_Mutation_p.G37*|MAP4K4_uc002tbe.2_Nonsense_Mutation_p.G37*|MAP4K4_uc002tbf.2_Nonsense_Mutation_p.G37*|MAP4K4_uc010yvy.1_Nonsense_Mutation_p.G37*|MAP4K4_uc002tbh.2_Nonsense_Mutation_p.G37*|MAP4K4_uc002tbi.2_Nonsense_Mutation_p.G37*	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase	37	Protein kinase.|ATP (By similarity).				intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						TGGCACCTATGGACAAGTCTA	0.488													12	492	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109379712	109379712	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109379712A>G	uc002tem.3	+	20	2843	c.2717A>G	c.(2716-2718)AAT>AGT	p.N906S		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	906					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						TATGGCATGAATAGGCTTCCA	0.408													33	51	---	---	---	---	PASS
SAP130	79595	broad.mit.edu	37	2	128767876	128767876	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128767876G>A	uc002tpp.2	-	7	1046	c.914C>T	c.(913-915)ACG>ATG	p.T305M	SAP130_uc002tpn.2_Missense_Mutation_p.T66M|SAP130_uc002tpo.2_Missense_Mutation_p.T50M|SAP130_uc010fmd.2_Missense_Mutation_p.T305M|SAP130_uc002tpq.1_Missense_Mutation_p.T279M	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b	305					histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		CGCCGCTGTCGTAGTGATGAC	0.512													47	7	---	---	---	---	PASS
TUBA3D	113457	broad.mit.edu	37	2	132237812	132237812	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132237812G>T	uc002tsu.3	+	4	653	c.546G>T	c.(544-546)GTG>GTT	p.V182V		NM_080386	NP_525125	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	182					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(221;0.13)		CAGCCGTGGTGGAGCCCTACA	0.552													6	128	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168107064	168107064	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168107064C>A	uc002udx.2	+	8	9180	c.9162C>A	c.(9160-9162)TCC>TCA	p.S3054S	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.S2879S|XIRP2_uc010fpq.2_Silent_p.S2832S|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2879					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						AAACATCATCCAAAGTATCTA	0.353													6	133	---	---	---	---	PASS
HOXD10	3236	broad.mit.edu	37	2	176983941	176983941	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176983941C>A	uc002ukj.2	+	2	1075	c.1005C>A	c.(1003-1005)GCC>GCA	p.A335A		NM_002148	NP_002139	P28358	HXD10_HUMAN	homeobox D10	335						nucleus	sequence-specific DNA binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		AACTGACCGCCAACCTCACGT	0.463													5	82	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178098960	178098960	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178098960C>G	uc002ulh.3	-	2	640	c.85G>C	c.(85-87)GAT>CAT	p.D29H	NFE2L2_uc002ulg.3_Missense_Mutation_p.D13H|NFE2L2_uc010zfa.1_Missense_Mutation_p.D13H|NFE2L2_uc002uli.3_Missense_Mutation_p.D13H|NFE2L2_uc010fra.2_Missense_Mutation_p.D13H|NFE2L2_uc010frb.2_Missense_Mutation_p.D13H	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	29					transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ACTCCAAGATCTATATCTTGC	0.363			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			39	5	---	---	---	---	PASS
TTC30B	150737	broad.mit.edu	37	2	178415699	178415699	+	Nonsense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178415699G>C	uc002uln.2	-	1	1826	c.1793C>G	c.(1792-1794)TCA>TGA	p.S598*	TTC30B_uc010zfc.1_Nonsense_Mutation_p.S370*	NM_152517	NP_689730	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	598					cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			TGTGTGTTTTGACATGTTTTC	0.388													7	165	---	---	---	---	PASS
PLCL1	5334	broad.mit.edu	37	2	198949015	198949015	+	Silent	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198949015T>C	uc010fsp.2	+	2	1065	c.774T>C	c.(772-774)ATT>ATC	p.I258I	PLCL1_uc002uuv.3_Silent_p.I179I	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	258					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)	GGAATGGGATTATGTTGGAAG	0.423													15	114	---	---	---	---	PASS
COL4A3	1285	broad.mit.edu	37	2	228148491	228148491	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228148491G>T	uc002vom.1	+	33	2827	c.2665G>T	c.(2665-2667)GGA>TGA	p.G889*	COL4A3_uc002von.1_Nonsense_Mutation_p.G889*|COL4A3_uc002voo.1_Nonsense_Mutation_p.G889*|COL4A3_uc002vop.1_Nonsense_Mutation_p.G889*|uc002voq.1_Intron|uc002vor.1_Intron	NM_000091	NP_000082	Q01955	CO4A3_HUMAN	alpha 3 type IV collagen isoform 1 precursor	889	Triple-helical region.				activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		AGGTGAAGATGGAGTGATTGG	0.458													5	71	---	---	---	---	PASS
BTD	686	broad.mit.edu	37	3	15677003	15677003	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15677003C>T	uc003cah.2	+	2	220	c.117C>T	c.(115-117)GCC>GCT	p.A39A	BTD_uc011avv.1_Silent_p.A41A|BTD_uc011avw.1_Silent_p.A41A|BTD_uc011avx.1_Silent_p.A19A	NM_000060	NP_000051	P43251	BTD_HUMAN	biotinidase precursor	39					central nervous system development|epidermis development|nitrogen compound metabolic process	extracellular space	biotin carboxylase activity|biotinidase activity				0						ACGTGGTTGCCCTGGGAGCCC	0.537													6	59	---	---	---	---	PASS
KCNH8	131096	broad.mit.edu	37	3	19554758	19554758	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19554758G>T	uc003cbk.1	+	13	2571	c.2376G>T	c.(2374-2376)AAG>AAT	p.K792N	KCNH8_uc010hex.1_Missense_Mutation_p.K253N	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	792	Cytoplasmic (Potential).					integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5						GGAAAGAGAAGAACTTGAAAT	0.448													19	28	---	---	---	---	PASS
ITGA9	3680	broad.mit.edu	37	3	37523104	37523104	+	Intron	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37523104C>T	uc003chd.2	+						ITGA9_uc003chc.2_Intron	NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		TGAAGGTGAGCATGGATTGAT	0.547													26	12	---	---	---	---	PASS
LAMB2	3913	broad.mit.edu	37	3	49161317	49161317	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49161317C>A	uc003cwe.2	-	24	3940	c.3641G>T	c.(3640-3642)CGG>CTG	p.R1214L		NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	1214	Domain II.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CTCCTGCGCCCGCTGCTCTAG	0.612													4	19	---	---	---	---	PASS
BSN	8927	broad.mit.edu	37	3	49692819	49692819	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49692819C>T	uc003cxe.3	+	5	5944	c.5830C>T	c.(5830-5832)CCC>TCC	p.P1944S		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	1944					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CTTCTATGGTCCCCGGGACCC	0.687													7	12	---	---	---	---	PASS
SLMAP	7871	broad.mit.edu	37	3	57908716	57908716	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57908716A>G	uc003dje.1	+	21	2565	c.2360A>G	c.(2359-2361)AAC>AGC	p.N787S	SLMAP_uc003djd.1_Missense_Mutation_p.N770S|SLMAP_uc003djf.1_Missense_Mutation_p.N749S|SLMAP_uc003djg.1_Missense_Mutation_p.N381S|SLMAP_uc011bez.1_Missense_Mutation_p.N255S|SLMAP_uc011bfa.1_Missense_Mutation_p.N321S|SLMAP_uc003dji.1_Missense_Mutation_p.N321S|SLMAP_uc011bfb.1_Missense_Mutation_p.N321S|SLMAP_uc011bfc.1_Missense_Mutation_p.N280S	NM_007159	NP_009090	Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	787	Cytoplasmic (Potential).|Potential.				muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		CAGTGTAAAAACAACCTGAAG	0.383													49	13	---	---	---	---	PASS
FLNB	2317	broad.mit.edu	37	3	58089694	58089694	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58089694G>T	uc003djj.2	+	10	1657	c.1492G>T	c.(1492-1494)GAG>TAG	p.E498*	FLNB_uc010hne.2_Nonsense_Mutation_p.E498*|FLNB_uc003djk.2_Nonsense_Mutation_p.E498*|FLNB_uc010hnf.2_Nonsense_Mutation_p.E498*|FLNB_uc003djl.2_Nonsense_Mutation_p.E329*|FLNB_uc003djm.2_Nonsense_Mutation_p.E329*	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2	498	Filamin 3.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		AGAGGGTCTGGAGGAGCTGGT	0.517													5	47	---	---	---	---	PASS
MINA	84864	broad.mit.edu	37	3	97664061	97664061	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97664061G>T	uc003drz.1	-	10	1871	c.1365C>A	c.(1363-1365)TCC>TCA	p.S455S	MINA_uc003dry.1_Silent_p.S126S|MINA_uc003dsa.1_Silent_p.S454S|MINA_uc003dsb.1_Silent_p.S455S|MINA_uc003dsc.1_Silent_p.S454S	NM_001042533	NP_001035998	Q8IUF8	MINA_HUMAN	MYC induced nuclear antigen isoform a	455					ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1						CTGTCCAGAGGGATAATACCA	0.373													12	176	---	---	---	---	PASS
TMEM45A	55076	broad.mit.edu	37	3	100295772	100295772	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100295772G>T	uc003dtz.1	+	6	1051	c.738G>T	c.(736-738)TTG>TTT	p.L246F	TMEM45A_uc003dua.1_Missense_Mutation_p.L262F|TMEM45A_uc003dub.1_RNA	NM_018004	NP_060474	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	246						integral to membrane				skin(2)|ovary(1)	3						TCCTCAGGTTGGTTAAATCTA	0.383													6	87	---	---	---	---	PASS
CEP97	79598	broad.mit.edu	37	3	101476034	101476034	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101476034G>A	uc003dvk.1	+	8	1048	c.1021G>A	c.(1021-1023)GAA>AAA	p.E341K	CEP97_uc010hpm.1_Missense_Mutation_p.E307K|CEP97_uc011bhf.1_Missense_Mutation_p.E341K|CEP97_uc003dvl.1_Missense_Mutation_p.E37K|CEP97_uc003dvm.1_Missense_Mutation_p.E179K	NM_024548	NP_078824	Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	341	CEP110 binding.					centrosome|nucleus	protein binding			ovary(2)	2						GATATCCCAGGAAAGTGGTAA	0.378													5	93	---	---	---	---	PASS
MYH15	22989	broad.mit.edu	37	3	108129421	108129421	+	Intron	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108129421T>A	uc003dxa.1	-							NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						TGAGCCCAGCTCGGTGTACCT	0.532													18	38	---	---	---	---	PASS
BOC	91653	broad.mit.edu	37	3	112993496	112993496	+	Silent	SNP	G	C	C	rs139797362		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112993496G>C	uc003dzx.2	+	9	2130	c.1509G>C	c.(1507-1509)GCG>GCC	p.A503A	BOC_uc003dzy.2_Silent_p.A503A|BOC_uc003dzz.2_Silent_p.A503A|BOC_uc003eab.2_Silent_p.A204A	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	503	Fibronectin type-III 1.|Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)			GTGGCCGGGCGCCAATCCTCT	0.632													8	28	---	---	---	---	PASS
DRD3	1814	broad.mit.edu	37	3	113858465	113858465	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113858465C>A	uc003ebd.2	-	6	1028	c.605G>T	c.(604-606)GGA>GTA	p.G202V	DRD3_uc010hqn.1_Missense_Mutation_p.G202V|DRD3_uc003ebb.1_Missense_Mutation_p.G202V|DRD3_uc003ebc.1_Missense_Mutation_p.G202V	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a	202	Helical; Name=5.				activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)	GACAGTCACTCCAAAGGGCAG	0.512													62	147	---	---	---	---	PASS
GOLGB1	2804	broad.mit.edu	37	3	121410336	121410336	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121410336G>T	uc003eei.3	-	14	7986	c.7860C>A	c.(7858-7860)GCC>GCA	p.A2620A	GOLGB1_uc010hrc.2_Silent_p.A2625A|GOLGB1_uc003eej.3_Silent_p.A2586A	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	2620	Cytoplasmic (Potential).|Potential.				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)		CTTCTTGCAAGGCTGTTACTT	0.378													7	106	---	---	---	---	PASS
GOLGB1	2804	broad.mit.edu	37	3	121417435	121417435	+	Silent	SNP	C	A	A	rs112783488	byFrequency	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121417435C>A	uc003eei.3	-	13	2046	c.1920G>T	c.(1918-1920)GCG>GCT	p.A640A	GOLGB1_uc010hrc.2_Silent_p.A645A|GOLGB1_uc003eej.3_Silent_p.A606A|GOLGB1_uc011bjm.1_Silent_p.A526A|GOLGB1_uc010hrd.1_Silent_p.A604A	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	640	Cytoplasmic (Potential).				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)		GTTCAGTGCTCGCCTGTTCTT	0.373													6	102	---	---	---	---	PASS
CD86	942	broad.mit.edu	37	3	121825266	121825266	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121825266C>A	uc003eet.2	+	4	738	c.622C>A	c.(622-624)CCT>ACT	p.P208T	CD86_uc011bjo.1_Missense_Mutation_p.P126T|CD86_uc011bjp.1_Missense_Mutation_p.P96T|CD86_uc003eeu.2_Missense_Mutation_p.P202T	NM_175862	NP_787058	P42081	CD86_HUMAN	CD86 antigen isoform 1	208	Ig-like C2-type.|Extracellular (Potential).				interspecies interaction between organisms|positive regulation of cell proliferation|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of lymphotoxin A biosynthetic process|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation		coreceptor activity|protein binding			pancreas(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)	TGTTTCATTCCCTGATGTTAC	0.393													9	220	---	---	---	---	PASS
MCM2	4171	broad.mit.edu	37	3	127337913	127337913	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127337913A>T	uc003ejp.2	+	13	2114	c.2057A>T	c.(2056-2058)CAC>CTC	p.H686L	MCM2_uc011bkm.1_Missense_Mutation_p.H556L|MCM2_uc010hsl.2_RNA|MCM2_uc011bkn.1_Missense_Mutation_p.H639L	NM_004526	NP_004517	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	686					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding			ovary(3)|skin(1)	4						CACGTCAGACACCACCCCAGC	0.647													11	6	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	3	129130176	129130176	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129130176C>G	uc003emg.2	-	5	1023	c.860G>C	c.(859-861)AGA>ACA	p.R287T		NM_207307	NP_997190			hypothetical protein LOC90288																		CAGGGAATCTCTGTGCTTGGC	0.557													63	44	---	---	---	---	PASS
DNAJC13	23317	broad.mit.edu	37	3	132169490	132169490	+	Splice_Site	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132169490G>C	uc003eor.2	+	6	402	c.337_splice	c.e6-1	p.R113_splice	DNAJC13_uc010htq.1_Splice_Site_p.R113_splice	NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2						TCTGTCTTTAGAGATACAACT	0.313													14	45	---	---	---	---	PASS
DNAJC13	23317	broad.mit.edu	37	3	132257136	132257136	+	3'UTR	SNP	G	T	T	rs73860746	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132257136G>T	uc003eor.2	+	56						NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2						AAATATTCACGAGAGACAATA	0.483													4	41	---	---	---	---	PASS
A4GNT	51146	broad.mit.edu	37	3	137849890	137849890	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137849890G>T	uc003ers.2	-	2	411	c.209C>A	c.(208-210)TCC>TAC	p.S70Y		NM_016161	NP_057245	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	70	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	acetylglucosaminyltransferase activity|galactosyltransferase activity			central_nervous_system(1)	1						AGACTCTACGGAACAGGAGAC	0.527													7	138	---	---	---	---	PASS
MRAS	22808	broad.mit.edu	37	3	138119441	138119441	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138119441C>A	uc003esh.3	+	5	1074	c.513C>A	c.(511-513)CTC>CTA	p.L171L	MRAS_uc011bmi.1_Silent_p.L95L|MRAS_uc003esi.3_Silent_p.L171L|MRAS_uc011bmj.1_Silent_p.L95L	NM_012219	NP_036351	O14807	RASM_HUMAN	muscle RAS oncogene homolog precursor	171					actin cytoskeleton organization|muscle organ development|Ras protein signal transduction	intracellular|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity			lung(2)|upper_aerodigestive_tract(1)|ovary(1)	4						TCCATGACCTCGTTAGAGTAA	0.542													6	239	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164760854	164760854	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164760854C>G	uc003fei.2	-	17	2059	c.1997G>C	c.(1996-1998)GGA>GCA	p.G666A		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	666	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	TACTTCATATCCGTCAGAATT	0.353										HNSCC(35;0.089)			7	204	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164793766	164793766	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164793766G>C	uc003fei.2	-	2	97	c.35C>G	c.(34-36)TCT>TGT	p.S12C		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	12	Cytoplasmic.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	GACAATCAGAGAGATTTCCAA	0.264										HNSCC(35;0.089)			112	12	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164907978	164907978	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164907978C>A	uc003fej.3	-	2	1085	c.641G>T	c.(640-642)CGA>CTA	p.R214L	SLITRK3_uc003fek.2_Missense_Mutation_p.R214L	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	214	Extracellular (Potential).|LRR 6.					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						TAGCATTCCTCGGTAAAAAAG	0.418										HNSCC(40;0.11)			5	171	---	---	---	---	PASS
PHC3	80012	broad.mit.edu	37	3	169846536	169846536	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169846536G>C	uc010hws.1	-	8	1752	c.1688C>G	c.(1687-1689)CCT>CGT	p.P563R	PHC3_uc003fgl.2_Missense_Mutation_p.P575R|PHC3_uc011bpq.1_Missense_Mutation_p.P522R|PHC3_uc011bpr.1_Missense_Mutation_p.P489R	NM_024947	NP_079223	Q8NDX5	PHC3_HUMAN	polyhomeotic like 3	563	Pro-rich.				multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			CTGTGGAGGAGGAAGAGTCTG	0.502													334	65	---	---	---	---	PASS
PHC3	80012	broad.mit.edu	37	3	169896648	169896648	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169896648G>T	uc010hws.1	-	2	121	c.57C>A	c.(55-57)ACC>ACA	p.T19T	PHC3_uc003fgl.2_Silent_p.T31T|PHC3_uc011bpq.1_Silent_p.T31T|PHC3_uc011bpr.1_Silent_p.T31T|PHC3_uc003fgm.2_Silent_p.T31T|PHC3_uc003fgo.1_Silent_p.T19T|PHC3_uc003fgp.3_Silent_p.T31T|PHC3_uc003fgq.3_Silent_p.T31T|PHC3_uc003fgr.1_RNA	NM_024947	NP_079223	Q8NDX5	PHC3_HUMAN	polyhomeotic like 3	19	Poly-Thr.				multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			tggtggtggtggtACTGCTGG	0.418													11	656	---	---	---	---	PASS
SKIL	6498	broad.mit.edu	37	3	170078995	170078995	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170078995G>T	uc003fgu.2	+	2	1588	c.876G>T	c.(874-876)CTG>CTT	p.L292L	SKIL_uc011bps.1_Silent_p.L272L|SKIL_uc003fgv.2_Silent_p.L292L|SKIL_uc003fgw.2_Silent_p.L292L	NM_005414	NP_005405	P12757	SKIL_HUMAN	SKI-like isoform 1	292					cell cycle arrest|negative regulation of cell differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of axonogenesis|protein heterotrimerization|protein homotrimerization|regulation of apoptosis|regulation of apoptosis|response to antibiotic|response to growth factor stimulus|skeletal muscle tissue development	cytoplasm|PML body	chromatin binding|nucleotide binding|protein complex binding|protein domain specific binding|SMAD binding|transcription corepressor activity|transcription repressor activity			ovary(2)|skin(1)	3	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			TTCAATGTCTGGAGTGTTGTG	0.468													7	269	---	---	---	---	PASS
NLGN1	22871	broad.mit.edu	37	3	173997089	173997089	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173997089G>T	uc003fio.1	+	6	1721	c.1298G>T	c.(1297-1299)AGA>ATA	p.R433I	NLGN1_uc010hww.1_Missense_Mutation_p.R473I|NLGN1_uc003fip.1_Missense_Mutation_p.R433I	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	450	Extracellular (Potential).				calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			GATGTTTTGAGAGAAACCATT	0.383													7	249	---	---	---	---	PASS
ACTL6A	86	broad.mit.edu	37	3	179292177	179292177	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179292177G>T	uc003fjw.2	+	5	571	c.398G>T	c.(397-399)AGA>ATA	p.R133I	ACTL6A_uc003fjx.2_Missense_Mutation_p.R91I|ACTL6A_uc003fjy.2_Missense_Mutation_p.R91I	NM_004301	NP_004292	O96019	ACL6A_HUMAN	actin-like 6A isoform 1	133					chromatin remodeling|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|nervous system development|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	Ino80 complex|npBAF complex|NuA4 histone acetyltransferase complex|plasma membrane|SWI/SNF complex	ATP binding|chromatin binding			ovary(1)	1	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			AGAGCAAAGAGAGAGAAACTG	0.353													8	439	---	---	---	---	PASS
USP13	8975	broad.mit.edu	37	3	179481915	179481915	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179481915G>T	uc003fkh.2	+	18	2299	c.2218G>T	c.(2218-2220)GGA>TGA	p.G740*		NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13	740	UBA 2.				ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			CACCTCCATGGGATTTCAGCG	0.408													10	391	---	---	---	---	PASS
ATP11B	23200	broad.mit.edu	37	3	182554253	182554253	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182554253C>A	uc003flb.2	+	6	804	c.547C>A	c.(547-549)CTG>ATG	p.L183M	ATP11B_uc003fla.2_Missense_Mutation_p.L183M	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	183	Cytoplasmic (Potential).				aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			AGAAACTAACCTGAAGGTTTG	0.388													10	617	---	---	---	---	PASS
EIF2B5	8893	broad.mit.edu	37	3	183860854	183860854	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183860854G>A	uc003fmp.2	+	12	2033	c.1669G>A	c.(1669-1671)GTT>ATT	p.V557I	EIF2B5_uc003fmq.2_Missense_Mutation_p.V278I|EIF2B5_uc003fmr.2_5'Flank	NM_003907	NP_003898	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B,	557	W2.				astrocyte development|myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|positive regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus|RNA metabolic process	cytosol|eukaryotic translation initiation factor 2B complex|nucleus	guanyl-nucleotide exchange factor activity|transferase activity|translation initiation factor activity|translation initiation factor binding			ovary(5)	5	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			CCAGAATGAAGTTTTAGGAAC	0.438													8	106	---	---	---	---	PASS
ECE2	9718	broad.mit.edu	37	3	184003289	184003289	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184003289G>T	uc003fni.3	+	10	1564	c.1526G>T	c.(1525-1527)TGG>TTG	p.W509L	ECE2_uc011brh.1_Missense_Mutation_p.W362L|ECE2_uc003fnl.3_Missense_Mutation_p.W437L|ECE2_uc003fnm.3_Missense_Mutation_p.W391L|ECE2_uc003fnk.3_Missense_Mutation_p.W362L|ECE2_uc011bri.1_Missense_Mutation_p.W424L|ECE2_uc010hxv.2_Missense_Mutation_p.W153L	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A	509	Lumenal (Potential).|Endothelin-converting enzyme 2 region.				brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TACCTGATCTGGAACCTGGTG	0.517											OREG0015945	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	313	---	---	---	---	PASS
PSMD2	5708	broad.mit.edu	37	3	184021421	184021421	+	Intron	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184021421C>A	uc003fnn.1	+						PSMD2_uc011brj.1_Intron|PSMD2_uc011brk.1_Intron	NM_002808	NP_002799	Q13200	PSMD2_HUMAN	proteasome 26S non-ATPase subunit 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding				0	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	TAGATTCTTCCCTGGTATAGG	0.453													7	142	---	---	---	---	PASS
SENP2	59343	broad.mit.edu	37	3	185316246	185316246	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185316246C>T	uc003fpn.2	+	3	375	c.204C>T	c.(202-204)AGC>AGT	p.S68S	SENP2_uc011brv.1_Silent_p.S58S|SENP2_uc011brw.1_5'UTR	NM_021627	NP_067640	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific protease 2	68					mRNA transport|protein desumoylation|protein transport|proteolysis|regulation of Wnt receptor signaling pathway|transmembrane transport|Wnt receptor signaling pathway	cytoplasm|nuclear membrane|nuclear pore	protein binding|SUMO-specific protease activity				0	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			ATGCTGCCAGCTTATTTGGAT	0.413													15	143	---	---	---	---	PASS
MASP1	5648	broad.mit.edu	37	3	186980345	186980345	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186980345T>A	uc003frh.1	-	3	733	c.401A>T	c.(400-402)CAC>CTC	p.H134L	MASP1_uc003fri.2_Missense_Mutation_p.H134L|MASP1_uc003frj.2_Missense_Mutation_p.H103L|MASP1_uc003frk.1_Missense_Mutation_p.H134L|MASP1_uc011bse.1_Missense_Mutation_p.H108L	NM_001879	NP_001870	P48740	MASP1_HUMAN	mannan-binding lectin serine protease 1 isoform	134	Interaction with FCN2.|Interaction with MBL2.|Homodimerization (By similarity).|CUB 1.				complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		AGCCATGTAGTGGGCATCAAA	0.507													43	179	---	---	---	---	PASS
ATP13A3	79572	broad.mit.edu	37	3	194151920	194151920	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194151920C>T	uc003fty.3	-	22	2859	c.2457G>A	c.(2455-2457)GAG>GAA	p.E819E	ATP13A3_uc003ftz.1_Silent_p.E525E	NM_024524	NP_078800	Q9H7F0	AT133_HUMAN	ATPase type 13A3	819					ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)	1	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		TTTGAAGATCCTCTAAGCTAT	0.348													16	136	---	---	---	---	PASS
LRCH3	84859	broad.mit.edu	37	3	197598320	197598320	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197598320C>A	uc011bul.1	+	19	2122	c.2117C>A	c.(2116-2118)CCC>CAC	p.P706H	LRCH3_uc003fyj.1_Missense_Mutation_p.P706H|LRCH3_uc011bum.1_Missense_Mutation_p.P654H|LRCH3_uc011bun.1_Missense_Mutation_p.P552H|LRCH3_uc003fyk.2_Missense_Mutation_p.P301H	NM_032773	NP_116162	Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH)	706	CH.					extracellular region				ovary(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		ATTCATGTTCCCTCACCAGCT	0.393													8	290	---	---	---	---	PASS
ZNF518B	85460	broad.mit.edu	37	4	10445265	10445265	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10445265T>A	uc003gmn.2	-	3	3175	c.2688A>T	c.(2686-2688)TTA>TTT	p.L896F		NM_053042	NP_444270	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	896					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)	4						TCTTCCTGGATAAGTGTACTT	0.393													11	52	---	---	---	---	PASS
MED28	80306	broad.mit.edu	37	4	17623283	17623283	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17623283G>T	uc003gpi.1	+	3	312	c.300G>T	c.(298-300)TTG>TTT	p.L100F	MED28_uc003gpj.2_RNA	NM_025205	NP_079481	Q9H204	MED28_HUMAN	mediator complex subunit 28	100					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|membrane|nucleus	actin binding				0						AAAAAAGATTGCAGTTATCTG	0.353													4	26	---	---	---	---	PASS
KIT	3815	broad.mit.edu	37	4	55564640	55564640	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55564640A>T	uc010igr.2	+	3	615	c.528A>T	c.(526-528)AAA>AAT	p.K176N	KIT_uc010igs.2_Missense_Mutation_p.K176N	NM_000222	NP_000213	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral	176	Extracellular (Potential).|Ig-like C2-type 2.				male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	AAAGTGTGAAACGCGCCTACC	0.527		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				22	23	---	---	---	---	PASS
KDR	3791	broad.mit.edu	37	4	55964865	55964865	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55964865C>G	uc003has.2	-	16	2674	c.2372G>C	c.(2371-2373)CGG>CCG	p.R791P	KDR_uc003hat.1_Missense_Mutation_p.R791P	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	791	Cytoplasmic (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	TTTTTTTACCCGCTTAACGGT	0.418			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			17	42	---	---	---	---	PASS
REST	5978	broad.mit.edu	37	4	57796520	57796520	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57796520T>A	uc003hch.2	+	4	1843	c.1496T>A	c.(1495-1497)GTG>GAG	p.V499E	REST_uc003hci.2_Missense_Mutation_p.V499E|REST_uc010ihf.2_Missense_Mutation_p.V173E	NM_005612	NP_005603	Q13127	REST_HUMAN	RE1-silencing transcription factor	499	Lys-rich.				cardiac muscle cell myoblast differentiation|cellular response to drug|cellular response to electrical stimulus|cellular response to glucocorticoid stimulus|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of aldosterone biosynthetic process|negative regulation of calcium ion-dependent exocytosis|negative regulation of cell proliferation|negative regulation of cortisol biosynthetic process|negative regulation of dense core granule biogenesis|negative regulation of insulin secretion|negative regulation of mesenchymal stem cell differentiation|negative regulation of neurogenesis|negative regulation of neuron differentiation|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of transcription, DNA-dependent	cytoplasm|transcriptional repressor complex	calcium channel activity|chromatin binding|core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|outward rectifier potassium channel activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|zinc ion binding			skin(5)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	9	Glioma(25;0.08)|all_neural(26;0.181)					GTAACAGAGGTGAAAGAGATG	0.383													6	67	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62775359	62775359	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62775359A>G	uc010ihh.2	+	9	1938	c.1765A>G	c.(1765-1767)ACC>GCC	p.T589A	LPHN3_uc003hcq.3_Missense_Mutation_p.T589A|LPHN3_uc003hct.2_5'UTR|LPHN3_uc003hcs.1_Missense_Mutation_p.T418A	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	589	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						TGGGGACATCACCTACTCTGT	0.478													7	9	---	---	---	---	PASS
ENAM	10117	broad.mit.edu	37	4	71508091	71508091	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71508091T>G	uc011caw.1	+	9	1229	c.948T>G	c.(946-948)ATT>ATG	p.I316M		NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin precursor	316					bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)			AGCCAAATATTCGTGAAAATC	0.468													36	16	---	---	---	---	PASS
CCDC158	339965	broad.mit.edu	37	4	77290776	77290776	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77290776C>A	uc003hkb.3	-	10	1303	c.1150G>T	c.(1150-1152)GCT>TCT	p.A384S		NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	384	Potential.									skin(3)|ovary(2)|pancreas(1)	6						TGTAGATCAGCCTAAAAAAAG	0.393													15	9	---	---	---	---	PASS
CCDC158	339965	broad.mit.edu	37	4	77290777	77290777	+	Splice_Site	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77290777C>A	uc003hkb.3	-	10	1303	c.1150_splice	c.e10-1	p.A384_splice		NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158											skin(3)|ovary(2)|pancreas(1)	6						GTAGATCAGCCTAAAAAAAGA	0.393													14	9	---	---	---	---	PASS
DDX60	55601	broad.mit.edu	37	4	169197228	169197228	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169197228T>C	uc003irp.2	-	15	2375	c.2083A>G	c.(2083-2085)ATA>GTA	p.I695V		NM_017631	NP_060101	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	695							ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		CATCTGGCTATGAGTTGCCGA	0.373													29	11	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13793634	13793634	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13793634G>T	uc003jfd.2	-	49	8256	c.8214C>A	c.(8212-8214)GAC>GAA	p.D2738E		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2738	AAA 3 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					CAAAGATCTTGTCCACAGAAG	0.478									Kartagener_syndrome				15	99	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14507302	14507302	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14507302A>T	uc003jff.2	+	56	8690	c.8684A>T	c.(8683-8685)CAC>CTC	p.H2895L	TRIO_uc003jfg.2_RNA	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2895	Protein kinase.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					ATCAGGGCGCACCTGGGGGAG	0.622													13	17	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19544111	19544111	+	Nonsense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19544111G>C	uc003jgc.2	-	8	1634	c.1257C>G	c.(1255-1257)TAC>TAG	p.Y419*	CDH18_uc003jgd.2_Nonsense_Mutation_p.Y419*|CDH18_uc011cnm.1_Nonsense_Mutation_p.Y419*	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	419	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					AGTTGATGAAGTATCTAGAGA	0.308													5	40	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21760696	21760696	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21760696T>A	uc010iuc.2	-	10	2062	c.1604A>T	c.(1603-1605)AAA>ATA	p.K535I	CDH12_uc011cno.1_Missense_Mutation_p.K495I|CDH12_uc003jgk.2_Missense_Mutation_p.K535I|uc003jgj.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	535	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						AAAATTTGGTTTGATAGCAGC	0.388										HNSCC(59;0.17)			8	125	---	---	---	---	PASS
PDZD2	23037	broad.mit.edu	37	5	31983601	31983601	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31983601C>G	uc003jhl.2	+	3	1205	c.817C>G	c.(817-819)CTC>GTC	p.L273V	PDZD2_uc003jhm.2_Missense_Mutation_p.L273V|PDZD2_uc011cnx.1_Missense_Mutation_p.L99V	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	273					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						CCCAGATTCTCTCAAGGAGGT	0.532													9	127	---	---	---	---	PASS
PDZD2	23037	broad.mit.edu	37	5	32090546	32090546	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32090546C>A	uc003jhl.2	+	20	7380	c.6992C>A	c.(6991-6993)TCA>TAA	p.S2331*	PDZD2_uc003jhm.2_Nonsense_Mutation_p.S2331*	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	2331					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						GAATCTACCTCATTTTTCTCT	0.507													6	188	---	---	---	---	PASS
C5orf42	65250	broad.mit.edu	37	5	37107698	37107698	+	3'UTR	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37107698C>A	uc011cpa.1	-	52					C5orf42_uc003jko.1_3'UTR|C5orf42_uc003jkp.1_RNA|C5orf42_uc011coy.1_3'UTR|C5orf42_uc003jks.2_RNA|C5orf42_uc011coz.1_3'UTR	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CAATGATATCCAGGTCTTACA	0.517													18	11	---	---	---	---	PASS
HEATR7B2	133558	broad.mit.edu	37	5	40998243	40998243	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40998243G>T	uc003jmj.3	-	42	5159	c.4669C>A	c.(4669-4671)CAA>AAA	p.Q1557K	HEATR7B2_uc003jmi.3_Missense_Mutation_p.Q1112K	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	1557							binding			ovary(6)|central_nervous_system(2)	8						CACGGATCTTGACGAAGTGCT	0.488													124	119	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45262722	45262722	+	Silent	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45262722G>C	uc003jok.2	-	8	1999	c.1974C>G	c.(1972-1974)TCC>TCG	p.S658S		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	658	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						TCCTCATGCGGGAGGTCGGGG	0.557													20	44	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45267206	45267206	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45267206G>A	uc003jok.2	-	7	1793	c.1768C>T	c.(1768-1770)CGA>TGA	p.R590*		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	590	cAMP.|Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						CGATCTAGTCGGTCAATGGCA	0.388													53	33	---	---	---	---	PASS
IL6ST	3572	broad.mit.edu	37	5	55247854	55247854	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55247854T>A	uc003jqq.2	-	13	1857	c.1602A>T	c.(1600-1602)GAA>GAT	p.E534D	IL6ST_uc010iwb.2_Missense_Mutation_p.E473D|IL6ST_uc010iwc.2_Intron|IL6ST_uc010iwd.2_Intron|IL6ST_uc011cqk.1_Missense_Mutation_p.E245D|IL6ST_uc003jqr.2_3'UTR|IL6ST_uc010iwe.1_5'Flank	NM_002184	NP_002175	P40189	IL6RB_HUMAN	interleukin 6 signal transducer isoform 1	534	Extracellular (Potential).|Fibronectin type-III 5.				interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production	ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex	ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity			large_intestine(1)|ovary(1)	2		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				CTAAGACAGCTTCGTTTTTCC	0.353			O		hepatocellular ca								12	5	---	---	---	---	PASS
PIK3R1	5295	broad.mit.edu	37	5	67593336	67593336	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67593336G>T	uc003jva.2	+	16	2642	c.2082G>T	c.(2080-2082)CTG>CTT	p.L694L	PIK3R1_uc003jvb.2_Silent_p.L694L|PIK3R1_uc003jvc.2_Silent_p.L394L|PIK3R1_uc003jvd.2_Silent_p.L424L|PIK3R1_uc003jve.2_Silent_p.L373L	NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1	694	SH2 2.				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.?(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)	TGAAAGAACTGGTGCTACATT	0.493			Mis|F|O		gliobastoma|ovarian|colorectal					TCGA GBM(4;<1E-08)			7	150	---	---	---	---	PASS
CMYA5	202333	broad.mit.edu	37	5	79031807	79031807	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79031807C>T	uc003kgc.2	+	2	7291	c.7219C>T	c.(7219-7221)CCA>TCA	p.P2407S		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2407						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		ATCAGAGAAACCAGAGTCAAT	0.358													9	25	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127800548	127800548	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127800548A>T	uc003kuu.2	-	6	1134	c.695T>A	c.(694-696)ATT>AAT	p.I232N	FBN2_uc003kuv.2_Missense_Mutation_p.I199N|FBN2_uc003kuw.3_Missense_Mutation_p.I232N|FBN2_uc003kux.1_Missense_Mutation_p.I232N	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	232	TB 1.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CGTGCAGACAATGCCTGTCAG	0.567													31	6	---	---	---	---	PASS
HSPA4	3308	broad.mit.edu	37	5	132424810	132424810	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132424810C>T	uc003kyj.2	+	10	1482	c.1201C>T	c.(1201-1203)CCA>TCA	p.P401S		NM_002154	NP_002145	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	401					cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein	cytoplasm|nucleus	ATP binding			lung(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGTACCATATCCAATATCTCT	0.328													5	32	---	---	---	---	PASS
TRPC7	57113	broad.mit.edu	37	5	135692600	135692600	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135692600G>A	uc003lbn.1	-	1	476	c.473C>T	c.(472-474)ACG>ATG	p.T158M	TRPC7_uc010jef.1_Missense_Mutation_p.T150M|TRPC7_uc010jeg.1_RNA|TRPC7_uc010jeh.1_Missense_Mutation_p.T150M|TRPC7_uc010jei.1_Missense_Mutation_p.T150M|TRPC7_uc010jej.1_Translation_Start_Site	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,	159	Cytoplasmic (Potential).				axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GGAGAAGCGCGTGCCGTCCTC	0.667													49	11	---	---	---	---	PASS
FLT4	2324	broad.mit.edu	37	5	180048825	180048825	+	Silent	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180048825T>C	uc003mma.3	-	13	1816	c.1737A>G	c.(1735-1737)CAA>CAG	p.Q579Q	FLT4_uc003mlz.3_Silent_p.Q579Q|FLT4_uc003mmb.1_Silent_p.Q112Q|FLT4_uc011dgy.1_Silent_p.Q579Q	NM_002020	NP_002011	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 2	579	Ig-like C2-type 6.|Extracellular (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)	AGCTGTCGGCTTGGCAGCTCA	0.622									Congenital_Hereditary_Lymphedema				10	8	---	---	---	---	PASS
C6orf145	221749	broad.mit.edu	37	6	3737340	3737340	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3737340T>A	uc003mvt.2	-	3	920	c.439A>T	c.(439-441)AGC>TGC	p.S147C		NM_183373	NP_899229	Q5TGL8	CF145_HUMAN	hypothetical protein LOC221749	147					cell communication		phosphatidylinositol binding			breast(1)	1	Ovarian(93;0.0925)	all_hematologic(90;0.108)				CTTTGAAAGCTGGGTTGAATT	0.448													11	78	---	---	---	---	PASS
FAM65B	9750	broad.mit.edu	37	6	24861267	24861267	+	Intron	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24861267G>T	uc003neo.1	-						FAM65B_uc011djs.1_Intron|FAM65B_uc011dju.1_Intron|FAM65B_uc003nep.2_Intron|FAM65B_uc011djt.1_Intron	NM_014722	NP_055537	Q9Y4F9	FA65B_HUMAN	hypothetical protein LOC9750 isoform 1						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1						CACATATTCTGCAAAGAGGAC	0.458													8	5	---	---	---	---	PASS
BTN3A1	11119	broad.mit.edu	37	6	26413559	26413559	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26413559G>T	uc003nhv.2	+	10	1549	c.1181G>T	c.(1180-1182)AGA>ATA	p.R394I	BTN3A1_uc011dkj.1_3'UTR|BTN3A1_uc011dkk.1_Missense_Mutation_p.R342I|BTN3A1_uc010jqj.2_3'UTR	NM_007048	NP_008979	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1 isoform a	394	Cytoplasmic (Potential).|B30.2/SPRY.				lipid metabolic process	integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2						ATATCAGGGAGACATTACTGG	0.507													38	26	---	---	---	---	PASS
HIST1H1B	3009	broad.mit.edu	37	6	27835316	27835316	+	5'UTR	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27835316G>A	uc003njx.2	-	1						NM_005322	NP_005313	P16401	H15_HUMAN	histone cluster 1, H1b						nucleosome assembly	nucleosome|nucleus	DNA binding			large_intestine(2)|lung(1)	3						ATGGTGGCAAGAAACTGCTAG	0.572													8	8	---	---	---	---	PASS
OR2B2	81697	broad.mit.edu	37	6	27879772	27879772	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27879772G>T	uc011dkw.1	-	1	326	c.326C>A	c.(325-327)TCC>TAC	p.S109Y		NM_033057	NP_149046	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B,	109	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						ACATTCTGTGGAACCCAAGGC	0.463													26	20	---	---	---	---	PASS
GABBR1	2550	broad.mit.edu	37	6	29574776	29574776	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29574776C>A	uc003nmt.3	-	18	2451	c.2115G>T	c.(2113-2115)CTG>CTT	p.L705L	GABBR1_uc003nmp.3_Silent_p.L588L|GABBR1_uc003nms.3_Silent_p.L588L|GABBR1_uc003nmu.3_Silent_p.L643L|GABBR1_uc011dlr.1_Silent_p.L528L	NM_001470	NP_001461	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor 1	705	Cytoplasmic (Potential).				gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(5)|liver(1)|skin(1)	7					Baclofen(DB00181)|Progabide(DB00837)	TCCAGGGTTCCAGAGTCTGGA	0.592													5	35	---	---	---	---	PASS
FLOT1	10211	broad.mit.edu	37	6	30708458	30708458	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30708458G>T	uc003nrm.2	-	6	636	c.472C>A	c.(472-474)CAG>AAG	p.Q158K	FLOT1_uc011dmr.1_Missense_Mutation_p.Q110K	NM_005803	NP_005794	O75955	FLOT1_HUMAN	flotillin 1	158						centriolar satellite|endosome|integral to membrane|melanosome|membrane fraction					0						AGTTTTACCTGGTCATCGTGA	0.468													5	79	---	---	---	---	PASS
LY6G5C	80741	broad.mit.edu	37	6	31644735	31644735	+	Nonstop_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31644735T>A	uc003nvu.1	-	3	443	c.443A>T	c.(442-444)TAG>TTG	p.*148L	LY6G5C_uc003nvw.1_RNA|LY6G5C_uc010jtb.1_RNA	NM_025262	NP_079538	Q5SRR4	LY65C_HUMAN	lymphocyte antigen 6 complex G5C	148	UPAR/Ly6.					extracellular region					0						GCAGTCACACTAAGGAGTATA	0.478													8	69	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	6	32427855	32427855	+	IGR	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32427855C>G								HLA-DRA (15034 upstream) : HLA-DRB1 (57308 downstream)																							TTAATCTGCTCCAAGAAATGT	0.542													14	28	---	---	---	---	PASS
TNFRSF21	27242	broad.mit.edu	37	6	47200539	47200539	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47200539G>T	uc003oyv.2	-	6	2363	c.1930C>A	c.(1930-1932)CTG>ATG	p.L644M		NM_014452	NP_055267	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily,	644	Cytoplasmic (Potential).				cellular lipid metabolic process	cytoplasm|integral to membrane	protein binding|receptor activity				0			Lung(136;0.189)			ACAGAGTCCAGGAGGGTCTGG	0.468													6	145	---	---	---	---	PASS
PAQR8	85315	broad.mit.edu	37	6	52268753	52268753	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52268753C>A	uc003pao.3	+	2	916	c.742C>A	c.(742-744)CAC>AAC	p.H248N		NM_133367	NP_588608	Q8TEZ7	MPRB_HUMAN	progestin and adipoQ receptor family member	248	Helical; Name=5; (Potential).				cell differentiation|multicellular organismal development|oogenesis	integral to membrane|plasma membrane	receptor activity|steroid binding				0	Lung NSC(77;0.0875)					AGCCTGGTACCACACCCTCCA	0.592													5	53	---	---	---	---	PASS
GCLC	2729	broad.mit.edu	37	6	53385711	53385711	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53385711C>A	uc003pbw.1	-	3	699	c.311G>T	c.(310-312)GGG>GTG	p.G104V	GCLC_uc003pbx.2_Missense_Mutation_p.G104V	NM_001498	NP_001489	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	104					anti-apoptosis|cell redox homeostasis|cysteine metabolic process|glutamate metabolic process|glutathione biosynthetic process|negative regulation of transcription, DNA-dependent|regulation of blood vessel size|response to heat|response to hormone stimulus|response to oxidative stress|xenobiotic metabolic process	cytosol	ADP binding|ATP binding|coenzyme binding|glutamate binding|glutamate-cysteine ligase activity|magnesium ion binding			ovary(1)|central_nervous_system(1)	2	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)	TCCTGGTGTCCCTTCAATCAT	0.458													8	264	---	---	---	---	PASS
LRRC1	55227	broad.mit.edu	37	6	53784346	53784346	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53784346G>T	uc003pcd.1	+	12	1434	c.1157G>T	c.(1156-1158)TGG>TTG	p.W386L		NM_018214	NP_060684	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	386	LRR 17.					cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		AAGGCTCTGTGGCTATCTGAC	0.418													6	72	---	---	---	---	PASS
IBTK	25998	broad.mit.edu	37	6	82950160	82950160	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82950160A>C	uc003pjl.1	-	2	571	c.44T>G	c.(43-45)CTG>CGG	p.L15R	IBTK_uc011dyv.1_Missense_Mutation_p.L15R|IBTK_uc011dyw.1_Missense_Mutation_p.L15R|IBTK_uc010kbi.1_5'UTR|IBTK_uc003pjm.2_Missense_Mutation_p.L15R	NM_015525	NP_056340	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton's tyrosine kinase	15					negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		AGCATGCTTCAGGGATCGACA	0.403													7	90	---	---	---	---	PASS
CASP8AP2	9994	broad.mit.edu	37	6	90572028	90572028	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90572028G>T	uc003pnr.2	+	7	796	c.600G>T	c.(598-600)AAG>AAT	p.K200N	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Missense_Mutation_p.K200N|CASP8AP2_uc011dzz.1_Missense_Mutation_p.K200N	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	200					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		ATCTGGAAAAGGAAGGAAAAC	0.383													7	203	---	---	---	---	PASS
C6orf167	253714	broad.mit.edu	37	6	97679333	97679333	+	Missense_Mutation	SNP	C	A	A	rs138260692		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97679333C>A	uc003ppb.2	-	13	1764	c.1498G>T	c.(1498-1500)GGC>TGC	p.G500C	C6orf167_uc011eaf.1_Missense_Mutation_p.G460C|C6orf167_uc010kcn.1_Missense_Mutation_p.G274C	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714	500					double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)		GGATGAGGGCCATTGCTCTTC	0.348													5	16	---	---	---	---	PASS
PRDM13	59336	broad.mit.edu	37	6	100062259	100062259	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100062259C>A	uc003pqg.1	+	4	2009	c.1748C>A	c.(1747-1749)TCG>TAG	p.S583*		NM_021620	NP_067633	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	583	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		AAGCTGTACTCGCGCAAGTAT	0.453													13	13	---	---	---	---	PASS
SIM1	6492	broad.mit.edu	37	6	100896428	100896428	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100896428C>T	uc003pqj.3	-	6	877	c.670G>A	c.(670-672)GAG>AAG	p.E224K	SIM1_uc010kcu.2_Missense_Mutation_p.E224K	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	224	PAS 2.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		AGCTTGATCTCCGTGACGGCG	0.617													10	20	---	---	---	---	PASS
LAMA4	3910	broad.mit.edu	37	6	112486384	112486384	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112486384G>T	uc003pvu.2	-	13	1955	c.1646C>A	c.(1645-1647)TCA>TAA	p.S549*	LAMA4_uc003pvv.2_Nonsense_Mutation_p.S542*|LAMA4_uc003pvt.2_Nonsense_Mutation_p.S542*	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	549	Domain II and I.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		ATCAAGTTCTGAAAGAGTTAG	0.433													6	63	---	---	---	---	PASS
FRK	2444	broad.mit.edu	37	6	116381198	116381198	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116381198T>C	uc003pwi.1	-	1	724	c.277A>G	c.(277-279)AGT>GGT	p.S93G		NM_002031	NP_002022	P42685	FRK_HUMAN	fyn-related kinase	93	SH3.				negative regulation of cell proliferation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|lung(3)	6		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)		AGTTGCTGACTGGAGCCATCT	0.473													62	118	---	---	---	---	PASS
KPNA5	3841	broad.mit.edu	37	6	117043288	117043288	+	Splice_Site	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117043288G>T	uc003pxh.2	+	9	888	c.757_splice	c.e9-1	p.V253_splice		NM_002269	NP_002260	O15131	IMA5_HUMAN	karyopherin alpha 5						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)|skin(1)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		TTCCCTTACAGGTTTCACCTT	0.323													4	27	---	---	---	---	PASS
THEMIS	387357	broad.mit.edu	37	6	128222064	128222064	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128222064A>G	uc003qbi.2	-	2	333	c.14T>C	c.(13-15)CTG>CCG	p.L5P	THEMIS_uc011ebt.1_Missense_Mutation_p.L5P|THEMIS_uc010kfb.2_Intron	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	thymocyte selection pathway associated isoform	5	CABIT 1.				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)|skin(2)	4						GAATTCTTCCAGTGATAATGC	0.493													24	72	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129712691	129712691	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129712691C>T	uc003qbn.2	+	36	5232	c.5127C>T	c.(5125-5127)GCC>GCT	p.A1709A	LAMA2_uc003qbo.2_Silent_p.A1709A	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	1709	Domain II and I.|Potential.				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)		GAGACGAGGCCTTTGAGAGAA	0.363													36	95	---	---	---	---	PASS
VNN3	55350	broad.mit.edu	37	6	133044143	133044143	+	3'UTR	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133044143G>A	uc003qdp.2	-	8					VNN3_uc010kfs.2_Silent_p.V184V|VNN3_uc011ecl.1_RNA|VNN3_uc011ecm.1_Silent_p.V218V|VNN3_uc011ecn.1_Silent_p.V218V|VNN3_uc010kfu.2_Silent_p.V218V|VNN3_uc010kfv.2_RNA|VNN3_uc010kfw.2_Silent_p.V218V|VNN3_uc010kfx.2_Silent_p.V184V|VNN3_uc010kfy.2_Silent_p.V184V|VNN3_uc010kfz.2_3'UTR	NM_078625	NP_523239			SubName: Full=PAGEL-beta;												0	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00242)|GBM - Glioblastoma multiforme(226;0.0168)		CCATAACTAAGACAGGCAAAG	0.483													52	53	---	---	---	---	PASS
LTV1	84946	broad.mit.edu	37	6	144164604	144164604	+	5'UTR	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144164604G>A	uc003qjs.2	+	1						NM_032860	NP_116249	Q96GA3	LTV1_HUMAN	LTV1 homolog											ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)		TGAGCGCCGCGCGGCTGCAGC	0.652													9	20	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152734570	152734570	+	Silent	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152734570A>G	uc010kiw.2	-	42	6749	c.6147T>C	c.(6145-6147)GAT>GAC	p.D2049D	SYNE1_uc003qot.3_Silent_p.D2056D|SYNE1_uc003qou.3_Silent_p.D2049D|SYNE1_uc010kjb.1_Silent_p.D2032D	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2049	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CAAAAGCTACATCTTTCTGGG	0.403										HNSCC(10;0.0054)			28	53	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	6	153603625	153603625	+	IGR	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153603625C>A								RGS17 (151236 upstream) : OPRM1 (728011 downstream)																							TGTTCACTGACCAAAGTCCAC	0.483													43	86	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	6	153603626	153603626	+	IGR	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153603626C>A								RGS17 (151237 upstream) : OPRM1 (728010 downstream)																							GTTCACTGACCAAAGTCCACA	0.478													43	86	---	---	---	---	PASS
TULP4	56995	broad.mit.edu	37	6	158923577	158923577	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158923577A>G	uc003qrf.2	+	13	4239	c.2882A>G	c.(2881-2883)TAT>TGT	p.Y961C	TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	961					intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CCACCCCCGTATCCTGAAATT	0.662													10	11	---	---	---	---	PASS
MAP3K4	4216	broad.mit.edu	37	6	161470015	161470015	+	Silent	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161470015A>T	uc003qtn.2	+	3	853	c.711A>T	c.(709-711)TCA>TCT	p.S237S	MAP3K4_uc010kkc.1_Silent_p.S237S|MAP3K4_uc003qto.2_Silent_p.S237S|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_5'UTR	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	237					activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AGCTTACCTCAGTCTCAAAGA	0.433													17	22	---	---	---	---	PASS
TCTE3	6991	broad.mit.edu	37	6	170151566	170151566	+	5'UTR	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170151566C>T	uc003qxe.1	-	1					TCTE3_uc003qxf.2_RNA|C6orf70_uc003qxg.1_5'Flank|C6orf70_uc011ehb.1_5'Flank|C6orf70_uc003qxh.1_5'Flank|C6orf70_uc010kky.1_5'Flank	NM_174910	NP_777570	Q8IZS6	TC1D3_HUMAN	t-complex-associated-testis-expressed 3						transport	cytoplasm|dynein complex|membrane|microtubule	motor activity				0		Breast(66;0.000338)		OV - Ovarian serous cystadenocarcinoma(33;1.08e-21)|BRCA - Breast invasive adenocarcinoma(81;1.32e-07)|GBM - Glioblastoma multiforme(31;0.00157)		TCGCTCTGTTCTCCAAGACGC	0.662													6	47	---	---	---	---	PASS
KIAA0415	9907	broad.mit.edu	37	7	4820834	4820834	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4820834T>A	uc003sne.2	+	2	153	c.70T>A	c.(70-72)TTC>ATC	p.F24I	KIAA0415_uc010ksp.2_RNA	NM_014855	NP_055670	O43299	K0415_HUMAN	hypothetical protein LOC9907	24					cell death|double-strand break repair via homologous recombination	cytoplasm|nucleus	protein binding			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.091)|OV - Ovarian serous cystadenocarcinoma(56;8.35e-15)		GCTGAAGAAGTTCTGTTCCCG	0.542													29	29	---	---	---	---	PASS
SP4	6671	broad.mit.edu	37	7	21521591	21521591	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21521591G>A	uc003sva.2	+	5	2138	c.1957G>A	c.(1957-1959)GGA>AGA	p.G653R	SP4_uc003svb.2_Missense_Mutation_p.G340R	NM_003112	NP_003103	Q02446	SP4_HUMAN	Sp4 transcription factor	653	C2H2-type 1.				regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(3)|skin(2)	5						TCATATTGAAGGATGTGGTAA	0.373													8	69	---	---	---	---	PASS
KLHL7	55975	broad.mit.edu	37	7	23207573	23207573	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23207573C>G	uc003svs.3	+	9	1589	c.1296C>G	c.(1294-1296)ATC>ATG	p.I432M	KLHL7_uc003svr.3_Missense_Mutation_p.I410M|KLHL7_uc011jys.1_Missense_Mutation_p.I356M|KLHL7_uc011jyt.1_Missense_Mutation_p.I207M|KLHL7_uc003svt.2_Missense_Mutation_p.I384M|KLHL7_uc011jyv.1_Intron	NM_001031710	NP_001026880	Q8IXQ5	KLHL7_HUMAN	kelch-like 7 isoform 1	432	Kelch 4.					Golgi apparatus|nucleolus|plasma membrane					0						ATGGCCTAATCTATGTTTGTG	0.443													31	58	---	---	---	---	PASS
HOXA2	3199	broad.mit.edu	37	7	27141032	27141032	+	Silent	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27141032A>T	uc003syh.2	-	2	719	c.444T>A	c.(442-444)ACT>ACA	p.T148T		NM_006735	NP_006726	O43364	HXA2_HUMAN	homeobox A2	148	Homeobox.					nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2						TGGTGTAAGCAGTTCTCAGGC	0.537													11	10	---	---	---	---	PASS
C7orf16	10842	broad.mit.edu	37	7	31736665	31736665	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31736665G>C	uc003tcl.2	+	4	480	c.322G>C	c.(322-324)GAC>CAC	p.D108H	C7orf16_uc011kaf.1_Missense_Mutation_p.D57H	NM_006658	NP_006649	O96001	GSUB_HUMAN	G-substrate isoform 1	108					behavior|central nervous system development|intracellular protein kinase cascade|protein phosphorylation	soluble fraction				ovary(2)|central_nervous_system(1)	3			GBM - Glioblastoma multiforme(11;0.216)			TCATAACACTGACCTGGAACA	0.458													29	59	---	---	---	---	PASS
PKD1L1	168507	broad.mit.edu	37	7	47979871	47979871	+	Silent	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47979871A>G	uc003tny.1	-	3	204	c.204T>C	c.(202-204)TGT>TGC	p.C68C		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	68	Extracellular (Potential).				cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						AAGGACAGCCACACTTCCCAT	0.473													38	37	---	---	---	---	PASS
FKBP6	8468	broad.mit.edu	37	7	72756882	72756882	+	Silent	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72756882A>T	uc003tya.2	+	8	1101	c.969A>T	c.(967-969)ACA>ACT	p.T323T	FKBP6_uc003twz.2_Silent_p.T293T|FKBP6_uc011kew.1_Silent_p.T318T	NM_003602	NP_003593	O75344	FKBP6_HUMAN	FK506 binding protein 6 isoform a	323					protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)				ATGGTTCTACAGCAGGAGAAA	0.537											OREG0018106	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	49	68	---	---	---	---	PASS
PHTF2	57157	broad.mit.edu	37	7	77539631	77539631	+	Silent	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77539631A>G	uc003ugs.3	+	8	807	c.681A>G	c.(679-681)ACA>ACG	p.T227T	PHTF2_uc003ugo.3_Silent_p.T189T|PHTF2_uc003ugp.2_Silent_p.T189T|PHTF2_uc003ugq.3_Silent_p.T189T|PHTF2_uc010ldv.2_Silent_p.T189T|PHTF2_uc003ugr.3_Silent_p.T193T|PHTF2_uc003ugt.3_Silent_p.T193T|PHTF2_uc003ugu.3_Silent_p.T189T|PHTF2_uc003ugv.2_Silent_p.T52T|PHTF2_uc010ldw.1_Silent_p.T52T	NM_001127357	NP_001120829	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	227					regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1						CAGATAACACACAAGAGGGAG	0.448													45	49	---	---	---	---	PASS
ABCB1	5243	broad.mit.edu	37	7	87196249	87196249	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87196249C>A	uc003uiz.1	-	7	800	c.382G>T	c.(382-384)GCT>TCT	p.A128S	ABCB1_uc011khc.1_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	128	ABC transmembrane type-1 1.|Helical; (Potential).				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	ATGTAAGCAGCAACCAGCACC	0.403													9	53	---	---	---	---	PASS
CLDN12	9069	broad.mit.edu	37	7	90042424	90042424	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90042424C>G	uc003ukp.2	+	5	1070	c.434C>G	c.(433-435)ACT>AGT	p.T145S	CLDN12_uc003ukq.2_Missense_Mutation_p.T145S|CLDN12_uc010leq.2_Missense_Mutation_p.T145S|CLDN12_uc003ukr.2_Missense_Mutation_p.T145S|CLDN12_uc003uks.2_Missense_Mutation_p.T145S	NM_012129	NP_036261	P56749	CLD12_HUMAN	claudin 12	145	Helical; (Potential).				calcium-independent cell-cell adhesion|tight junction assembly	integral to membrane|tight junction	identical protein binding|structural molecule activity				0						CTGGCAGGTACTGTGAGCCTC	0.488													11	68	---	---	---	---	PASS
CASD1	64921	broad.mit.edu	37	7	94174935	94174935	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94174935C>T	uc003uni.3	+	12	1782	c.1555C>T	c.(1555-1557)CCC>TCC	p.P519S	CASD1_uc003unj.3_Missense_Mutation_p.P519S	NM_022900	NP_075051	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1 precursor	519	Helical; (Potential).					integral to membrane				ovary(2)	2	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			TTACTTTGTCCCCTTGGTCAC	0.328													29	21	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	100552224	100552224	+	RNA	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100552224T>C	uc003uxk.1	+	1		c.1475T>C			uc003uxl.1_Silent_p.T225T					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																		GTCCAGGAACTATAACAATTA	0.493													77	304	---	---	---	---	PASS
MOGAT3	346606	broad.mit.edu	37	7	100843591	100843591	+	Intron	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100843591G>A	uc003uyc.2	-						MOGAT3_uc010lhr.2_Intron	NM_178176	NP_835470	Q86VF5	MOGT3_HUMAN	monoacylglycerol O-acyltransferase 3						glycerol metabolic process|lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity|diacylglycerol O-acyltransferase activity			ovary(2)	2	Lung NSC(181;0.168)|all_lung(186;0.215)					TCCACCTGCGGACAATGAGAT	0.567													50	56	---	---	---	---	PASS
PLOD3	8985	broad.mit.edu	37	7	100853802	100853802	+	Intron	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100853802C>A	uc003uyd.2	-						PLOD3_uc010lhs.2_Intron	NM_001084	NP_001075	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase						protein modification process	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein binding			ovary(1)|skin(1)	2	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)	AGACCGTGCACCCGCGCTCAC	0.627													4	19	---	---	---	---	PASS
ZNHIT1	10467	broad.mit.edu	37	7	100866982	100866982	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100866982A>G	uc003uye.2	+	4	794	c.302A>G	c.(301-303)TAC>TGC	p.Y101C	ZNHIT1_uc003uyf.2_RNA	NM_006349	NP_006340	O43257	ZNHI1_HUMAN	zinc finger, HIT domain containing 1	101							metal ion binding|protein binding			large_intestine(1)	1	Lung NSC(181;0.168)|all_lung(186;0.215)					GGCCCTAACTACCTGACGGCC	0.682													17	21	---	---	---	---	PASS
SLC26A4	5172	broad.mit.edu	37	7	107323902	107323902	+	Silent	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107323902G>C	uc003vep.2	+	8	1145	c.921G>C	c.(919-921)ACG>ACC	p.T307T		NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin	307	Helical; (Potential).				regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7						TATTTCAGACGATAATTGCTA	0.348									Pendred_syndrome				19	35	---	---	---	---	PASS
PPP1R3A	5506	broad.mit.edu	37	7	113519573	113519573	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113519573C>T	uc010ljy.1	-	4	1605	c.1574G>A	c.(1573-1575)GGT>GAT	p.G525D		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	525					glycogen metabolic process	integral to membrane				lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1)	34						TTCATTAACACCTAAATATAT	0.353													12	23	---	---	---	---	PASS
FOXP2	93986	broad.mit.edu	37	7	114271687	114271687	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114271687C>T	uc003vhb.2	+	6	1076	c.702C>T	c.(700-702)CTC>CTT	p.L234L	FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_Silent_p.L259L|FOXP2_uc003vha.2_Silent_p.L142L|FOXP2_uc011kmu.1_Silent_p.L251L|FOXP2_uc011kmv.1_Silent_p.L233L|FOXP2_uc010ljz.1_Silent_p.L142L|FOXP2_uc003vgt.1_RNA|FOXP2_uc003vgv.1_Silent_p.L234L|FOXP2_uc003vgx.2_Silent_p.L234L|FOXP2_uc003vhd.2_Silent_p.L234L|FOXP2_uc003vhc.2_Silent_p.L259L	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I	234	Gln-rich.				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8						AGCATCTGCTCAGCCTTCAGC	0.478													14	18	---	---	---	---	PASS
TES	26136	broad.mit.edu	37	7	115892000	115892000	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115892000G>T	uc003vho.2	+	5	1070	c.889G>T	c.(889-891)GAG>TAG	p.E297*	TES_uc011kmy.1_Nonsense_Mutation_p.E55*|TES_uc003vhp.2_Nonsense_Mutation_p.E288*|uc003vhq.1_5'Flank	NM_015641	NP_056456	Q9UGI8	TES_HUMAN	testin isoform 1	297	LIM zinc-binding 1.				negative regulation of cell proliferation	cytoplasm|focal adhesion|nucleus|protein complex	zinc ion binding				0	Lung NSC(10;0.0137)|all_lung(10;0.0148)	Breast(660;0.0602)	STAD - Stomach adenocarcinoma(10;0.00878)			CTGTGACAGCGAGAAACCCCG	0.493													31	32	---	---	---	---	PASS
AASS	10157	broad.mit.edu	37	7	121753271	121753271	+	Silent	SNP	C	G	G	rs139733515		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121753271C>G	uc003vka.2	-	10	1275	c.1179G>C	c.(1177-1179)TCG>TCC	p.S393S	AASS_uc011knu.1_RNA|AASS_uc011knv.1_RNA|AASS_uc003vkb.2_Silent_p.S393S|AASS_uc011knw.1_Intron	NM_005763	NP_005754	Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase precursor	393	Lysine-ketoglutarate reductase.				protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)	TCAGGATCCCCGAGCCTTCAA	0.408													12	16	---	---	---	---	PASS
LUC7L2	51631	broad.mit.edu	37	7	139030286	139030286	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139030286C>T	uc011kqt.1	+	2	412	c.178C>T	c.(178-180)CAT>TAT	p.H60Y	LUC7L2_uc011kqs.1_Intron|C7orf55_uc003vuw.3_Missense_Mutation_p.H60Y	NM_016019	NP_057103	Q9Y383	LC7L2_HUMAN	LUC7-like 2	Error:Variant_position_missing_in_Q9Y383_after_alignment							enzyme binding|metal ion binding				0	Melanoma(164;0.242)					ACATGAGCTTCATTTCCAAGC	0.507													14	42	---	---	---	---	PASS
DENND2A	27147	broad.mit.edu	37	7	140301390	140301390	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140301390G>A	uc010lnj.2	-	1	953	c.808C>T	c.(808-810)CGG>TGG	p.R270W	DENND2A_uc011kre.1_RNA|DENND2A_uc010lnk.2_Missense_Mutation_p.R270W|DENND2A_uc003vvw.2_Missense_Mutation_p.R270W|DENND2A_uc003vvx.2_Missense_Mutation_p.R270W	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	270										ovary(3)|breast(1)	4	Melanoma(164;0.00956)					AACGTTCTCCGGGGTTTTGGC	0.498													65	96	---	---	---	---	PASS
TAS2R38	5726	broad.mit.edu	37	7	141673168	141673168	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141673168A>T	uc003vwx.1	-	1	406	c.322T>A	c.(322-324)TGG>AGG	p.W108R		NM_176817	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	108	Helical; Name=3; (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			kidney(1)|skin(1)	2	Melanoma(164;0.0171)					GCAGCAAGCCAGAGGTTGGCT	0.517													30	33	---	---	---	---	PASS
MGAM	8972	broad.mit.edu	37	7	141800656	141800656	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141800656G>A	uc003vwy.2	+	45	5295	c.5241G>A	c.(5239-5241)GGG>GGA	p.G1747G		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	1747	Glucoamylase.|Lumenal (Potential).				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GAACTGCTGGGGGCTGGCTCT	0.498													5	25	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142379005	142379005	+	Intron	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142379005G>A	uc011krp.1	+						uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc011ksg.1_Intron|uc003waa.1_Silent_p.E91E					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																		TAAGGACGGAGCATTTTCCCC	0.498													11	90	---	---	---	---	PASS
OR9A2	135924	broad.mit.edu	37	7	142723686	142723686	+	Silent	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142723686C>G	uc003wcc.1	-	1	534	c.534G>C	c.(532-534)GGG>GGC	p.G178G		NM_001001658	NP_001001658	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A,	178	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	Melanoma(164;0.059)					TGAGCAATTGCCCTCGGTCAC	0.398													33	49	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151878701	151878701	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151878701T>C	uc003wla.2	-	36	6463	c.6244A>G	c.(6244-6246)ATA>GTA	p.I2082V	MLL3_uc003wkz.2_Missense_Mutation_p.I1143V	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	2082	Pro-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)		AAATTATCTATAGGTCTTGGT	0.458			N		medulloblastoma								27	35	---	---	---	---	PASS
UBE3C	9690	broad.mit.edu	37	7	156981640	156981640	+	Intron	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156981640C>G	uc010lqs.2	+						UBE3C_uc003wnf.2_Intron|UBE3C_uc003wng.2_Intron	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C						protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		CACTGATTGTCAGGGTGTACA	0.403													14	5	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	2876056	2876056	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2876056G>T	uc011kwk.1	-	52	8365	c.7975C>A	c.(7975-7977)CAT>AAT	p.H2659N	CSMD1_uc011kwj.1_Missense_Mutation_p.H1988N|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2659	Extracellular (Potential).|Sushi 17.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TCTCTGACATGAGACCCCACA	0.488													101	44	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	3245035	3245035	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3245035G>A	uc011kwk.1	-	18	3156	c.2766C>T	c.(2764-2766)CAC>CAT	p.H922H	CSMD1_uc011kwj.1_Silent_p.H314H|CSMD1_uc003wqe.2_Silent_p.H78H	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	922	Extracellular (Potential).|Sushi 5.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TGGGCAAGGCGTGGTTCCACT	0.582													4	1	---	---	---	---	PASS
DLC1	10395	broad.mit.edu	37	8	12957525	12957525	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12957525A>T	uc003wwm.2	-	9	2765	c.2321T>A	c.(2320-2322)ATG>AAG	p.M774K	DLC1_uc003wwk.1_Missense_Mutation_p.M337K|DLC1_uc003wwl.1_Missense_Mutation_p.M371K|DLC1_uc011kxx.1_Missense_Mutation_p.M263K	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	774					actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						CTCTAAGTACATGCCCACCCG	0.577													16	3	---	---	---	---	PASS
TEX15	56154	broad.mit.edu	37	8	30703523	30703523	+	Nonsense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30703523A>T	uc003xil.2	-	1	3011	c.3011T>A	c.(3010-3012)TTA>TAA	p.L1004*		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	1004										ovary(3)|upper_aerodigestive_tract(2)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AGCTTTTTTTAAGTGAACAAC	0.338													54	19	---	---	---	---	PASS
HTRA4	203100	broad.mit.edu	37	8	38832580	38832580	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38832580A>G	uc003xmj.2	+	2	612	c.497A>G	c.(496-498)AAT>AGT	p.N166S		NM_153692	NP_710159	P83105	HTRA4_HUMAN	HtrA serine peptidase 4 precursor	166					proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)			CTCAGGAGGAATTACAACTTC	0.557													59	27	---	---	---	---	PASS
PCMTD1	115294	broad.mit.edu	37	8	52733199	52733199	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52733199C>T	uc003xqx.3	-	6	1127	c.786G>A	c.(784-786)GAG>GAA	p.E262E	PCMTD1_uc011ldm.1_Silent_p.E132E|PCMTD1_uc003xqw.3_Silent_p.E262E|PCMTD1_uc011ldn.1_Silent_p.E74E|PCMTD1_uc010lya.2_Silent_p.E186E	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)	262						cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)				TGGCCTGCATCTCATCATTTA	0.408													7	102	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55534821	55534821	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55534821G>T	uc003xsd.1	+	3	908	c.760G>T	c.(760-762)GGA>TGA	p.G254*	RP1_uc011ldy.1_Nonsense_Mutation_p.G254*	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	254					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			GTACCCCAAGGGAAATGCAAA	0.423													39	12	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77616390	77616390	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77616390G>T	uc003yav.2	+	2	454	c.67G>T	c.(67-69)GGA>TGA	p.G23*	ZFHX4_uc003yat.1_Nonsense_Mutation_p.G23*|ZFHX4_uc003yau.1_Nonsense_Mutation_p.G23*|ZFHX4_uc003yaw.1_Nonsense_Mutation_p.G23*	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	23						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAAGCTATGTGGAACGACACA	0.493										HNSCC(33;0.089)			5	53	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77775461	77775461	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77775461C>A	uc003yav.2	+	11	9763	c.9376C>A	c.(9376-9378)CCT>ACT	p.P3126T		NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3122	Pro-rich.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			tcctcctcctcctcctccttc	0.358										HNSCC(33;0.089)			18	9	---	---	---	---	PASS
RALYL	138046	broad.mit.edu	37	8	85799928	85799928	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85799928G>A	uc003ycq.3	+	9	1191	c.775G>A	c.(775-777)GCT>ACT	p.A259T	RALYL_uc003ycr.3_Missense_Mutation_p.A259T|RALYL_uc003ycs.3_Missense_Mutation_p.A259T|RALYL_uc010lzy.2_Missense_Mutation_p.A248T|RALYL_uc003yct.3_Missense_Mutation_p.A272T|RALYL_uc003ycu.3_Missense_Mutation_p.A186T|RALYL_uc003ycv.3_Intron	NM_001100392	NP_001093862	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like isoform 2	259							identical protein binding|nucleotide binding|RNA binding			ovary(1)	1						AGAGGAGCCTGCTGAAGGAGG	0.507													9	137	---	---	---	---	PASS
CTHRC1	115908	broad.mit.edu	37	8	104390442	104390442	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104390442C>T	uc003ylk.2	+	3	659	c.560C>T	c.(559-561)TCA>TTA	p.S187L		NM_138455	NP_612464	Q96CG8	CTHR1_HUMAN	collagen triple helix repeat containing 1	187						collagen				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)			GAAATGAATTCAACAATTAAT	0.373													8	46	---	---	---	---	PASS
ZFPM2	23414	broad.mit.edu	37	8	106815050	106815050	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106815050A>G	uc003ymd.2	+	8	2763	c.2740A>G	c.(2740-2742)ATA>GTA	p.I914V	ZFPM2_uc011lhs.1_Missense_Mutation_p.I645V	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	914					blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			AAGAAGCATAATAAAATGTGA	0.453													23	22	---	---	---	---	PASS
TAF2	6873	broad.mit.edu	37	8	120759010	120759010	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120759010C>G	uc003you.2	-	23	3313	c.3043G>C	c.(3043-3045)GCA>CCA	p.A1015P		NM_003184	NP_003175	Q6P1X5	TAF2_HUMAN	TBP-associated factor 2	1015					G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TGGTTGCCTGCTACTGACTCT	0.428													17	125	---	---	---	---	PASS
MTBP	27085	broad.mit.edu	37	8	121463572	121463572	+	Intron	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121463572T>C	uc003ypc.1	+						MTBP_uc003ypb.1_Silent_p.Y145Y|MTBP_uc011lie.1_Intron	NM_022045	NP_071328	Q96DY7	MTBP_HUMAN	Mdm2, transformed 3T3 cell double minute 2, p53						cell cycle arrest					skin(2)|ovary(1)	3	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			AGTATGCTTATATGGTTTTTG	0.299													3	27	---	---	---	---	PASS
EFR3A	23167	broad.mit.edu	37	8	132957123	132957123	+	Intron	SNP	A	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132957123A>C	uc003yte.2	+							NM_015137	NP_055952	Q14156	EFR3A_HUMAN	EFR3 homolog A							plasma membrane	binding			ovary(3)|breast(1)|central_nervous_system(1)	5	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			GTTCTGGGTAAGGAAACTAAT	0.358													4	21	---	---	---	---	PASS
ZNF34	80778	broad.mit.edu	37	8	145999031	145999031	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145999031C>A	uc003zdy.3	-	6	1405	c.1303G>T	c.(1303-1305)GTG>TTG	p.V435L	ZNF34_uc010mgb.2_Missense_Mutation_p.V332L|ZNF34_uc003zdx.3_Missense_Mutation_p.V414L	NM_030580	NP_085057	Q8IZ26	ZNF34_HUMAN	zinc finger protein 34	435	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.221)	OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;5.18e-38)|all cancers(56;4.41e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.0179)		TGATGTTCCACGAGTTTGGTT	0.413													39	13	---	---	---	---	PASS
DMRT1	1761	broad.mit.edu	37	9	893917	893917	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:893917C>T	uc003zgv.2	+	3	693	c.544C>T	c.(544-546)CGT>TGT	p.R182C	DMRT1_uc003zgu.1_Missense_Mutation_p.R182C	NM_021951	NP_068770	Q9Y5R6	DMRT1_HUMAN	doublesex and mab-3 related transcription factor	182					cell differentiation|male gonad development|sex determination	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232)		Lung(218;0.037)		TTTAGAGGGACGTATGGTCAT	0.448											OREG0019071	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	18	---	---	---	---	PASS
C9orf68	55064	broad.mit.edu	37	9	4605351	4605351	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4605351T>C	uc011llz.1	-	9	1149	c.911A>G	c.(910-912)AAC>AGC	p.N304S	C9orf68_uc003zik.2_RNA|C9orf68_uc003zil.2_RNA|C9orf68_uc010mhj.2_Missense_Mutation_p.N362S|C9orf68_uc011lly.1_Missense_Mutation_p.N239S	NM_001039395	NP_001034484	B4DIY4	B4DIY4_HUMAN	hypothetical protein LOC55064	304											0		Breast(48;0.0456)		GBM - Glioblastoma multiforme(50;0.0222)		TCTAACCTTGTTTTGGTGCAG	0.328													29	7	---	---	---	---	PASS
C9orf72	203228	broad.mit.edu	37	9	27556758	27556758	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27556758C>T	uc003zqq.2	-	8	989	c.892G>A	c.(892-894)GTC>ATC	p.V298I		NM_018325	NP_060795	Q96LT7	CI072_HUMAN	hypothetical protein LOC203228 isoform a	298										ovary(3)|central_nervous_system(1)	4		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		GCATACATGACTTGCCGGAAA	0.378													46	27	---	---	---	---	PASS
UBAP1	51271	broad.mit.edu	37	9	34241647	34241647	+	Silent	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34241647G>C	uc003ztx.2	+	4	859	c.624G>C	c.(622-624)GTG>GTC	p.V208V	UBAP1_uc010mka.1_Silent_p.V244V|UBAP1_uc003zty.2_Silent_p.V208V|UBAP1_uc011loi.1_Silent_p.V244V|UBAP1_uc011loj.1_Silent_p.V272V|KIF24_uc010mkb.2_Intron|UBAP1_uc003ztz.2_Silent_p.V208V	NM_016525	NP_057609	Q9NZ09	UBAP1_HUMAN	ubiquitin associated protein 1	208						cytoplasm					0			LUSC - Lung squamous cell carcinoma(29;0.00272)			CTGGGTCTGTGTTACAGGATG	0.483													13	162	---	---	---	---	PASS
KIF24	347240	broad.mit.edu	37	9	34254519	34254519	+	Intron	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34254519C>A	uc003zua.3	-						KIF24_uc010mkb.2_Intron	NM_194313	NP_919289	Q5T7B8	KIF24_HUMAN	kinesin family member 24						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0107)			CTTCAAAATCCTGAGAAGGAA	0.488													11	532	---	---	---	---	PASS
KIF24	347240	broad.mit.edu	37	9	34257596	34257596	+	Missense_Mutation	SNP	G	T	T	rs10972026		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34257596G>T	uc003zua.3	-	11	2129	c.2009C>A	c.(2008-2010)TCT>TAT	p.S670Y	KIF24_uc010mkb.2_Intron	NM_194313	NP_919289	Q5T7B8	KIF24_HUMAN	kinesin family member 24	670					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0107)			ATTTTTCTCAGAGCACAATGG	0.527													11	443	---	---	---	---	PASS
VCP	7415	broad.mit.edu	37	9	35061053	35061053	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35061053C>A	uc003zvy.2	-	11	1707	c.1318G>T	c.(1318-1320)GAG>TAG	p.E440*	VCP_uc003zvz.2_RNA|VCP_uc010mkh.1_Nonsense_Mutation_p.E109*|VCP_uc010mki.1_Nonsense_Mutation_p.E395*	NM_007126	NP_009057	P55072	TERA_HUMAN	valosin-containing protein	440					activation of caspase activity|double-strand break repair|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|retrograde protein transport, ER to cytosol	cytosol|endoplasmic reticulum|microsome|nucleus|proteasome complex	ATP binding|ATPase activity|lipid binding|polyubiquitin binding|protein domain specific binding|protein phosphatase binding			upper_aerodigestive_tract(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TTCATGACCTCGGCATCAATG	0.527													11	882	---	---	---	---	PASS
FAM166B	730112	broad.mit.edu	37	9	35563227	35563227	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35563227C>A	uc010mkr.2	-	2	293	c.222G>T	c.(220-222)AGG>AGT	p.R74S	FAM166B_uc011lov.1_Missense_Mutation_p.R74S|FAM166B_uc011low.1_Missense_Mutation_p.R74S|FAM166B_uc003zwy.2_Missense_Mutation_p.R74S	NM_001164310	NP_001157782	A8MTA8	F166B_HUMAN	hypothetical protein LOC730112 isoform 1	74											0						GTAGACTCTCCCTGGGAACCT	0.617													12	552	---	---	---	---	PASS
MSMP	692094	broad.mit.edu	37	9	35753243	35753243	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35753243C>A	uc003zyb.1	-	3	420	c.274G>T	c.(274-276)GAG>TAG	p.E92*		NM_001044264	NP_001037729	Q1L6U9	MSMP_HUMAN	PC3-secreted microprotein precursor	92						extracellular region					0						TGACGTACCTCACACCCAGCC	0.602													6	129	---	---	---	---	PASS
NPR2	4882	broad.mit.edu	37	9	35807326	35807326	+	Splice_Site	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35807326G>T	uc003zyd.2	+	18	2644	c.2644_splice	c.e18-1	p.V882_splice	NPR2_uc010mlb.2_Splice_Site_p.V858_splice	NM_003995	NP_003986	P20594	ANPRB_HUMAN	natriuretic peptide receptor B precursor						intracellular signal transduction|ossification|receptor guanylyl cyclase signaling pathway|regulation of blood pressure	integral to membrane|plasma membrane	GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|protein kinase activity|transmembrane receptor activity			ovary(2)|stomach(1)	3	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	ATCCCTTTTAGGTAGTGACAC	0.423													12	689	---	---	---	---	PASS
SPAG8	26206	broad.mit.edu	37	9	35810135	35810135	+	Intron	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35810135G>T	uc003zye.2	-						SPAG8_uc003zyf.2_Intron|SPAG8_uc003zyg.2_Intron	NM_172312	NP_758516	Q99932	SPAG8_HUMAN	sperm associated antigen 8 isoform 2							acrosomal vesicle|membrane				ovary(1)	1	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)			ACACCCTGGAGGAGTGCCAGG	0.547													13	777	---	---	---	---	PASS
TMEM8B	51754	broad.mit.edu	37	9	35853137	35853137	+	Splice_Site	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35853137G>T	uc003zym.2	+	13	1982	c.967_splice	c.e13-1	p.V323_splice	TMEM8B_uc003zyo.2_Splice_Site_p.V323_splice	NM_001042589	NP_001036054	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B isoform a						cell-matrix adhesion|regulation of growth|regulation of mitotic cell cycle	cell surface|endoplasmic reticulum|integral to membrane|mitochondrion|nucleus|plasma membrane	protein binding			ovary(1)	1						TCTTTCTCTAGGTGCTGTATT	0.582													11	831	---	---	---	---	PASS
TRPM3	80036	broad.mit.edu	37	9	73235238	73235238	+	Missense_Mutation	SNP	C	A	A	rs145000157		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73235238C>A	uc004aid.2	-	15	2091	c.1847G>T	c.(1846-1848)CGT>CTT	p.R616L	TRPM3_uc004ahu.2_Missense_Mutation_p.R446L|TRPM3_uc004ahv.2_Missense_Mutation_p.R418L|TRPM3_uc004ahw.2_Missense_Mutation_p.R488L|TRPM3_uc004ahx.2_Missense_Mutation_p.R475L|TRPM3_uc004ahy.2_Missense_Mutation_p.R478L|TRPM3_uc004ahz.2_Missense_Mutation_p.R465L|TRPM3_uc004aia.2_Missense_Mutation_p.R463L|TRPM3_uc004aib.2_Missense_Mutation_p.R453L|TRPM3_uc004aic.2_Missense_Mutation_p.R616L	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,	641	Cytoplasmic (Potential).					integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9						CTCTTCTTCACGTTTCTTGGT	0.433													129	26	---	---	---	---	PASS
TMEM2	23670	broad.mit.edu	37	9	74345833	74345833	+	Intron	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74345833G>C	uc011lsa.1	-						TMEM2_uc010mos.2_Intron|TMEM2_uc011lsb.1_Intron	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a							integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		TTCATTATCTGTAAGTCAAGG	0.343													8	30	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79324805	79324805	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79324805C>A	uc010mpk.2	-	8	2509	c.2385G>T	c.(2383-2385)GCG>GCT	p.A795A		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	795					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						CTGGGAATGGCGCCACAGCTG	0.488													7	35	---	---	---	---	PASS
GKAP1	80318	broad.mit.edu	37	9	86403544	86403544	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86403544C>A	uc004amy.2	-	5	906	c.410G>T	c.(409-411)AGT>ATT	p.S137I	GKAP1_uc004amz.2_Missense_Mutation_p.S137I|GKAP1_uc011lsu.1_RNA	NM_025211	NP_079487	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1 isoform a	137	Potential.				signal transduction	Golgi apparatus					0						TTCTAGTTTACTTAGTAACAA	0.303													4	107	---	---	---	---	PASS
C9orf79	286234	broad.mit.edu	37	9	90500668	90500668	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90500668C>A	uc004app.3	+	4	1301	c.1266C>A	c.(1264-1266)GTC>GTA	p.V422V	C9orf79_uc004apo.1_Silent_p.V234V	NM_178828	NP_849150	Q6ZUB1	CI079_HUMAN	chromosome 9 open reading frame 79	422						integral to membrane				ovary(3)	3						CTCAGCAAGTCTCTGATGCCA	0.577													75	19	---	---	---	---	PASS
FANCC	2176	broad.mit.edu	37	9	97864116	97864116	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97864116T>A	uc004avh.2	-	15	1812	c.1550A>T	c.(1549-1551)GAG>GTG	p.E517V		NM_000136	NP_000127	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C	517					protein complex assembly	cytosol|nucleoplasm	protein binding			kidney(1)	1		Acute lymphoblastic leukemia(62;0.138)				GTGAGTTATCTCAGCAGTGTG	0.473			D|Mis|N|F|S			AML|leukemia		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				17	64	---	---	---	---	PASS
IKBKAP	8518	broad.mit.edu	37	9	111640903	111640903	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111640903C>A	uc004bdm.3	-	34	4220	c.3700G>T	c.(3700-3702)GAT>TAT	p.D1234Y	IKBKAP_uc004bdl.2_Missense_Mutation_p.D885Y|IKBKAP_uc011lwc.1_Missense_Mutation_p.D1120Y|IKBKAP_uc010mtq.2_Missense_Mutation_p.D885Y|IKBKAP_uc004bdk.2_Missense_Mutation_p.D238Y|IKBKAP_uc010mtp.2_RNA	NM_003640	NP_003631	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene	1234					immune response|protein complex assembly|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding|signal transducer activity			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	7						GAGAATATACCTTTCAGGTTT	0.498													8	175	---	---	---	---	PASS
ZNF483	158399	broad.mit.edu	37	9	114296103	114296103	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114296103A>C	uc004bff.2	+	4	810	c.586A>C	c.(586-588)AAG>CAG	p.K196Q	ZNF483_uc011lwq.1_Missense_Mutation_p.K196Q|ZNF483_uc004bfg.2_Missense_Mutation_p.K196Q	NM_133464	NP_597721	Q8TF39	ZN483_HUMAN	zinc finger protein 483 isoform a	196	KRAB.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1						GGAGCTATATAAGGAAGTGCT	0.408													6	64	---	---	---	---	PASS
C10orf18	54906	broad.mit.edu	37	10	5799560	5799560	+	Silent	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5799560T>C	uc001iij.2	+	17	7435	c.6810T>C	c.(6808-6810)GAT>GAC	p.D2270D	C10orf18_uc001iik.2_Silent_p.D1114D	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	2270										ovary(1)|central_nervous_system(1)	2						ATGTTCTTGATCACACCTACC	0.438													43	159	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	17156039	17156039	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17156039C>A	uc001ioo.2	-	8	922	c.870G>T	c.(868-870)GGG>GGT	p.G290G		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	290	EGF-like 3; calcium-binding (Potential).				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)	TTGGACAGGCCCCACAGTAGA	0.552													7	12	---	---	---	---	PASS
ZEB1	6935	broad.mit.edu	37	10	31810412	31810412	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31810412C>A	uc001ivs.3	+	7	2212	c.2149C>A	c.(2149-2151)CAG>AAG	p.Q717K	ZEB1_uc001ivr.3_Missense_Mutation_p.Q499K|ZEB1_uc010qee.1_Missense_Mutation_p.Q499K|ZEB1_uc010qef.1_Missense_Mutation_p.Q499K|ZEB1_uc009xlj.1_Missense_Mutation_p.Q643K|ZEB1_uc010qeg.1_Missense_Mutation_p.Q576K|ZEB1_uc009xlk.1_Missense_Mutation_p.Q499K|ZEB1_uc001ivt.3_Missense_Mutation_p.Q499K|ZEB1_uc001ivu.3_Missense_Mutation_p.Q718K|ZEB1_uc001ivv.3_Missense_Mutation_p.Q697K|ZEB1_uc010qeh.1_Missense_Mutation_p.Q650K|ZEB1_uc009xlo.1_Missense_Mutation_p.Q700K|ZEB1_uc009xlp.2_Missense_Mutation_p.Q701K	NM_030751	NP_110378	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b	717					cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)				CAGAAATACACAGGGTTACTT	0.453													16	41	---	---	---	---	PASS
ZNF33A	7581	broad.mit.edu	37	10	38345348	38345348	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38345348G>C	uc001izh.2	+	5	2471	c.2293G>C	c.(2293-2295)GTA>CTA	p.V765L	ZNF33A_uc001izg.2_Missense_Mutation_p.V766L|ZNF33A_uc010qev.1_Missense_Mutation_p.V772L|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	765	C2H2-type 16.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3						AAATCTCATTGTACATCAGAG	0.378													25	39	---	---	---	---	PASS
FRMPD2	143162	broad.mit.edu	37	10	49392662	49392662	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49392662C>G	uc001jgi.2	-	20	2638	c.2531G>C	c.(2530-2532)AGG>ACG	p.R844T	FRMPD2_uc001jgh.2_Missense_Mutation_p.R812T|FRMPD2_uc001jgj.2_Missense_Mutation_p.R822T	NM_001018071	NP_001018081	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2 isoform 3	844	PDZ 1.				tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)		CTGGATCATCCTAACAGCCAT	0.408													16	25	---	---	---	---	PASS
SAMD8	142891	broad.mit.edu	37	10	76910349	76910349	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76910349G>A	uc001jwx.1	+	2	166	c.63G>A	c.(61-63)CTG>CTA	p.L21L	SAMD8_uc001jwy.1_Silent_p.L21L	NM_144660	NP_653261	Q96LT4	SAMD8_HUMAN	sterile alpha motif domain containing 8	21	SAM.				sphingomyelin biosynthetic process	integral to membrane					0	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					CTGTGTGGCTGAAGGATGAAG	0.453													23	26	---	---	---	---	PASS
C10orf11	83938	broad.mit.edu	37	10	77806919	77806919	+	Intron	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77806919C>T	uc001jxi.2	+							NM_032024	NP_114413	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)					TAACCTTTGTCACATCACTGA	0.517													30	30	---	---	---	---	PASS
GBF1	8729	broad.mit.edu	37	10	104135269	104135269	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104135269G>C	uc001kux.1	+	30	4051	c.3811G>C	c.(3811-3813)GAG>CAG	p.E1271Q	GBF1_uc001kuy.1_Missense_Mutation_p.E1271Q|GBF1_uc001kuz.1_Missense_Mutation_p.E1272Q	NM_004193	NP_004184	Q92538	GBF1_HUMAN	golgi-specific brefeldin A resistant guanine	1271					COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CACACTGCTGGAGTGCATCGG	0.592													16	8	---	---	---	---	PASS
SORCS3	22986	broad.mit.edu	37	10	106907389	106907389	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106907389C>T	uc001kyi.1	+	9	1544	c.1317C>T	c.(1315-1317)ATC>ATT	p.I439I		NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	439	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TGCACATCATCAGTACAGACG	0.458													11	19	---	---	---	---	PASS
SORCS1	114815	broad.mit.edu	37	10	108339011	108339011	+	Intron	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108339011T>C	uc001kym.2	-						SORCS1_uc001kyl.2_Splice_Site_p.R1124_splice|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_3'UTR	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GGGATCTTCCTAAAATATTAA	0.468													14	43	---	---	---	---	PASS
ABLIM1	3983	broad.mit.edu	37	10	116232760	116232760	+	Silent	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116232760T>C	uc010qsg.1	-	10	1350	c.1251A>G	c.(1249-1251)AAA>AAG	p.K417K	ABLIM1_uc010qsh.1_Silent_p.K385K|ABLIM1_uc010qsi.1_Silent_p.K357K|ABLIM1_uc010qsk.1_Silent_p.K341K|ABLIM1_uc009xyp.2_Silent_p.K379K|ABLIM1_uc010qsf.1_Silent_p.K129K|ABLIM1_uc009xyn.2_Silent_p.K68K|ABLIM1_uc010qsj.1_Silent_p.K94K|ABLIM1_uc009xyo.2_Silent_p.K265K	NM_002313	NP_002304	O14639	ABLM1_HUMAN	actin-binding LIM protein 1 isoform a	417					axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		GTCTCTCCTGTTTGTCATCAT	0.403													44	14	---	---	---	---	PASS
MKI67	4288	broad.mit.edu	37	10	129913759	129913759	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129913759C>G	uc001lke.2	-	7	1108	c.913G>C	c.(913-915)GAG>CAG	p.E305Q	MKI67_uc001lkf.2_Intron|MKI67_uc009yav.1_Intron|MKI67_uc009yaw.1_Intron	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	305					cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GAAGCAGGCTCTGCCACAGCG	0.552													4	20	---	---	---	---	PASS
TCERG1L	256536	broad.mit.edu	37	10	133106547	133106547	+	Silent	SNP	A	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133106547A>C	uc001lkp.2	-	3	683	c.597T>G	c.(595-597)GCT>GCG	p.A199A		NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	199										large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		ACAGAGACACAGCTACTTGAT	0.522													21	8	---	---	---	---	PASS
MUC6	4588	broad.mit.edu	37	11	1020215	1020215	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1020215G>T	uc001lsw.2	-	29	3734	c.3683C>A	c.(3682-3684)ACC>AAC	p.T1228N		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	1228					maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCCGATGGTGGTGGAGGTTCC	0.657													16	6	---	---	---	---	PASS
OR51M1	390059	broad.mit.edu	37	11	5411036	5411036	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5411036G>T	uc010qzc.1	+	1	408	c.408G>T	c.(406-408)GTG>GTT	p.V136V	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001004756	NP_001004756	B2RNI9	B2RNI9_HUMAN	olfactory receptor, family 51, subfamily M,	136						integral to membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.98e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCGCCTTGTGGCCATCTGCC	0.517													83	37	---	---	---	---	PASS
OR52H1	390067	broad.mit.edu	37	11	5566079	5566079	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5566079G>T	uc010qzh.1	-	1	675	c.675C>A	c.(673-675)TCC>TCA	p.S225S	HBG2_uc001mak.1_Intron	NM_001005289	NP_001005289	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H,	225	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTGTGCGTAGGAAACAGCAA	0.507													4	28	---	---	---	---	PASS
FAR1	84188	broad.mit.edu	37	11	13729455	13729455	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13729455T>C	uc001mld.2	+	4	529	c.374T>C	c.(373-375)GTT>GCT	p.V125A	FAR1_uc009ygp.2_Missense_Mutation_p.V125A	NM_032228	NP_115604	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	125					ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2						AGAGATGCTGTTCAGTTAAAT	0.343													16	1	---	---	---	---	PASS
SPON1	10418	broad.mit.edu	37	11	14280884	14280884	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14280884C>A	uc001mle.2	+	13	2089	c.1551C>A	c.(1549-1551)TGC>TGA	p.C517*		NM_006108	NP_006099	Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein	517	TSP type-1 2.				cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)		GCATCTCCTGCGGCATGGGCA	0.632													8	3	---	---	---	---	PASS
SLC6A5	9152	broad.mit.edu	37	11	20668427	20668427	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20668427C>G	uc001mqd.2	+	14	2290	c.2017C>G	c.(2017-2019)CCT>GCT	p.P673A	SLC6A5_uc009yic.2_Missense_Mutation_p.P438A	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	673					synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	TGGATTCCAGCCTAACATCTT	0.433													23	12	---	---	---	---	PASS
SLC6A5	9152	broad.mit.edu	37	11	20668428	20668428	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20668428C>G	uc001mqd.2	+	14	2291	c.2018C>G	c.(2017-2019)CCT>CGT	p.P673R	SLC6A5_uc009yic.2_Missense_Mutation_p.P438R	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	673					synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	GGATTCCAGCCTAACATCTTC	0.428													23	12	---	---	---	---	PASS
ANO3	63982	broad.mit.edu	37	11	26620410	26620410	+	Silent	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26620410A>T	uc001mqt.3	+	16	1681	c.1536A>T	c.(1534-1536)ACA>ACT	p.T512T	ANO3_uc010rdr.1_Silent_p.T496T|ANO3_uc010rds.1_Silent_p.T351T|ANO3_uc010rdt.1_Silent_p.T366T	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C	512	Cytoplasmic (Potential).					chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CATAGGAAACACTTCGTCCCC	0.393													6	14	---	---	---	---	PASS
OR4C6	219432	broad.mit.edu	37	11	55433025	55433025	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55433025T>A	uc001nht.3	+	3	648	c.383T>A	c.(382-384)CTG>CAG	p.L128Q	OR4C6_uc010rik.1_Missense_Mutation_p.L128Q	NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C,	128	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						TGTAAGCCCCTGCACTACACG	0.537													26	11	---	---	---	---	PASS
TMEM132A	54972	broad.mit.edu	37	11	60704035	60704035	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60704035G>C	uc001nqj.2	+	11	2921	c.2728G>C	c.(2728-2730)GAC>CAC	p.D910H	TMEM132A_uc001nqi.2_Missense_Mutation_p.D911H|TMEM132A_uc001nqm.2_Missense_Mutation_p.D120H	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b	910	Binds to HSPA5/GRP78 (By similarity).|Cytoplasmic (Potential).|Confers cellular localization similar to full-length form (By similarity).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1						CCGCCAGCTGGACCGGCAGTC	0.721													3	7	---	---	---	---	PASS
INTS5	80789	broad.mit.edu	37	11	62416108	62416108	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62416108C>A	uc001nud.2	-	2	1497	c.1444G>T	c.(1444-1446)GGA>TGA	p.G482*	GANAB_uc001nua.2_5'Flank|GANAB_uc001nub.2_5'Flank|GANAB_uc001nuc.2_5'Flank|GANAB_uc010rma.1_5'Flank|GANAB_uc010rmb.1_5'Flank	NM_030628	NP_085131	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	482					snRNA processing	integral to membrane|integrator complex	protein binding			ovary(2)	2						CACAGCTCTCCAACATGGTTT	0.602													5	76	---	---	---	---	PASS
MRGPRF	116535	broad.mit.edu	37	11	68773711	68773711	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68773711C>A	uc001ooo.3	-	3	434	c.67G>T	c.(67-69)GAG>TAG	p.E23*	MRGPRF_uc001oop.3_Nonsense_Mutation_p.E23*	NM_001098515	NP_001091985	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	23	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TCCGGGGCCTCGCTCAGGCCA	0.667													3	9	---	---	---	---	PASS
ANO1	55107	broad.mit.edu	37	11	70009436	70009436	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70009436G>A	uc001opj.2	+	19	2245	c.1940G>A	c.(1939-1941)CGA>CAA	p.R647Q	ANO1_uc001opk.1_Missense_Mutation_p.R589Q|ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_Missense_Mutation_p.R356Q	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	647	Extracellular (Potential).				multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						CGTTCCTTCCGAATGGAAGAG	0.517													10	13	---	---	---	---	PASS
CNTN5	53942	broad.mit.edu	37	11	100061878	100061878	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100061878G>T	uc001pga.2	+	14	1940	c.1601G>T	c.(1600-1602)GGG>GTG	p.G534V	CNTN5_uc009ywv.1_Missense_Mutation_p.G534V|CNTN5_uc001pfz.2_Missense_Mutation_p.G534V|CNTN5_uc001pgb.2_Missense_Mutation_p.G460V|CNTN5_uc010ruk.1_5'UTR	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	534	Ig-like C2-type 5.				cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		CTTCCAGACGGGAGTCTACGG	0.368													18	11	---	---	---	---	PASS
GRIA4	2893	broad.mit.edu	37	11	105623843	105623843	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105623843C>G	uc001pix.2	+	4	830	c.384C>G	c.(382-384)AGC>AGG	p.S128R	GRIA4_uc001piu.1_Missense_Mutation_p.S128R|GRIA4_uc001piw.2_Missense_Mutation_p.S128R|GRIA4_uc001piv.2_Missense_Mutation_p.S128R|GRIA4_uc009yxk.1_Missense_Mutation_p.S128R	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform	128	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	AGGGGGAGAGCCAGTTTGTGC	0.473													26	11	---	---	---	---	PASS
GRIA4	2893	broad.mit.edu	37	11	105795143	105795143	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105795143G>T	uc001pix.2	+	12	1941	c.1495G>T	c.(1495-1497)GCC>TCC	p.A499S	GRIA4_uc001piw.2_Missense_Mutation_p.A499S	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform	499	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	GATTGCTATTGCCCCTCTGAC	0.383													36	10	---	---	---	---	PASS
GUCY1A2	2977	broad.mit.edu	37	11	106680751	106680751	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106680751C>G	uc001pjg.1	-	5	2050	c.1660G>C	c.(1660-1662)GAC>CAC	p.D554H	GUCY1A2_uc010rvo.1_Missense_Mutation_p.D575H|GUCY1A2_uc009yxn.1_Missense_Mutation_p.D554H	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	554	Guanylate cyclase.				intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)		CACTGGTGGTCAAATCTGGTG	0.358													4	18	---	---	---	---	PASS
EXPH5	23086	broad.mit.edu	37	11	108380315	108380315	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108380315G>T	uc001pkk.2	-	6	6030	c.5919C>A	c.(5917-5919)ACC>ACA	p.T1973T	EXPH5_uc010rvy.1_Silent_p.T1785T|EXPH5_uc010rvz.1_Silent_p.T1817T|EXPH5_uc010rwa.1_Silent_p.T1897T	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	1973					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CATCATCTGTGGTTGTGTCTG	0.403													6	76	---	---	---	---	PASS
BACE1	23621	broad.mit.edu	37	11	117160476	117160476	+	Silent	SNP	A	G	G	rs138594731	byFrequency	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117160476A>G	uc001pqz.2	-	9	1773	c.1312T>C	c.(1312-1314)TTG>CTG	p.L438L	BACE1_uc001pqw.2_Silent_p.L413L|BACE1_uc001pqx.2_Silent_p.L369L|BACE1_uc001pqy.2_Silent_p.L394L|BACE1_uc010rxg.1_Silent_p.L313L|BACE1_uc010rxh.1_Silent_p.L338L|uc010rxi.1_5'Flank	NM_012104	NP_036236	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1 isoform A	438	Extracellular (Potential).				beta-amyloid metabolic process|membrane protein ectodomain proteolysis	cell surface|cytoplasmic vesicle membrane|endoplasmic reticulum|endosome|integral to plasma membrane|trans-Golgi network	aspartic-type endopeptidase activity|beta-aspartyl-peptidase activity|protein binding			ovary(1)	1	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		TCCATGTCCAAGGTGACAAAA	0.368													15	7	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	122848348	122848348	+	IGR	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122848348C>A								C11orf63 (17919 upstream) : BSX (10 downstream)																							CCCTCCCCAGCCTGGCGGCTC	0.687													7	4	---	---	---	---	PASS
OR8A1	390275	broad.mit.edu	37	11	124440879	124440879	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124440879C>A	uc010san.1	+	1	915	c.915C>A	c.(913-915)ATC>ATA	p.I305I		NM_001005194	NP_001005194	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A,	305	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.0115)|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;0.0214)		ATCCCCTAATCTACAGCCTGA	0.443													20	8	---	---	---	---	PASS
PATE1	160065	broad.mit.edu	37	11	125618497	125618497	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125618497G>T	uc001qct.2	+	5	262	c.250G>T	c.(250-252)GAT>TAT	p.D84Y	PATE1_uc009zbr.2_Missense_Mutation_p.D72Y	NM_138294	NP_612151	Q8WXA2	PATE1_HUMAN	expressed in prostate and testis precursor	84						extracellular region					0						CTCCACAGGGGATGGTAATCC	0.448													13	8	---	---	---	---	PASS
FAM118B	79607	broad.mit.edu	37	11	126126634	126126634	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126126634G>T	uc001qdf.2	+	7	1052	c.869G>T	c.(868-870)CGA>CTA	p.R290L	FAM118B_uc009zca.2_Missense_Mutation_p.R294L|FAM118B_uc001qdg.2_Missense_Mutation_p.R290L	NM_024556	NP_078832	Q9BPY3	F118B_HUMAN	hypothetical protein LOC79607	290											0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		AAAAAGCTTCGAGAAAACATG	0.443													4	99	---	---	---	---	PASS
ANO2	57101	broad.mit.edu	37	12	5939597	5939597	+	Intron	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5939597T>A	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						ATCCATTTACTTACAATGCGG	0.478													12	18	---	---	---	---	PASS
ACSM4	341392	broad.mit.edu	37	12	7479568	7479568	+	Intron	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7479568G>T	uc001qsx.1	+							NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0						CTTTTCTGTTGCAGGTGGTGA	0.353													9	11	---	---	---	---	PASS
ZNF705A	440077	broad.mit.edu	37	12	8330139	8330139	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8330139T>A	uc001qud.1	+	5	935	c.863T>A	c.(862-864)CTA>CAA	p.L288Q	FAM66C_uc001que.3_5'Flank|FAM66C_uc001quf.3_5'Flank|FAM66C_uc009zgc.2_5'Flank|FAM66C_uc001qug.3_5'Flank	NM_001004328	NP_001004328	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	288					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				Kidney(36;0.0877)		GCTTGTCTTCTATGTGGGAAG	0.418													9	46	---	---	---	---	PASS
CLEC4E	26253	broad.mit.edu	37	12	8689737	8689737	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8689737C>A	uc001quo.1	-	4	511	c.346G>T	c.(346-348)GTG>TTG	p.V116L		NM_014358	NP_055173	Q9ULY5	CLC4E_HUMAN	C-type lectin domain family 4, member E	116	C-type lectin.|Extracellular (Potential).					integral to membrane	sugar binding			central_nervous_system(1)	1	Lung SC(5;0.184)					TTGATAACCACCAGGTGAGCC	0.478													20	14	---	---	---	---	PASS
CLEC1B	51266	broad.mit.edu	37	12	10149584	10149584	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10149584C>A	uc001qwu.2	-	4	499	c.299G>T	c.(298-300)AGC>ATC	p.S100I	CLEC1B_uc009zhd.2_Missense_Mutation_p.S67I	NM_016509	NP_057593	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B isoform	100	Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	protein binding|sugar binding|transmembrane receptor activity				0						GTCACAGGGGCTGCATTTATG	0.413													33	44	---	---	---	---	PASS
ATF7IP	55729	broad.mit.edu	37	12	14633957	14633957	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14633957A>G	uc001rbw.2	+	13	3276	c.3118A>G	c.(3118-3120)ACA>GCA	p.T1040A	ATF7IP_uc001rbv.1_Missense_Mutation_p.T1039A|ATF7IP_uc001rbx.2_Missense_Mutation_p.T1039A|ATF7IP_uc001rby.3_Missense_Mutation_p.T1040A|ATF7IP_uc001rca.2_Missense_Mutation_p.T1040A	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	1040					DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5						CGTGAATGTAACACATCGTCC	0.423													41	65	---	---	---	---	PASS
FAM60A	58516	broad.mit.edu	37	12	31448254	31448254	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31448254G>T	uc010sjz.1	-	3	381	c.142C>A	c.(142-144)CGT>AGT	p.R48S	FAM60A_uc001rkd.2_Missense_Mutation_p.R48S|FAM60A_uc010ska.1_Missense_Mutation_p.R48S|FAM60A_uc001rke.2_Missense_Mutation_p.R48S|FAM60A_uc010skb.1_Intron|FAM60A_uc001rkc.2_Missense_Mutation_p.R73S	NM_021238	NP_067061	Q9NP50	FA60A_HUMAN	family with sequence similarity 60, member A	48											0	all_cancers(9;5.22e-13)|all_epithelial(9;4e-13)|all_lung(12;1.2e-11)|Lung NSC(12;2.17e-09)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0207)|Lung SC(12;0.0592)|Esophageal squamous(101;0.162)					TCTCCTGAACGAGTCTCATGC	0.383													4	44	---	---	---	---	PASS
LRRK2	120892	broad.mit.edu	37	12	40692290	40692290	+	Missense_Mutation	SNP	A	T	T	rs35808389		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40692290A>T	uc001rmg.3	+	24	3463	c.3342A>T	c.(3340-3342)TTA>TTT	p.L1114F	LRRK2_uc001rmh.1_Missense_Mutation_p.L736F|LRRK2_uc009zjw.2_5'UTR	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1114	LRR 6.				activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AGCTCATTTTAGAAGGGTAAG	0.343													46	61	---	---	---	---	PASS
PPHLN1	51535	broad.mit.edu	37	12	42729762	42729762	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42729762C>A	uc001rng.1	+	2	163	c.58C>A	c.(58-60)CGA>AGA	p.R20R	PPHLN1_uc001rmy.2_Silent_p.R38R|PPHLN1_uc001rna.2_Silent_p.R27R|PPHLN1_uc001rne.2_Silent_p.R27R|PPHLN1_uc001rnb.2_Silent_p.R27R|PPHLN1_uc001rnd.2_Silent_p.R27R|PPHLN1_uc001rnc.2_Silent_p.R20R|PPHLN1_uc001rnf.2_Silent_p.R20R|PPHLN1_uc010skq.1_Silent_p.R20R|PPHLN1_uc010skr.1_Silent_p.R20R|PPHLN1_uc010sks.1_Silent_p.R20R|PPHLN1_uc010skt.1_Intron|PPHLN1_uc001rni.1_Silent_p.R20R|PPHLN1_uc001rnh.1_RNA|PPHLN1_uc010sku.1_Silent_p.R27R	NM_016488	NP_057572	Q8NEY8	PPHLN_HUMAN	periphilin 1 isoform 1	20					keratinization	cytoplasm|nucleus				ovary(1)|breast(1)	2	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		AGCACCTCCTCGAAGTCATCC	0.368													4	97	---	---	---	---	PASS
KCNH3	23416	broad.mit.edu	37	12	49949466	49949466	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49949466G>C	uc001ruh.1	+	12	2460	c.2200G>C	c.(2200-2202)GAT>CAT	p.D734H	KCNH3_uc010smj.1_Missense_Mutation_p.D674H	NM_012284	NP_036416	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H	734	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity				0						GAAGGAGACAGATGGGGAGCA	0.637													5	20	---	---	---	---	PASS
KRT84	3890	broad.mit.edu	37	12	52778981	52778981	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52778981C>A	uc001sah.1	-	1	437	c.389G>T	c.(388-390)GGA>GTA	p.G130V		NM_033045	NP_149034	Q9NSB2	KRT84_HUMAN	keratin, hair, basic, 4	130	Head.					keratin filament	structural constituent of epidermis			skin(1)	1	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TGCTGGGACTCCAACCCCTCC	0.572													58	81	---	---	---	---	PASS
KRT74	121391	broad.mit.edu	37	12	52962040	52962040	+	Missense_Mutation	SNP	C	G	G	rs139298074		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52962040C>G	uc001sap.1	-	7	1316	c.1268G>C	c.(1267-1269)CGC>CCC	p.R423P		NM_175053	NP_778223	Q7RTS7	K2C74_HUMAN	keratin 6 irs4	423	Rod.|Coil 2.					keratin filament	structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.191)		CTGGTACTCGCGCAGCATCCG	0.652													24	44	---	---	---	---	PASS
KRT74	121391	broad.mit.edu	37	12	52967522	52967522	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52967522C>A	uc001sap.1	-	1	88	c.40G>T	c.(40-42)GGC>TGC	p.G14C		NM_175053	NP_778223	Q7RTS7	K2C74_HUMAN	keratin 6 irs4	14	Head.|Gly-rich.					keratin filament	structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.191)		CTGAAGTTGCCCTTGTCACCA	0.557													32	37	---	---	---	---	PASS
KRT77	374454	broad.mit.edu	37	12	53091506	53091506	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53091506C>A	uc001saw.2	-	2	747	c.718G>T	c.(718-720)GTC>TTC	p.V240F	KRT77_uc009zmi.2_5'UTR	NM_175078	NP_778253	Q7Z794	K2C1B_HUMAN	keratin 77	240	Coil 1B.|Rod.					keratin filament	structural molecule activity			ovary(1)	1						ATGCTCCTGACCTCCGCGTTC	0.592													30	331	---	---	---	---	PASS
OR6C75	390323	broad.mit.edu	37	12	55759748	55759748	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55759748C>T	uc010spk.1	+	1	854	c.854C>T	c.(853-855)CCC>CTC	p.P285L		NM_001005497	NP_001005497	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C,	285	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|large_intestine(1)	3						CTCTTGAATCCCTTCATATAC	0.383													12	49	---	---	---	---	PASS
PRIM1	5557	broad.mit.edu	37	12	57135524	57135524	+	Intron	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57135524A>G	uc001smd.2	-							NM_000946	NP_000937	P49642	PRI1_HUMAN	DNA primase polypeptide 1						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	DNA primase activity|metal ion binding				0						TTTCAGTGGCATATACCTGAT	0.348													16	156	---	---	---	---	PASS
MON2	23041	broad.mit.edu	37	12	62894643	62894643	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62894643G>T	uc001sre.2	+	6	1037	c.646G>T	c.(646-648)GCA>TCA	p.A216S	MON2_uc009zqj.2_Missense_Mutation_p.A216S|MON2_uc010ssl.1_Missense_Mutation_p.A144S|MON2_uc010ssm.1_Missense_Mutation_p.A216S|MON2_uc010ssn.1_Missense_Mutation_p.A216S|MON2_uc001srf.2_5'Flank|MON2_uc001srd.1_Missense_Mutation_p.A108S	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	216					Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TGCTAAAGATGCATATATGCT	0.303													32	41	---	---	---	---	PASS
MON2	23041	broad.mit.edu	37	12	62894645	62894645	+	Silent	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62894645A>T	uc001sre.2	+	6	1039	c.648A>T	c.(646-648)GCA>GCT	p.A216A	MON2_uc009zqj.2_Silent_p.A216A|MON2_uc010ssl.1_Silent_p.A144A|MON2_uc010ssm.1_Silent_p.A216A|MON2_uc010ssn.1_Silent_p.A216A|MON2_uc001srf.2_5'Flank|MON2_uc001srd.1_Silent_p.A108A	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	216					Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		CTAAAGATGCATATATGCTTT	0.294													32	41	---	---	---	---	PASS
PTPRR	5801	broad.mit.edu	37	12	71095029	71095029	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71095029G>A	uc001swi.1	-	7	1498	c.1082C>T	c.(1081-1083)ACA>ATA	p.T361I	PTPRR_uc001swh.1_Missense_Mutation_p.T116I|PTPRR_uc009zrs.2_Missense_Mutation_p.T210I|PTPRR_uc010stq.1_Missense_Mutation_p.T249I|PTPRR_uc010str.1_Missense_Mutation_p.T210I	NM_002849	NP_002840	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	361	Cytoplasmic (Potential).				in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		CTCCCGTGGTGTTGGTATAGA	0.463													6	78	---	---	---	---	PASS
E2F7	144455	broad.mit.edu	37	12	77419463	77419463	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77419463G>A	uc001sym.3	-	12	2676	c.2440C>T	c.(2440-2442)CCT>TCT	p.P814S	E2F7_uc009zse.2_Intron	NM_203394	NP_976328	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	814					cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3						TGAAGCTGAGGGTCTGCAGAA	0.537													17	52	---	---	---	---	PASS
MGAT4C	25834	broad.mit.edu	37	12	86373490	86373490	+	Silent	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86373490A>T	uc001tai.3	-	8	2264	c.1014T>A	c.(1012-1014)CCT>CCA	p.P338P	MGAT4C_uc001tal.3_Silent_p.P338P|MGAT4C_uc001taj.3_Silent_p.P338P|MGAT4C_uc001tak.3_Silent_p.P338P|MGAT4C_uc010sum.1_Silent_p.P362P|MGAT4C_uc001tah.3_Silent_p.P338P	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein	338	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						GGGGGTTATCAGGAATGTCAA	0.408													20	34	---	---	---	---	PASS
FGD6	55785	broad.mit.edu	37	12	95488424	95488424	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95488424T>A	uc001tdp.3	-	15	3768	c.3544A>T	c.(3544-3546)ATA>TTA	p.I1182L	FGD6_uc009zsx.2_Missense_Mutation_p.I315L|FGD6_uc001tdq.1_Missense_Mutation_p.I218L	NM_018351	NP_060821	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1182	PH 1.				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3						TACTCTTCTATTGCCCTGGAA	0.378													12	44	---	---	---	---	PASS
NUP37	79023	broad.mit.edu	37	12	102492903	102492903	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102492903T>A	uc001tjc.2	-	4	495	c.430A>T	c.(430-432)AGT>TGT	p.S144C	NUP37_uc009zub.1_Missense_Mutation_p.S144C	NM_024057	NP_076962	Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	144	WD 2.				carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			ovary(1)	1						TGATCGTCACTCACACTTGCA	0.343													18	20	---	---	---	---	PASS
KIAA1033	23325	broad.mit.edu	37	12	105551091	105551091	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105551091A>G	uc001tld.2	+	28	2990	c.2903A>G	c.(2902-2904)AAA>AGA	p.K968R	KIAA1033_uc010swr.1_Missense_Mutation_p.K969R|KIAA1033_uc010sws.1_Missense_Mutation_p.K780R	NM_015275	NP_056090	Q2M389	WAHS7_HUMAN	hypothetical protein LOC23325	968					endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2						GAAACATTAAAAGCAGCAAGG	0.303													26	31	---	---	---	---	PASS
SSH1	54434	broad.mit.edu	37	12	109201450	109201450	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109201450C>A	uc001tnm.2	-	8	777	c.690G>T	c.(688-690)CTG>CTT	p.L230L	SSH1_uc001tnl.2_5'Flank|SSH1_uc010sxg.1_Silent_p.L241L|SSH1_uc001tnn.3_Silent_p.L230L|SSH1_uc001tno.1_Silent_p.L134L	NM_018984	NP_061857	Q8WYL5	SSH1_HUMAN	slingshot 1 isoform 1	230				L -> P (in Ref. 1; BAB84116).	actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(4)	4						GCGTAGACTCCAGGTCCTGCA	0.617													6	49	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112688130	112688130	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112688130C>A	uc009zwc.2	-	18	2520	c.2502G>T	c.(2500-2502)CCG>CCT	p.P834P	C12orf51_uc010syk.1_Silent_p.P656P|C12orf51_uc001tts.2_Silent_p.P647P|C12orf51_uc001ttt.3_Silent_p.P645P	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						GAGAGGGGCTCGGAGTAAGGG	0.542													4	55	---	---	---	---	PASS
SDS	10993	broad.mit.edu	37	12	113837484	113837484	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113837484C>A	uc001tvg.2	-	2	152	c.30G>T	c.(28-30)AAG>AAT	p.K10N	SDS_uc001tvh.1_Missense_Mutation_p.K10N	NM_006843	NP_006834	P20132	SDHL_HUMAN	serine dehydratase	10					gluconeogenesis|L-serine catabolic process|pyruvate biosynthetic process	cytoplasm	L-serine ammonia-lyase activity|L-threonine ammonia-lyase activity|protein homodimerization activity|pyridoxal phosphate binding			pancreas(1)	1					L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	GGATGGGGGTCTTCACGTGCA	0.602													6	7	---	---	---	---	PASS
P2RX7	5027	broad.mit.edu	37	12	121592748	121592748	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121592748C>A	uc001tzm.2	+	2	382	c.286C>A	c.(286-288)CCT>ACT	p.P96T	P2RX7_uc001tzn.2_5'UTR|P2RX7_uc001tzo.2_RNA|P2RX7_uc001tzp.2_5'UTR|P2RX7_uc001tzq.2_5'UTR	NM_002562	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X7	96						integral to membrane	ATP binding|ion channel activity|receptor activity			large_intestine(2)|lung(1)|breast(1)|skin(1)	5	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CTACACCTTCCCTTTGCAGGT	0.567													5	64	---	---	---	---	PASS
WDR66	144406	broad.mit.edu	37	12	122372222	122372222	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122372222G>T	uc009zxk.2	+	5	1100	c.958G>T	c.(958-960)GGG>TGG	p.G320W		NM_144668	NP_653269	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	320	WD 1.						calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		AGCAGACAAAGGGCCAGACTG	0.498													5	20	---	---	---	---	PASS
DNAH10	196385	broad.mit.edu	37	12	124317842	124317842	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124317842A>G	uc001uft.3	+	26	4398	c.4373A>G	c.(4372-4374)CAA>CGA	p.Q1458R		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1458	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CCTTTTCTGCAAACTGTTCAC	0.423													17	18	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	129558710	129558710	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129558710G>T	uc009zyl.1	-	9	3338	c.3010C>A	c.(3010-3012)CTC>ATC	p.L1004I	TMEM132D_uc001uia.2_Missense_Mutation_p.L542I	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	1004	Cytoplasmic (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TTTGTGCTGAGGAGATATTTA	0.463													5	68	---	---	---	---	PASS
PIWIL1	9271	broad.mit.edu	37	12	130846036	130846036	+	Intron	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130846036A>G	uc001uik.2	+						PIWIL1_uc001uij.1_Intron	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1						gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|P granule	mRNA binding|piRNA binding|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		CCATATTTGTATTGAAGCTGA	0.378													26	33	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23906110	23906110	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23906110G>A	uc001uon.2	-	10	12494	c.11905C>T	c.(11905-11907)CTT>TTT	p.L3969F	SACS_uc001uoo.2_Missense_Mutation_p.L3822F|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	3969					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CGAGGTCTAAGTTTTTGAGGA	0.393													10	76	---	---	---	---	PASS
MIPEP	4285	broad.mit.edu	37	13	24380178	24380178	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24380178G>T	uc001uox.3	-	16	1859	c.1759C>A	c.(1759-1761)CAT>AAT	p.H587N		NM_005932	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase precursor	587					protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		TGCTTCCCATGGTAGATTTGA	0.413													6	83	---	---	---	---	PASS
PARP4	143	broad.mit.edu	37	13	25026687	25026687	+	Silent	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25026687G>C	uc001upl.2	-	24	2977	c.2871C>G	c.(2869-2871)CTC>CTG	p.L957L	PARP4_uc010tdc.1_Silent_p.L957L	NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	957	VWFA.				cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TAAGATATCGGAGTGTTTTCC	0.493													39	42	---	---	---	---	PASS
PAN3	255967	broad.mit.edu	37	13	28794441	28794441	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28794441C>A	uc001urz.2	+	5	496	c.488C>A	c.(487-489)TCA>TAA	p.S163*	PAN3_uc010tdo.1_Nonsense_Mutation_p.S309*|PAN3_uc001ury.2_5'UTR|PAN3_uc001urx.2_Nonsense_Mutation_p.S109*	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	309	Interaction with polyadenylate-binding protein.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		GTGTCCCAGTCAAATATGTCT	0.428													34	203	---	---	---	---	PASS
KL	9365	broad.mit.edu	37	13	33638087	33638087	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33638087T>A	uc001uus.2	+	5	2811	c.2803T>A	c.(2803-2805)TTT>ATT	p.F935I		NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho precursor	935	Glycosyl hydrolase-1 2.|Extracellular (Potential).				aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TGCAGATCAGTTTGAGCCCAA	0.448													40	32	---	---	---	---	PASS
NBEA	26960	broad.mit.edu	37	13	35517158	35517158	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35517158C>T	uc001uvb.2	+	2	407	c.201C>T	c.(199-201)ATC>ATT	p.I67I		NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	67						cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CGGTGCCGATCCGCAACATCC	0.532													20	44	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39271908	39271908	+	Silent	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39271908T>C	uc001uwv.2	+	2	5556	c.5247T>C	c.(5245-5247)TTT>TTC	p.F1749F		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	1749	Extracellular (Potential).|CSPG 12.				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TGTTCTATTTTGCAGTTGAAG	0.393													4	33	---	---	---	---	PASS
KIAA0564	23078	broad.mit.edu	37	13	42385440	42385440	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42385440G>C	uc001uyj.2	-	17	2054	c.1984C>G	c.(1984-1986)CTG>GTG	p.L662V	KIAA0564_uc001uyk.2_Missense_Mutation_p.L662V	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a	662						extracellular region	ATP binding|ATPase activity	p.L662L(1)		ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)		ATTCGCAACAGTTGTCTGGTA	0.393													4	73	---	---	---	---	PASS
COG3	83548	broad.mit.edu	37	13	46085956	46085956	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46085956A>T	uc001vak.2	+	16	1877	c.1776A>T	c.(1774-1776)TTA>TTT	p.L592F	COG3_uc001vaj.1_Missense_Mutation_p.L592F|COG3_uc010tfv.1_Missense_Mutation_p.L429F|COG3_uc010aci.2_Missense_Mutation_p.L368F	NM_031431	NP_113619	Q96JB2	COG3_HUMAN	component of golgi transport complex 3	592					ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity			breast(1)|skin(1)	2		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		TTCAGTCCTTACTTGGAGCGT	0.398													17	16	---	---	---	---	PASS
PCDH9	5101	broad.mit.edu	37	13	67800610	67800610	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67800610G>T	uc001vik.2	-	2	2655	c.1963C>A	c.(1963-1965)CGT>AGT	p.R655S	PCDH9_uc001vil.2_Missense_Mutation_p.R655S|PCDH9_uc010thl.1_Missense_Mutation_p.R655S|PCDH9_uc001vin.3_Missense_Mutation_p.R655S	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	655	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GTAGAGGAACGAGGTGGTTGT	0.433													4	60	---	---	---	---	PASS
LMO7	4008	broad.mit.edu	37	13	76382282	76382282	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76382282G>T	uc001vjv.2	+	7	1924	c.1164G>T	c.(1162-1164)GAG>GAT	p.E388D	LMO7_uc010thv.1_Intron|LMO7_uc001vjt.1_Intron|LMO7_uc010thw.1_Intron|LMO7_uc001vjw.1_Missense_Mutation_p.E294D	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2	673						cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AGAGATGGGAGGCCATCCGGG	0.532													16	17	---	---	---	---	PASS
ITGBL1	9358	broad.mit.edu	37	13	102235561	102235561	+	Intron	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102235561C>A	uc001vpb.2	+						ITGBL1_uc010agb.2_Intron|ITGBL1_uc001vpc.3_Intron	NM_004791	NP_004782	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTTCTTCCCACCTAGGGACTT	0.398													26	27	---	---	---	---	PASS
LIG4	3981	broad.mit.edu	37	13	108861116	108861116	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108861116T>A	uc001vqn.2	-	2	2774	c.2501A>T	c.(2500-2502)GAG>GTG	p.E834V	LIG4_uc001vqo.2_Missense_Mutation_p.E834V|LIG4_uc010agg.1_Missense_Mutation_p.E767V|LIG4_uc010agf.2_Missense_Mutation_p.E834V|LIG4_uc001vqp.2_Missense_Mutation_p.E834V	NM_002312	NP_002303	P49917	DNLI4_HUMAN	DNA ligase IV	834	BRCT 2.				cell cycle|cell division|cell proliferation|central nervous system development|chromosome organization|DNA ligation involved in DNA recombination|DNA ligation involved in DNA repair|DNA replication|double-strand break repair via nonhomologous end joining|in utero embryonic development|initiation of viral infection|isotype switching|negative regulation of neuron apoptosis|neuron apoptosis|nucleotide-excision repair, DNA gap filling|positive regulation of fibroblast proliferation|positive regulation of neurogenesis|pro-B cell differentiation|provirus integration|response to gamma radiation|response to X-ray|single strand break repair|somatic stem cell maintenance|T cell differentiation in thymus|T cell receptor V(D)J recombination	condensed chromosome|cytoplasm|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|focal adhesion|nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding|protein C-terminus binding				0	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					CCTTGTCCCCTCATTTTTGGT	0.428								NHEJ					21	33	---	---	---	---	PASS
OR4Q3	441669	broad.mit.edu	37	14	20215703	20215703	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20215703C>A	uc010tkt.1	+	1	117	c.117C>A	c.(115-117)GTC>GTA	p.V39V		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	39	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTGCTATTGTCCTGGGAAACC	0.383													41	43	---	---	---	---	PASS
OR4Q3	441669	broad.mit.edu	37	14	20215704	20215704	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20215704C>G	uc010tkt.1	+	1	118	c.118C>G	c.(118-120)CTG>GTG	p.L40V		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	40	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.L40L(3)		breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TGCTATTGTCCTGGGAAACCT	0.388													44	41	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22037923	22037923	+	IGR	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22037923G>A								SALL2 (32586 upstream) : OR10G3 (12 downstream)																							CCTAGTGGGAGAAAGACACTT	0.408													14	6	---	---	---	---	PASS
NFATC4	4776	broad.mit.edu	37	14	24838700	24838700	+	Intron	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24838700G>C	uc001wpc.2	+						NFATC4_uc010tok.1_Intron|NFATC4_uc010tol.1_Intron|NFATC4_uc010alr.2_Intron|NFATC4_uc010als.2_Intron|NFATC4_uc010tom.1_Intron|NFATC4_uc010ton.1_Intron|NFATC4_uc010too.1_Intron|NFATC4_uc010alt.2_Intron|NFATC4_uc010top.1_Intron|NFATC4_uc010toq.1_Intron|NFATC4_uc010alu.2_Intron|NFATC4_uc010tor.1_Intron|NFATC4_uc010tos.1_Intron|NFATC4_uc010tot.1_Intron|NFATC4_uc010tou.1_5'UTR|NFATC4_uc010tov.1_Intron|NFATC4_uc010tow.1_5'UTR|NFATC4_uc010alv.2_Intron|NFATC4_uc010tox.1_5'UTR	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,						cell differentiation|inflammatory response|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(265;0.018)		TTCCCATTTTGACAGAACTGG	0.597													55	20	---	---	---	---	PASS
AP4S1	11154	broad.mit.edu	37	14	31549788	31549788	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31549788G>T	uc001wqy.3	+	5	686	c.304G>T	c.(304-306)GAT>TAT	p.D102Y	AP4S1_uc001wqw.3_Missense_Mutation_p.D102Y|AP4S1_uc001wqx.3_Missense_Mutation_p.D102Y|AP4S1_uc010amh.2_Intron|AP4S1_uc001wqz.3_Intron	NM_001128126	NP_001121598	Q9Y587	AP4S1_HUMAN	adaptor-related protein complex 4, sigma 1	102						coated pit|Golgi apparatus	protein transporter activity				0	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.221)	GBM - Glioblastoma multiforme(265;0.00553)		GAGTGAATTAGATGTATCCTT	0.443													4	22	---	---	---	---	PASS
SLC10A1	6554	broad.mit.edu	37	14	70245986	70245986	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70245986G>T	uc001xlr.2	-	3	793	c.659C>A	c.(658-660)CCA>CAA	p.P220Q		NM_003049	NP_003040	Q14973	NTCP_HUMAN	solute carrier family 10, member 1	220	Helical; (Potential).				bile acid metabolic process|organic anion transport	integral to plasma membrane	bile acid:sodium symporter activity			ovary(1)	1				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)		AATCAAGAGTGGTGTCATGGC	0.488													5	34	---	---	---	---	PASS
ADCK1	57143	broad.mit.edu	37	14	78353520	78353520	+	Silent	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78353520G>C	uc001xui.2	+	5	609	c.510G>C	c.(508-510)GGG>GGC	p.G170G	ADCK1_uc010tvo.1_Intron|ADCK1_uc001xuj.2_Silent_p.G102G|ADCK1_uc001xuk.1_Silent_p.G44G	NM_020421	NP_065154	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1 isoform a	177	Protein kinase.					extracellular region	ATP binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		TGCATGATGGGCGGACGGTGG	0.607													17	5	---	---	---	---	PASS
NRXN3	9369	broad.mit.edu	37	14	80130287	80130287	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80130287C>A	uc001xun.2	+	14	2983	c.2492C>A	c.(2491-2493)CCT>CAT	p.P831H	NRXN3_uc001xum.1_RNA|NRXN3_uc001xup.2_RNA|NRXN3_uc001xuq.2_Missense_Mutation_p.P199H|NRXN3_uc010asw.2_Missense_Mutation_p.P199H|NRXN3_uc001xur.3_Missense_Mutation_p.P199H	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	1204	Extracellular (Potential).|Laminin G-like 6.				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		GAACATTATCCTACAGGTACA	0.478													12	3	---	---	---	---	PASS
CINP	51550	broad.mit.edu	37	14	102816311	102816311	+	Silent	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102816311A>G	uc001ylv.1	-	4	446	c.381T>C	c.(379-381)TAT>TAC	p.Y127Y	CINP_uc001ylu.1_RNA	NM_032630	NP_116019	Q9BW66	CINP_HUMAN	cyclin-dependent kinase 2-interacting protein	127					cell cycle|cell division|DNA repair|DNA replication	nucleus	protein binding			large_intestine(1)	1						TCTCCTCCCCATAATGGTAGT	0.408													23	13	---	---	---	---	PASS
PAR4	347745	broad.mit.edu	37	15	25448376	25448376	+	Intron	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25448376G>A	uc001yzk.1	+						PAR4_uc010ayo.1_Intron|SNORD115-17_uc001yzo.1_RNA|SNORD115-17_uc001yzp.1_5'Flank					Homo sapiens clone Rt-13I SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0						CCTGGGTTGGGTCGATGATGA	0.512													51	165	---	---	---	---	PASS
VPS39	23339	broad.mit.edu	37	15	42459085	42459085	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42459085C>A	uc001zpd.2	-	15	1588	c.1437G>T	c.(1435-1437)TTG>TTT	p.L479F	VPS39_uc001zpc.2_Missense_Mutation_p.L468F|VPS39_uc001zpb.2_5'Flank	NM_015289	NP_056104	Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39	479					protein transport	HOPS complex|late endosome membrane|lysosomal membrane	small GTPase regulator activity			ovary(1)|pancreas(1)|skin(1)	3		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		CCAGGCGTAGCAAGGGGGCCA	0.562													10	28	---	---	---	---	PASS
SLC30A4	7782	broad.mit.edu	37	15	45814396	45814396	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45814396C>A	uc001zvj.2	-	2	469	c.157G>T	c.(157-159)GAC>TAC	p.D53Y	C15orf21_uc010beg.1_Intron|C15orf21_uc010beh.1_Intron|C15orf21_uc010bei.1_Intron|C15orf21_uc010bej.1_Intron|C15orf21_uc001zvm.1_Intron|C15orf21_uc001zvn.1_Intron	NM_013309	NP_037441	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter),	53	Cytoplasmic (Potential).|Asp-rich (acidic).				regulation of sequestering of zinc ion|response to toxin	endosome membrane|integral to membrane|late endosome	zinc ion transmembrane transporter activity				0		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		TCGGAACCGTCATCGGCCACC	0.572													21	30	---	---	---	---	PASS
SEMA6D	80031	broad.mit.edu	37	15	48056121	48056121	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48056121G>C	uc010bek.2	+	10	1182	c.822G>C	c.(820-822)TGG>TGC	p.W274C	SEMA6D_uc001zvw.2_Missense_Mutation_p.W274C|SEMA6D_uc001zvx.1_Missense_Mutation_p.W274C|SEMA6D_uc001zvy.2_Missense_Mutation_p.W274C|SEMA6D_uc001zvz.2_Missense_Mutation_p.W274C|SEMA6D_uc001zwa.2_Missense_Mutation_p.W274C|SEMA6D_uc001zwb.2_Missense_Mutation_p.W274C|SEMA6D_uc001zwc.2_Missense_Mutation_p.W274C	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor	274	Sema.|Extracellular (Potential).				axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AGAAACACTGGACTTCATTTC	0.468													32	48	---	---	---	---	PASS
ATP8B4	79895	broad.mit.edu	37	15	50190438	50190438	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50190438A>G	uc001zxu.2	-	22	2442	c.2300T>C	c.(2299-2301)CTA>CCA	p.L767P	ATP8B4_uc010ber.2_Missense_Mutation_p.L640P|ATP8B4_uc010ufd.1_Missense_Mutation_p.L577P|ATP8B4_uc010ufe.1_RNA|ATP8B4_uc001zxv.1_Missense_Mutation_p.L65P	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4	767	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		ATCACTTTCTAGGGCATGAGC	0.383													15	17	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54305821	54305821	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54305821G>A	uc002ack.2	+	1	721	c.721G>A	c.(721-723)GAT>AAT	p.D241N		NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	241					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CCAAACACATGATGTCATGGA	0.448													42	49	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54305932	54305932	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54305932T>A	uc002ack.2	+	1	832	c.832T>A	c.(832-834)TCC>ACC	p.S278T		NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	278					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CGATGAGATCTCCAGCAGTGT	0.438													42	67	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54592473	54592473	+	Silent	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54592473G>C	uc002ack.2	+	11	4170	c.4170G>C	c.(4168-4170)GGG>GGC	p.G1390G	UNC13C_uc002acl.2_Silent_p.G220G	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1390					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AAGTCAAAGGGGATGAAGCCT	0.368													9	5	---	---	---	---	PASS
SLTM	79811	broad.mit.edu	37	15	59225621	59225621	+	Silent	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59225621G>C	uc002afp.2	-	1	232	c.144C>G	c.(142-144)CTC>CTG	p.L48L	SLTM_uc002afo.2_Silent_p.L48L|SLTM_uc002afq.2_5'UTR|SLTM_uc010bgd.2_5'UTR|SLTM_uc002afr.1_Silent_p.L48L	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription	48	SAP.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1						GTCGGGAGATGAGCACGGTCT	0.637													3	7	---	---	---	---	PASS
CILP	8483	broad.mit.edu	37	15	65499327	65499327	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65499327G>T	uc002aon.2	-	4	398	c.217C>A	c.(217-219)CGG>AGG	p.R73R		NM_003613	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein	73					negative regulation of insulin-like growth factor receptor signaling pathway	extracellular matrix part|extracellular space|proteinaceous extracellular matrix		p.R73Q(1)		ovary(4)|pancreas(2)|skin(1)	7						GCGTCCAGCCGCTCATAGTCG	0.612													7	15	---	---	---	---	PASS
PIAS1	8554	broad.mit.edu	37	15	68378917	68378917	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68378917G>T	uc002aqz.2	+	2	394	c.298G>T	c.(298-300)GAT>TAT	p.D100Y	PIAS1_uc010ujx.1_Missense_Mutation_p.D100Y	NM_016166	NP_057250	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	100					androgen receptor signaling pathway|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|positive regulation of protein sumoylation|positive regulation of transcription, DNA-dependent|regulation of interferon-gamma-mediated signaling pathway|transcription, DNA-dependent	nuclear speck	androgen receptor binding|DNA binding|enzyme binding|SUMO ligase activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)	2						ACTCACTTACGATGGTCACCC	0.478													4	114	---	---	---	---	PASS
MSLNL	401827	broad.mit.edu	37	16	823224	823224	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:823224G>A	uc002cjz.1	-	10	2044	c.2044C>T	c.(2044-2046)CTG>TTG	p.L682L		NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like	331	Extracellular (Potential).				cell adhesion	integral to membrane				breast(3)|ovary(1)	4						CAGCCATCCAGGCAGGACTCA	0.632													21	14	---	---	---	---	PASS
TELO2	9894	broad.mit.edu	37	16	1557674	1557674	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1557674G>T	uc002cly.2	+	20	2655	c.2364G>T	c.(2362-2364)GAG>GAT	p.E788D		NM_016111	NP_057195	Q9Y4R8	TELO2_HUMAN	TEL2, telomere maintenance 2, homolog	788						chromosome, telomeric region|cytoplasm|membrane|nucleus	protein binding				0		Hepatocellular(780;0.219)				GCCTGCTGGAGGACCTGATGG	0.662													4	8	---	---	---	---	PASS
ABCA3	21	broad.mit.edu	37	16	2331382	2331382	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2331382C>A	uc002cpy.1	-	27	4876	c.4164G>T	c.(4162-4164)AAG>AAT	p.K1388N	ABCA3_uc010bsk.1_Missense_Mutation_p.K1330N	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3	1388	ABC transporter 2.				response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)				GCAAGGGTACCTTGGAGAGCT	0.607													5	62	---	---	---	---	PASS
ZNF213	7760	broad.mit.edu	37	16	3187644	3187644	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3187644G>A	uc010uws.1	+	2	810	c.363G>A	c.(361-363)GAG>GAA	p.E121E	ZNF213_uc002cud.2_RNA|ZNF213_uc010btf.2_Silent_p.E121E|ZNF213_uc010bth.2_Silent_p.E121E|ZNF213_uc010uwt.1_Silent_p.E121E	NM_004220	NP_004211	O14771	ZN213_HUMAN	zinc finger protein 213	121	SCAN box.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						CCTTGGTGGAGGACCTACAGA	0.627													8	4	---	---	---	---	PASS
NLRC3	197358	broad.mit.edu	37	16	3614540	3614540	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3614540C>T	uc010btn.2	-	5	809	c.398G>A	c.(397-399)CGG>CAG	p.R133Q		NM_178844	NP_849172	Q7RTR2	NLRC3_HUMAN	NOD3 protein	133					I-kappaB kinase/NF-kappaB cascade|negative regulation of NF-kappaB transcription factor activity|T cell activation	cytoplasm	ATP binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						GACAGACACCCGGGAGAGAGG	0.701													7	11	---	---	---	---	PASS
ADCY9	115	broad.mit.edu	37	16	4163760	4163760	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4163760G>T	uc002cvx.2	-	2	2223	c.1684C>A	c.(1684-1686)CAG>AAG	p.Q562K		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	562	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6						CCTTTCAACTGGTCAGCAACC	0.468													5	85	---	---	---	---	PASS
GP2	2813	broad.mit.edu	37	16	20335151	20335151	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20335151C>A	uc002dgv.2	-	3	605	c.522G>T	c.(520-522)CTG>CTT	p.L174L	GP2_uc002dgw.2_Silent_p.L174L|GP2_uc002dgx.2_Intron|GP2_uc002dgy.2_Intron	NM_001007240	NP_001007241	P55259	GP2_HUMAN	zymogen granule membrane glycoprotein 2 isoform	174						anchored to membrane|extracellular region|plasma membrane				ovary(3)|skin(1)	4						TGCAGTATCTCAGATTACACC	0.572													8	8	---	---	---	---	PASS
COG7	91949	broad.mit.edu	37	16	23456434	23456434	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23456434A>T	uc002dlo.2	-	3	558	c.370T>A	c.(370-372)TCT>ACT	p.S124T		NM_153603	NP_705831	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	124					intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)		TCCTGAAGAGATTCGGCAGCA	0.453													8	87	---	---	---	---	PASS
RBBP6	5930	broad.mit.edu	37	16	24583481	24583481	+	Silent	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24583481C>G	uc002dmh.2	+	18	6134	c.5094C>G	c.(5092-5094)GTC>GTG	p.V1698V	RBBP6_uc002dmi.2_Silent_p.V1664V|RBBP6_uc010bxr.2_Silent_p.V858V|RBBP6_uc002dmk.2_Silent_p.V1531V	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN	retinoblastoma-binding protein 6 isoform 1	1698					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0518)		GCCCCAGCGTCAGCCCCAGCA	0.443													8	31	---	---	---	---	PASS
SLC5A11	115584	broad.mit.edu	37	16	24922792	24922792	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24922792C>A	uc002dmu.2	+	16	2198	c.1966C>A	c.(1966-1968)CTG>ATG	p.L656M	SLC5A11_uc002dms.2_Missense_Mutation_p.L592M|SLC5A11_uc010vcd.1_Missense_Mutation_p.L621M|SLC5A11_uc002dmt.2_Missense_Mutation_p.L500M|SLC5A11_uc010vce.1_Missense_Mutation_p.L586M|SLC5A11_uc010bxt.2_Missense_Mutation_p.L592M|SLC5A11_uc002dmv.2_Missense_Mutation_p.L279M	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	656	Helical; (Potential).				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)		GAAGACCCTCCTGGACGTCAA	0.527													79	84	---	---	---	---	PASS
ATXN2L	11273	broad.mit.edu	37	16	28847341	28847341	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28847341C>T	uc002drc.2	+	22	3151	c.2983C>T	c.(2983-2985)CAG>TAG	p.Q995*	uc010vct.1_Intron|ATXN2L_uc002drb.2_Nonsense_Mutation_p.Q995*|ATXN2L_uc002dqy.2_Nonsense_Mutation_p.Q995*|ATXN2L_uc002dra.2_Nonsense_Mutation_p.Q995*|ATXN2L_uc002dqz.2_Nonsense_Mutation_p.Q995*|ATXN2L_uc010vdb.1_Nonsense_Mutation_p.Q1001*|ATXN2L_uc002dre.2_Nonsense_Mutation_p.Q995*|ATXN2L_uc002drf.2_Nonsense_Mutation_p.Q404*|ATXN2L_uc002drg.2_Nonsense_Mutation_p.Q278*	NM_007245	NP_009176	Q8WWM7	ATX2L_HUMAN	ataxin 2 related protein isoform A	995						membrane				upper_aerodigestive_tract(1)|ovary(1)	2						GCACCCACCCCAGAGTCATGG	0.672													6	28	---	---	---	---	PASS
ZNF646	9726	broad.mit.edu	37	16	31089893	31089893	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31089893G>A	uc002eap.2	+	2	2537	c.2248G>A	c.(2248-2250)GGT>AGT	p.G750S		NM_014699	NP_055514	O15015	ZN646_HUMAN	zinc finger protein 646	750					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2						CCATTTCCAGGGTGATAAAGA	0.532													15	79	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	33647796	33647796	+	5'Flank	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33647796G>T	uc010vga.1	-											Homo sapiens IGH mRNA for immunoglobulin heavy chain VHDJ region, partial cds, clone:kh0002h.																		GGGCTGGGCTGGTTTTTATCA	0.547													12	24	---	---	---	---	PASS
ABCC12	94160	broad.mit.edu	37	16	48119595	48119595	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48119595A>G	uc002efc.1	-	27	4083	c.3737T>C	c.(3736-3738)TTA>TCA	p.L1246S	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	1246	ABC transporter 2.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)				TTCTGCCTGTAATTTTTCTGG	0.403													12	40	---	---	---	---	PASS
RBL2	5934	broad.mit.edu	37	16	53499487	53499487	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53499487T>G	uc002ehi.3	+	13	1954	c.1836T>G	c.(1834-1836)AAT>AAG	p.N612K	RBL2_uc010vgv.1_Missense_Mutation_p.N538K|RBL2_uc002ehj.2_Missense_Mutation_p.N322K|RBL2_uc010vgw.1_Missense_Mutation_p.N396K	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)	612	Domain A.|Pocket; binds E1A.				cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						TTAGAGACAATGAAAACAGAG	0.338													12	34	---	---	---	---	PASS
RBL2	5934	broad.mit.edu	37	16	53499488	53499488	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53499488G>T	uc002ehi.3	+	13	1955	c.1837G>T	c.(1837-1839)GAA>TAA	p.E613*	RBL2_uc010vgv.1_Nonsense_Mutation_p.E539*|RBL2_uc002ehj.2_Nonsense_Mutation_p.E323*|RBL2_uc010vgw.1_Nonsense_Mutation_p.E397*	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)	613	Domain A.|Pocket; binds E1A.				cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						TAGAGACAATGAAAACAGAGT	0.338													12	34	---	---	---	---	PASS
PMFBP1	83449	broad.mit.edu	37	16	72157488	72157488	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72157488C>G	uc002fcc.3	-	18	2837	c.2665G>C	c.(2665-2667)GAT>CAT	p.D889H	PMFBP1_uc002fcd.2_Missense_Mutation_p.D884H|PMFBP1_uc002fce.2_RNA|PMFBP1_uc002fcf.2_Missense_Mutation_p.D739H	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	889										ovary(2)	2		Ovarian(137;0.179)				ATAATCTGATCATTCCCTCGG	0.557													24	18	---	---	---	---	PASS
MLYCD	23417	broad.mit.edu	37	16	83941731	83941731	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83941731G>T	uc002fgz.2	+	3	662	c.642G>T	c.(640-642)GAG>GAT	p.E214D		NM_012213	NP_036345	O95822	DCMC_HUMAN	malonyl-CoA decarboxylase precursor	214					acyl-CoA metabolic process|fatty acid biosynthetic process	mitochondrion|peroxisome	malonyl-CoA decarboxylase activity|methylmalonyl-CoA decarboxylase activity				0						TCCGCCCCAGGGCTGAGGCTG	0.468													21	13	---	---	---	---	PASS
TAF1C	9013	broad.mit.edu	37	16	84218511	84218511	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84218511C>A	uc002fhn.2	-	2	312	c.84G>T	c.(82-84)ATG>ATT	p.M28I	TAF1C_uc002fhm.2_Intron|TAF1C_uc010vnx.1_Missense_Mutation_p.M28I|TAF1C_uc010vny.1_Intron|TAF1C_uc010vnz.1_Intron|TAF1C_uc002fho.2_Intron|TAF1C_uc010voa.1_Intron|TAF1C_uc002fhp.1_RNA|TAF1C_uc010vob.1_Missense_Mutation_p.M28I	NM_005679	NP_005670	Q15572	TAF1C_HUMAN	TBP-associated factor 1C isoform 1	28					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding			ovary(1)	1						GCCAGCTGCACATGAAAGAGA	0.627													8	11	---	---	---	---	PASS
GAS8	2622	broad.mit.edu	37	16	90102917	90102917	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90102917G>T	uc002fqi.1	+	6	801	c.679G>T	c.(679-681)GAG>TAG	p.E227*	GAS8_uc010vps.1_Nonsense_Mutation_p.E202*|GAS8_uc002fqh.2_Nonsense_Mutation_p.E144*|GAS8_uc010vpt.1_3'UTR|GAS8_uc010vpu.1_Nonsense_Mutation_p.E144*|GAS8_uc010vpv.1_Nonsense_Mutation_p.E198*|GAS8_uc010cjc.1_Nonsense_Mutation_p.E144*|GAS8_uc010vpw.1_Nonsense_Mutation_p.E144*|GAS8_uc002fqj.1_Nonsense_Mutation_p.E35*	NM_001481	NP_001472	O95995	GAS8_HUMAN	growth arrest-specific 8	227	Microtubule-binding.				negative regulation of cell proliferation|sperm motility	cilium|Golgi apparatus|microtubule|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		GCAGCGCCACGAGGAGGCCTT	0.567													4	23	---	---	---	---	PASS
SMG6	23293	broad.mit.edu	37	17	2075968	2075968	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2075968T>A	uc002fub.1	-	13	3396	c.3341A>T	c.(3340-3342)GAG>GTG	p.E1114V	SMG6_uc010vqv.1_Missense_Mutation_p.E206V	NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay	1114					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4						CGAGGTTTTCTCCACGTAGCA	0.547													30	5	---	---	---	---	PASS
OR1A2	26189	broad.mit.edu	37	17	3101463	3101463	+	Silent	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3101463T>C	uc002fvd.1	+	1	651	c.651T>C	c.(649-651)TAT>TAC	p.Y217Y		NM_012352	NP_036484	Q9Y585	OR1A2_HUMAN	olfactory receptor, family 1, subfamily A,	217	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						TTGTCTCCTATGTTCAGGTCT	0.433													103	32	---	---	---	---	PASS
OR1E2	8388	broad.mit.edu	37	17	3337053	3337053	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3337053T>C	uc010vre.1	-	1	83	c.83A>G	c.(82-84)TAT>TGT	p.Y28C		NM_003554	NP_003545	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E,	28	Helical; Name=1; (Potential).				sensory perception of smell	integral to plasma membrane	olfactory receptor activity			large_intestine(1)	1						GAACAGGGCATAGCACAGGTT	0.522													40	12	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577538	7577538	+	Missense_Mutation	SNP	C	G	G	rs11540652		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577538C>G	uc002gim.2	-	7	937	c.743G>C	c.(742-744)CGG>CCG	p.R248P	TP53_uc002gig.1_Missense_Mutation_p.R248P|TP53_uc002gih.2_Missense_Mutation_p.R248P|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R116P|TP53_uc010cng.1_Missense_Mutation_p.R116P|TP53_uc002gii.1_Missense_Mutation_p.R116P|TP53_uc010cnh.1_Missense_Mutation_p.R248P|TP53_uc010cni.1_Missense_Mutation_p.R248P|TP53_uc002gij.2_Missense_Mutation_p.R248P|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.R155P|TP53_uc002gio.2_Missense_Mutation_p.R116P	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	248	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|NR -> IP (in a sporadic cancer; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|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 by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R248Q(523)|p.R248W(443)|p.R248L(63)|p.R248P(12)|p.R248G(11)|p.R248R(10)|p.0?(7)|p.R155Q(4)|p.N247_R248delNR(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248_P250delRRP(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GATGGGCCTCCGGTTCATGCC	0.572	R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIN87_STOMACH)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NIHOVCAR3_OVARY)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(HCC70_BREAST)|R248Q(KYSE150_OESOPHAGUS)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PC14_LUNG)	111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			25	8	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7710538	7710538	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7710538G>T	uc002giu.1	+	61	9527	c.9513G>T	c.(9511-9513)AAG>AAT	p.K3171N	DNAH2_uc010cnm.1_Missense_Mutation_p.K109N	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	3171	Stalk (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TTCTGAAGAAGATTGGGGCCT	0.527													54	16	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10412856	10412856	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10412856C>A	uc002gmo.2	-	15	1627	c.1533G>T	c.(1531-1533)TGG>TGT	p.W511C	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	511	Myosin head-like.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						CAATGAACGTCCACTCAATGC	0.483													44	29	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10412857	10412857	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10412857C>A	uc002gmo.2	-	15	1626	c.1532G>T	c.(1531-1533)TGG>TTG	p.W511L	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	511	Myosin head-like.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						AATGAACGTCCACTCAATGCC	0.488													45	27	---	---	---	---	PASS
RICH2	9912	broad.mit.edu	37	17	12860030	12860030	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12860030A>G	uc002gnr.3	+	15	1636	c.1309A>G	c.(1309-1311)ATC>GTC	p.I437V	RICH2_uc010vvk.1_Missense_Mutation_p.I437V|RICH2_uc010vvl.1_Missense_Mutation_p.I437V|RICH2_uc002gns.3_Missense_Mutation_p.I237V|RICH2_uc010vvm.1_Missense_Mutation_p.I437V|RICH2_uc010vvn.1_RNA|RICH2_uc002gnt.1_Missense_Mutation_p.I160V	NM_014859	NP_055674	Q17R89	RHG44_HUMAN	Rho GTPase-activating protein RICH2	437	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0						CATTGAACCTATCATCCAGCA	0.527													17	7	---	---	---	---	PASS
ZNF207	7756	broad.mit.edu	37	17	30696771	30696771	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30696771G>T	uc002hhh.3	+	11	1578	c.1430G>T	c.(1429-1431)CGT>CTT	p.R477L	ZNF207_uc002hhj.3_Missense_Mutation_p.R493L|ZNF207_uc002hhi.3_Missense_Mutation_p.R462L|ZNF207_uc010csz.2_Missense_Mutation_p.R496L|ZNF207_uc002hhk.1_Intron|ZNF207_uc002hhl.1_RNA	NM_003457	NP_003448	O43670	ZN207_HUMAN	zinc finger protein 207 isoform a	477						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			CAAGGTGGCCGTTACTGATCT	0.507													14	24	---	---	---	---	PASS
FBXO47	494188	broad.mit.edu	37	17	37099956	37099956	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37099956G>T	uc002hrc.2	-	8	1027	c.827C>A	c.(826-828)CCT>CAT	p.P276H		NM_001008777	NP_001008777	Q5MNV8	FBX47_HUMAN	F-box protein 47	276											0						TTCATCTGTAGGTTCTTCTAT	0.383													5	58	---	---	---	---	PASS
PLCD3	113026	broad.mit.edu	37	17	43195803	43195803	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43195803C>A	uc002iib.2	-	6	1084	c.970G>T	c.(970-972)GAG>TAG	p.E324*		NM_133373	NP_588614	Q8N3E9	PLCD3_HUMAN	phospholipase C delta 3	324					intracellular signal transduction|lipid catabolic process	cleavage furrow|cytoplasm|membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			breast(2)|lung(1)	3					Phosphatidylserine(DB00144)	GCAGCCCCCTCCGGCGACAAC	0.577													5	59	---	---	---	---	PASS
HOXB7	3217	broad.mit.edu	37	17	46688189	46688189	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46688189G>A	uc002inv.2	-	1	195	c.92C>T	c.(91-93)TCT>TTT	p.S31F		NM_004502	NP_004493	P09629	HXB7_HUMAN	homeobox B7	31						nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						AAACGCACAAGAAGTTTGTTC	0.552													13	37	---	---	---	---	PASS
COL1A1	1277	broad.mit.edu	37	17	48272584	48272584	+	Intron	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48272584G>C	uc002iqm.2	-							NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein						axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)	GGGAGAGTTTGGTACTCACGC	0.667			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta						4	13	---	---	---	---	PASS
PRR11	55771	broad.mit.edu	37	17	57262807	57262807	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57262807G>A	uc002ixf.1	+	4	365	c.286G>A	c.(286-288)GAA>AAA	p.E96K	PRR11_uc002ixg.1_RNA	NM_018304	NP_060774	Q96HE9	PRR11_HUMAN	proline rich 11	96										ovary(2)	2	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					TCAGAGTTTAGAAGTATTGAA	0.323													21	41	---	---	---	---	PASS
KIAA0195	9772	broad.mit.edu	37	17	73489806	73489806	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73489806G>T	uc002jnz.3	+	18	2491	c.2216G>T	c.(2215-2217)CGA>CTA	p.R739L	KIAA0195_uc010wsa.1_Missense_Mutation_p.R749L|KIAA0195_uc010wsb.1_Missense_Mutation_p.R379L|KIAA0195_uc002job.3_5'Flank	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	739					ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TTCTACCAGCGAGCCTGCCTG	0.607													4	103	---	---	---	---	PASS
RNF213	57674	broad.mit.edu	37	17	78337588	78337588	+	Silent	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78337588C>G	uc002jyh.1	+	16	6190	c.5967C>G	c.(5965-5967)GTC>GTG	p.V1989V	uc002jyi.1_Intron|RNF213_uc010dhw.1_Silent_p.V371V	NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TCAGGGAAGTCAGGTGAGACC	0.607													3	9	---	---	---	---	PASS
KIAA0802	23255	broad.mit.edu	37	18	8783855	8783855	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8783855G>T	uc002knr.2	+	6	887	c.745G>T	c.(745-747)GAG>TAG	p.E249*	KIAA0802_uc002knq.2_Nonsense_Mutation_p.E249*|KIAA0802_uc010dkw.1_Nonsense_Mutation_p.E87*	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	600	Potential.										0						GCAGGAGCGGGAGGGCCCGGG	0.647													6	31	---	---	---	---	PASS
MC5R	4161	broad.mit.edu	37	18	13826055	13826055	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13826055C>T	uc010xaf.1	+	1	291	c.291C>T	c.(289-291)TAC>TAT	p.Y97Y		NM_005913	NP_005904	P33032	MC5R_HUMAN	melanocortin 5 receptor	97	Helical; Name=2; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocortin receptor activity|protein binding			ovary(3)|lung(2)|breast(1)	6						TCACCATCTACCTACTCAACA	0.522													4	27	---	---	---	---	PASS
OSBPL1A	114876	broad.mit.edu	37	18	21758027	21758027	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21758027C>T	uc002kve.2	-	21	2217	c.2043G>A	c.(2041-2043)GGG>GGA	p.G681G	OSBPL1A_uc002kvd.2_Silent_p.G168G|OSBPL1A_uc010xbc.1_Silent_p.G299G	NM_080597	NP_542164	Q9BXW6	OSBL1_HUMAN	oxysterol-binding protein-like 1A isoform B	681					cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding			ovary(4)	4	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					CTACACTCTTCCCCCAGAATT	0.443													8	42	---	---	---	---	PASS
ASXL3	80816	broad.mit.edu	37	18	31324435	31324435	+	Silent	SNP	T	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31324435T>C	uc010dmg.1	+	12	4678	c.4623T>C	c.(4621-4623)GCT>GCC	p.A1541A	ASXL3_uc002kxq.2_Silent_p.A1248A	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1541					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						CTTTCATTGCTGCTTCGGCAG	0.507											OREG0024911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	12	---	---	---	---	PASS
RPRD1A	55197	broad.mit.edu	37	18	33613794	33613794	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33613794G>A	uc002kzf.1	-	2	164	c.158C>T	c.(157-159)CCA>CTA	p.P53L	RPRD1A_uc002kze.1_Missense_Mutation_p.P17L|RPRD1A_uc002kzg.2_Missense_Mutation_p.P53L|RPRD1A_uc010dmw.2_Missense_Mutation_p.P17L|RPRD1A_uc010dmx.2_Missense_Mutation_p.P53L	NM_018170	NP_060640	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing	53	CID.									ovary(1)|breast(1)	2						CTTCCTGTTTGGTTTGGCTGA	0.333													8	27	---	---	---	---	PASS
KIAA1632	57724	broad.mit.edu	37	18	43446904	43446904	+	Silent	SNP	C	A	A	rs142224776	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43446904C>A	uc002lbm.2	-	38	6580	c.6480G>T	c.(6478-6480)TCG>TCT	p.S2160S	KIAA1632_uc010xcq.1_Silent_p.S714S|KIAA1632_uc010xcr.1_RNA|KIAA1632_uc010xcs.1_RNA|KIAA1632_uc002lbn.2_Silent_p.S1035S	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	2160					autophagy						0						CACTCTGGTACGACACAATAT	0.398													34	18	---	---	---	---	PASS
DSEL	92126	broad.mit.edu	37	18	65181344	65181344	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65181344C>A	uc002lke.1	-	2	1756	c.532G>T	c.(532-534)GTT>TTT	p.V178F		NM_032160	NP_115536	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	168						integral to membrane	isomerase activity|sulfotransferase activity			ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	6		Esophageal squamous(42;0.129)				CCAATTGGAACCTCATCTCCT	0.383													26	14	---	---	---	---	PASS
DSEL	92126	broad.mit.edu	37	18	65181345	65181345	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65181345C>G	uc002lke.1	-	2	1755	c.531G>C	c.(529-531)GAG>GAC	p.E177D		NM_032160	NP_115536	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	167						integral to membrane	isomerase activity|sulfotransferase activity			ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	6		Esophageal squamous(42;0.129)				CAATTGGAACCTCATCTCCTG	0.378													27	14	---	---	---	---	PASS
MADCAM1	8174	broad.mit.edu	37	19	498595	498595	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:498595C>T	uc002los.2	+	3	447	c.437C>T	c.(436-438)GCG>GTG	p.A146V	MADCAM1_uc002lot.2_Missense_Mutation_p.A146V|MADCAM1_uc010drq.2_Missense_Mutation_p.A51V	NM_130760	NP_570116	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion	146	Extracellular (Potential).|Ig-like 2.				cell adhesion|immune response|regulation of immune response|signal transduction	integral to membrane|membrane fraction|plasma membrane					0		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)		GACCCCAACGCGCTCTCCTTC	0.716													11	2	---	---	---	---	PASS
DOT1L	84444	broad.mit.edu	37	19	2217007	2217007	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2217007G>C	uc002lvb.3	+	21	2498	c.2462G>C	c.(2461-2463)GGC>GCC	p.G821A	DOT1L_uc002lvc.1_Missense_Mutation_p.G115A|uc002lvd.1_5'Flank|DOT1L_uc002lve.1_Missense_Mutation_p.G115A	NM_032482	NP_115871	Q8TEK3	DOT1L_HUMAN	DOT1-like, histone H3 methyltransferase	821						nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		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)		AGCGTGCCTGGCAGCATGAAG	0.657													8	21	---	---	---	---	PASS
ZNF556	80032	broad.mit.edu	37	19	2877439	2877439	+	Silent	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2877439C>G	uc002lwp.1	+	4	570	c.483C>G	c.(481-483)TCC>TCG	p.S161S	ZNF556_uc002lwq.2_Silent_p.S160S	NM_024967	NP_079243	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	161	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)	3				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)		ATTCCTCATCCCTGATAAGGC	0.433													33	47	---	---	---	---	PASS
ZNF556	80032	broad.mit.edu	37	19	2877512	2877512	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2877512C>T	uc002lwp.1	+	4	643	c.556C>T	c.(556-558)CGC>TGC	p.R186C	ZNF556_uc002lwq.2_Missense_Mutation_p.R185C	NM_024967	NP_079243	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	186	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)	3				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)		AGCCTTCAGTCGCCCTTCCTA	0.453													45	38	---	---	---	---	PASS
UBXN6	80700	broad.mit.edu	37	19	4447574	4447574	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4447574C>T	uc002man.1	-	6	684	c.588G>A	c.(586-588)AAG>AAA	p.K196K	UBXN6_uc010dty.1_Silent_p.K100K|UBXN6_uc002mam.1_Silent_p.K143K	NM_025241	NP_079517	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	196	PUB.					microtubule organizing center|nucleus	protein binding				0						GCAGCTTGATCTTCCGGTACT	0.677													18	61	---	---	---	---	PASS
LRG1	116844	broad.mit.edu	37	19	4538248	4538248	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4538248T>A	uc002mau.2	-	2	759	c.748A>T	c.(748-750)AGG>TGG	p.R250W	PLIN5_uc002mat.1_Intron	NM_052972	NP_443204	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1 precursor	250	LRR 7.					extracellular region|membrane				ovary(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTGCCACCCTGGCCAGCTTG	0.607													77	38	---	---	---	---	PASS
PNPLA6	10908	broad.mit.edu	37	19	7605533	7605533	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7605533G>T	uc010xjq.1	+	8	954	c.759G>T	c.(757-759)GTG>GTT	p.V253V	PNPLA6_uc002mgq.1_Silent_p.V205V|PNPLA6_uc010xjp.1_Silent_p.V205V|PNPLA6_uc002mgr.1_Silent_p.V205V|PNPLA6_uc002mgs.2_Silent_p.V244V	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase isoform b	244	cNMP 1.|Cytoplasmic (Potential).				cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3						AGGAGTGTGTGGTGAAGGAAG	0.602													5	66	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9090237	9090237	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9090237C>T	uc002mkp.2	-	1	1782	c.1578G>A	c.(1576-1578)CAG>CAA	p.Q526Q		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	526	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						CACTAAATTGCTGAGCTGTGC	0.542													38	41	---	---	---	---	PASS
ZNF791	163049	broad.mit.edu	37	19	12739314	12739314	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12739314G>T	uc002mua.2	+	4	1133	c.971G>T	c.(970-972)GGA>GTA	p.G324V	ZNF791_uc010xml.1_Missense_Mutation_p.G292V|ZNF791_uc010dyu.1_Missense_Mutation_p.G215V|ZNF791_uc010xmm.1_Missense_Mutation_p.G215V	NM_153358	NP_699189	Q3KP31	ZN791_HUMAN	zinc finger protein 791	324					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						ATTCATACTGGAGAGAAGCCC	0.408													5	57	---	---	---	---	PASS
CCDC105	126402	broad.mit.edu	37	19	15124599	15124599	+	Intron	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15124599C>A	uc002nae.2	+							NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105						microtubule cytoskeleton organization	microtubule				ovary(1)	1						GTTAGGGGTGCCTGTGGACAA	0.502													7	9	---	---	---	---	PASS
CPAMD8	27151	broad.mit.edu	37	19	17091325	17091325	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17091325T>A	uc002nfb.2	-	14	1740	c.1708A>T	c.(1708-1710)ACA>TCA	p.T570S		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	523						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						GAAAGGTGTGTTAAACGAATC	0.587													9	25	---	---	---	---	PASS
FKBP8	23770	broad.mit.edu	37	19	18649073	18649073	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18649073G>A	uc002njk.1	-	5	835	c.722C>T	c.(721-723)GCC>GTC	p.A241V	FKBP8_uc002nji.1_Missense_Mutation_p.A79V|FKBP8_uc010xqi.1_Missense_Mutation_p.A270V|FKBP8_uc002njj.1_Missense_Mutation_p.A242V|FKBP8_uc002njl.1_Missense_Mutation_p.A242V|FKBP8_uc002njm.1_Missense_Mutation_p.A241V|FKBP8_uc010ebr.1_Missense_Mutation_p.A80V|FKBP8_uc002njn.2_RNA	NM_012181	NP_036313	Q14318	FKBP8_HUMAN	FK506-binding protein 8	241	TPR 1.				apoptosis|interspecies interaction between organisms|intracellular signal transduction|protein folding	integral to endoplasmic reticulum membrane|mitochondrial membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|protein binding			ovary(1)	1						GTAGGAGTTGGCGGCCAGGAC	0.662													7	41	---	---	---	---	PASS
ZNF85	7639	broad.mit.edu	37	19	21131712	21131712	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21131712G>T	uc002npg.3	+	4	519	c.392G>T	c.(391-393)TGT>TTT	p.C131F	ZNF85_uc010ecn.2_Missense_Mutation_p.C66F|ZNF85_uc010eco.2_Missense_Mutation_p.C79F|ZNF85_uc002npi.2_Missense_Mutation_p.C72F	NM_003429	NP_003420	Q03923	ZNF85_HUMAN	zinc finger protein 85	131						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			central_nervous_system(1)	1						AAAGGAGGTTGTAATGGACTT	0.328													4	71	---	---	---	---	PASS
ZNF714	148206	broad.mit.edu	37	19	21300186	21300186	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21300186A>G	uc002npo.3	+	6	1079	c.719A>G	c.(718-720)CAT>CGT	p.H240R	ZNF714_uc002npl.2_Missense_Mutation_p.H85R|ZNF714_uc010ecp.1_Missense_Mutation_p.H191R|ZNF714_uc002npn.2_RNA	NM_182515	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	240	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GCCTTCTACCATTCTTCACAC	0.413													26	16	---	---	---	---	PASS
ZNF599	148103	broad.mit.edu	37	19	35250747	35250747	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35250747A>G	uc010edn.1	-	4	1347	c.959T>C	c.(958-960)TTT>TCT	p.F320S	ZNF599_uc010edm.1_Missense_Mutation_p.F283S	NM_001007248	NP_001007249	Q96NL3	ZN599_HUMAN	zinc finger protein 599	320	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			GCTGTAGTAAAAAGCTTTCCC	0.433													3	69	---	---	---	---	PASS
HKR1	284459	broad.mit.edu	37	19	37854631	37854631	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37854631G>C	uc002ogb.2	+	6	2203	c.1934G>C	c.(1933-1935)AGT>ACT	p.S645T	HKR1_uc002ofx.2_Missense_Mutation_p.S361T|HKR1_uc002ofy.2_Missense_Mutation_p.S361T|HKR1_uc002oga.2_Missense_Mutation_p.S627T|HKR1_uc010xto.1_Missense_Mutation_p.S627T|HKR1_uc002ogc.2_Missense_Mutation_p.S626T|HKR1_uc010xtp.1_Missense_Mutation_p.S584T|HKR1_uc002ogd.2_Missense_Mutation_p.S584T	NM_181786	NP_861451	P10072	HKR1_HUMAN	GLI-Kruppel family member HKR1	645	C2H2-type 13.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CGGGGCTTTAGTCGGAAGTCC	0.473													4	49	---	---	---	---	PASS
CEACAM21	90273	broad.mit.edu	37	19	42085944	42085944	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42085944C>A	uc002ore.3	+	3	759	c.663C>A	c.(661-663)AGC>AGA	p.S221R	CEACAM21_uc002orc.1_RNA|CEACAM21_uc002ord.1_RNA|CEACAM21_uc002orf.2_RNA|CEACAM21_uc002org.3_Missense_Mutation_p.S221R	NM_001098506	NP_001091976	Q3KPI0	CEA21_HUMAN	carcinoembryonic antigen-related cell adhesion	221	Ig-like C2-type.|Extracellular (Potential).					integral to membrane				ovary(1)	1						ACCCAGTCAGCTCCAACAGGA	0.547													6	8	---	---	---	---	PASS
PSG6	5675	broad.mit.edu	37	19	43529139	43529139	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43529139A>T	uc002ovh.1	-	2	241	c.152T>A	c.(151-153)GTG>GAG	p.V51E	PSG11_uc002ouw.2_Missense_Mutation_p.V51E|PSG10_uc002ouv.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Missense_Mutation_p.V51E|PSG11_uc002ovm.1_Missense_Mutation_p.V45E|PSG11_uc002ovn.1_Missense_Mutation_p.V51E|PSG11_uc002ovo.1_Intron|PSG11_uc002ovp.1_Intron			Q00889	PSG6_HUMAN	SubName: Full=Putative uncharacterized protein PSG6;	45	Ig-like V-type.				female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)				CCCCTCGGACACTTTGGGTGG	0.468													80	117	---	---	---	---	PASS
ZNF227	7770	broad.mit.edu	37	19	44740694	44740694	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44740694G>T	uc002oyu.2	+	6	2316	c.2111G>T	c.(2110-2112)CGC>CTC	p.R704L	ZNF227_uc010xwu.1_Missense_Mutation_p.R653L|ZNF227_uc002oyv.2_Missense_Mutation_p.R704L|ZNF227_uc010xwv.1_Missense_Mutation_p.R653L|ZNF227_uc010xww.1_Missense_Mutation_p.R625L|ZNF227_uc002oyw.2_Missense_Mutation_p.R676L|ZNF227_uc010ejh.2_Missense_Mutation_p.R697L|ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_3'UTR	NM_182490	NP_872296	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	704	C2H2-type 16.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0435)				TTGAATCTTCGCCATCATCAG	0.483													4	82	---	---	---	---	PASS
CEACAM16	388551	broad.mit.edu	37	19	45211185	45211185	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45211185C>A	uc010xxd.1	+	6	1199	c.993C>A	c.(991-993)GGC>GGA	p.G331G	CEACAM16_uc002ozq.2_Silent_p.G390G	NM_001039213	NP_001034302	A7LI12	A7LI12_HUMAN	carcinoembryonic antigen-related cell adhesion	331										ovary(1)	1	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)				CAACGGAGGGCCAGGACGTAA	0.662													3	11	---	---	---	---	PASS
LIG1	3978	broad.mit.edu	37	19	48624466	48624466	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48624466G>T	uc002pia.1	-	24	2466	c.2346C>A	c.(2344-2346)TCC>TCA	p.S782S	LIG1_uc010xze.1_Silent_p.S475S|LIG1_uc002phz.1_RNA|LIG1_uc002pib.1_RNA|LIG1_uc010xzf.1_Silent_p.S714S|LIG1_uc010xzg.1_Silent_p.S751S	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I	782					anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	CCTCGTCGTAGGAGGCCAGCA	0.662								NER					6	67	---	---	---	---	PASS
CCDC155	147872	broad.mit.edu	37	19	49901368	49901368	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49901368G>T	uc002pnm.1	+	7	771	c.597G>T	c.(595-597)GAG>GAT	p.E199D	CCDC155_uc002pnl.1_Missense_Mutation_p.E199D|CCDC155_uc010emx.1_Missense_Mutation_p.E172D	NM_144688	NP_653289	Q8N6L0	CC155_HUMAN	coiled-coil domain containing 155	199	Potential.					integral to membrane	calcium ion binding			ovary(1)|central_nervous_system(1)	2						GCCTTGGGGAGGAGATCTTGG	0.647													4	22	---	---	---	---	PASS
PRR12	57479	broad.mit.edu	37	19	50099409	50099409	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50099409G>T	uc002poo.3	+	4	1817	c.1817G>T	c.(1816-1818)GGC>GTC	p.G606V		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CCGGGAGCTGGCAGCTATGCA	0.682													12	14	---	---	---	---	PASS
SHANK1	50944	broad.mit.edu	37	19	51192460	51192460	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51192460C>A	uc002psx.1	-	15	2060	c.2041G>T	c.(2041-2043)GCC>TCC	p.A681S	SHANK1_uc002psw.1_Missense_Mutation_p.A65S	NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	681	PDZ.				cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		TCACCCTTGGCCCCCCGGAGC	0.607													5	70	---	---	---	---	PASS
ZNF701	55762	broad.mit.edu	37	19	53085781	53085781	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53085781G>A	uc002pzs.1	+	4	596	c.469G>A	c.(469-471)GAA>AAA	p.E157K	ZNF701_uc010ydn.1_Missense_Mutation_p.E223K	NM_018260	NP_060730	Q9NV72	ZN701_HUMAN	zinc finger protein 701	157					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		ATTTCACCCCGAAGGGAAAAT	0.413													32	91	---	---	---	---	PASS
MBOAT7	79143	broad.mit.edu	37	19	54687471	54687471	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54687471C>T	uc002qdq.2	-	6	692	c.426G>A	c.(424-426)CTG>CTA	p.L142L	MBOAT7_uc010erg.2_5'UTR|MBOAT7_uc010yem.1_Silent_p.L124L|MBOAT7_uc002qdr.2_Silent_p.L142L|MBOAT7_uc002qds.2_Silent_p.L69L|MBOAT7_uc010yen.1_Silent_p.L69L|MBOAT7_uc002qdt.3_Silent_p.L142L	NM_024298	NP_077274	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain	142					phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CGTCGGGCAGCAGCCCCAGGG	0.627													17	27	---	---	---	---	PASS
KIR3DL1	3811	broad.mit.edu	37	19	55329031	55329031	+	Intron	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55329031C>A	uc002qhk.3	+						KIR2DS4_uc010yfj.1_Intron|KIR2DS4_uc010yfk.1_Intron|KIR3DL1_uc010yfn.1_Intron|KIR3DL1_uc010esf.2_Intron|KIR3DL1_uc010yfo.1_Intron|KIR3DL1_uc002qhl.3_Intron	NM_013289	NP_037421	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three						immune response|regulation of immune response	integral to plasma membrane	HLA-B specific inhibitory MHC class I receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|skin(1)	5				GBM - Glioblastoma multiforme(193;0.0192)		ATGGGTGAGTCCTTCCCCAAA	0.542													32	13	---	---	---	---	PASS
PTPRH	5794	broad.mit.edu	37	19	55711656	55711656	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55711656C>A	uc002qjq.2	-	7	1441	c.1368G>T	c.(1366-1368)TGG>TGT	p.W456C	PTPRH_uc010esv.2_Missense_Mutation_p.W278C|PTPRH_uc002qjs.2_Missense_Mutation_p.W463C	NM_002842	NP_002833	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	456	Extracellular (Potential).|Fibronectin type-III 5.				apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		TTTTTTCTGCCCATACAGAGA	0.517													18	16	---	---	---	---	PASS
ZNF835	90485	broad.mit.edu	37	19	57175601	57175601	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57175601G>A	uc010ygo.1	-	2	1032	c.1032C>T	c.(1030-1032)GCC>GCT	p.A344A	ZNF835_uc010ygn.1_Silent_p.A322A	NM_001005850	NP_001005850			zinc finger protein 835									p.G334fs*26(1)		pancreas(3)|skin(1)	4						GCCGGTGCTCGGCCAGAGAGG	0.701													11	18	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57344518	57344518	+	Intron	SNP	C	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57344518C>G	uc002qnv.2	-						ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnw.2_Intron|PEG3_uc002qnx.2_Intron|PEG3_uc010etr.2_Intron	NM_006210	NP_006201	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1						apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		TCCTGTGACTCCGGTTTGGCC	0.478													7	10	---	---	---	---	PASS
ZNF586	54807	broad.mit.edu	37	19	58290273	58290273	+	Silent	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58290273C>T	uc002qqd.2	+	3	504	c.318C>T	c.(316-318)CCC>CCT	p.P106P	ZNF587_uc002qqb.2_Intron|ZNF586_uc002qqe.2_Missense_Mutation_p.P64L|ZNF586_uc010euh.2_Silent_p.P63P|ZNF586_uc002qqf.1_Intron	NM_017652	NP_060122	Q9NXT0	ZN586_HUMAN	zinc finger protein 586	106	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TCACTGAACCCAGAAGAGATC	0.413													14	70	---	---	---	---	PASS
ZNF446	55663	broad.mit.edu	37	19	58991863	58991863	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58991863C>T	uc002qsz.2	+	7	1240	c.1123C>T	c.(1123-1125)CCA>TCA	p.P375S	ZNF446_uc002qta.2_3'UTR|ZNF446_uc010eur.2_3'UTR|SLC27A5_uc002qtb.2_RNA	NM_017908	NP_060378	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	375					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		AGAGAAGCCACCACAAGGGGA	0.647													7	7	---	---	---	---	PASS
CPXM1	56265	broad.mit.edu	37	20	2778860	2778860	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2778860C>A	uc002wgu.2	-	4	592	c.528G>T	c.(526-528)GTG>GTT	p.V176V	CPXM1_uc010gas.2_Silent_p.V176V	NM_019609	NP_062555	Q96SM3	CPXM1_HUMAN	carboxypeptidase X, member 1 precursor	176	F5/8 type C.				cell adhesion|proteolysis		metallocarboxypeptidase activity|zinc ion binding			ovary(2)|skin(2)	4						GCCCAGCGTCCACCTGAAACC	0.592													5	46	---	---	---	---	PASS
PLCB1	23236	broad.mit.edu	37	20	8769342	8769342	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8769342A>T	uc002wnb.2	+	29	3254	c.3251A>T	c.(3250-3252)AAA>ATA	p.K1084I	PLCB1_uc002wna.2_Missense_Mutation_p.K1084I	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	1084					activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						ACAGAAGCTAAATCCAAAGAC	0.363													10	28	---	---	---	---	PASS
PAX1	5075	broad.mit.edu	37	20	21687473	21687473	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21687473G>T	uc002wsj.2	+	2	738	c.684G>T	c.(682-684)CTG>CTT	p.L228L	PAX1_uc010zsl.1_Silent_p.L228L|PAX1_uc010zsm.1_Silent_p.L204L	NM_006192	NP_006183	P15863	PAX1_HUMAN	paired box 1	228					regulation of transcription, DNA-dependent|skeletal system development|transcription from RNA polymerase II promoter	nucleus	DNA binding			upper_aerodigestive_tract(1)|kidney(1)	2						TCGGCAGCCTGGCGCAGCCCG	0.642													26	10	---	---	---	---	PASS
MAPRE1	22919	broad.mit.edu	37	20	31421598	31421598	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31421598A>C	uc002wyh.2	+	3	336	c.197A>C	c.(196-198)AAG>ACG	p.K66T		NM_012325	NP_036457	Q15691	MARE1_HUMAN	microtubule-associated protein, RP/EB family,	66	CH.				cell division|cell proliferation|G2/M transition of mitotic cell cycle|mitotic prometaphase|negative regulation of microtubule polymerization|protein localization to microtubule	centrosome|cortical microtubule cytoskeleton|cytosol	microtubule plus-end binding|protein C-terminus binding				0						TTCCAAGCTAAGCTAGAACAC	0.398													51	62	---	---	---	---	PASS
SLC12A5	57468	broad.mit.edu	37	20	44663663	44663663	+	Silent	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44663663G>A	uc010zxl.1	+	2	274	c.198G>A	c.(196-198)AAG>AAA	p.K66K	SLC12A5_uc002xra.2_Silent_p.K43K|SLC12A5_uc010zxm.1_RNA|SLC12A5_uc002xrb.2_Silent_p.K43K	NM_001134771	NP_001128243	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	66	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	ATGATGGCAAGAACATGGCCT	0.547													43	74	---	---	---	---	PASS
PTPN1	5770	broad.mit.edu	37	20	49177930	49177930	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49177930T>G	uc002xvl.2	+	2	268	c.94T>G	c.(94-96)TGT>GGT	p.C32G	PTPN1_uc010zys.1_Intron	NM_002827	NP_002818	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type	32	Tyrosine-protein phosphatase.				blood coagulation|interferon-gamma-mediated signaling pathway|negative regulation of insulin receptor signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytosol|endoplasmic reticulum membrane	protein tyrosine phosphatase activity|zinc ion binding				0		Lung NSC(126;0.163)			Clodronate(DB00720)|Tiludronate(DB01133)	TGACTTCCCATGTAGAGTGGC	0.453													6	57	---	---	---	---	PASS
KRTAP13-1	140258	broad.mit.edu	37	21	31768868	31768868	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31768868G>A	uc002yoa.2	+	1	477	c.464G>A	c.(463-465)AGG>AAG	p.R155K		NM_181599	NP_853630	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	155						intermediate filament				ovary(1)	1						TTGGCTTCTAGGAGCTGCCAG	0.502													16	15	---	---	---	---	PASS
NDUFV3	4731	broad.mit.edu	37	21	44323851	44323851	+	Intron	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44323851G>T	uc002zcn.2	+						NDUFV3_uc002zcm.2_Silent_p.A243A	NM_001001503	NP_001001503	P56181	NDUV3_HUMAN	NADH-ubiquinone oxidoreductase flavoprotein 3						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I|nucleus	NADH dehydrogenase (ubiquinone) activity			ovary(2)	2				STAD - Stomach adenocarcinoma(101;0.0606)	NADH(DB00157)	GGGAAAATGCGAGACCAAAAA	0.428													6	268	---	---	---	---	PASS
CSF2RB	1439	broad.mit.edu	37	22	37333986	37333986	+	Silent	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37333986C>A	uc003aqa.3	+	14	2353	c.2136C>A	c.(2134-2136)GTC>GTA	p.V712V	CSF2RB_uc003aqc.3_Silent_p.V718V	NM_000395	NP_000386	P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta	712	Cytoplasmic (Potential).				respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			skin(2)|pancreas(1)	3					Sargramostim(DB00020)	CTGGTTATGTCTCCTCTGCAG	0.597													17	19	---	---	---	---	PASS
SH3BP1	23616	broad.mit.edu	37	22	38061567	38061567	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38061567G>T	uc003atj.1	+	17	2394	c.1507G>T	c.(1507-1509)GGG>TGG	p.G503W	PDXP_uc003atm.1_Missense_Mutation_p.G194W			Q9Y3L3	3BP1_HUMAN	SubName: Full=cDNA FLJ44925 fis, clone BRAMY3014613, highly similar to Homo sapiens SH3-domain binding protein 1 (SH3BP1);	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					signal transduction	cytoplasm	GTPase activator activity|SH3 domain binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					TACAGGCACCGGGAGCCTGGC	0.652													3	15	---	---	---	---	PASS
JOSD1	9929	broad.mit.edu	37	22	39085044	39085044	+	Silent	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39085044G>C	uc003awf.2	-	3	872	c.405C>G	c.(403-405)CTC>CTG	p.L135L		NM_014876	NP_055691	Q15040	JOS1_HUMAN	Josephin domain containing 1	135	Josephin.						peptidase activity				0	Melanoma(58;0.04)					GCTGCCTTTTGAGGGGCAGTT	0.572													27	33	---	---	---	---	PASS
PARVB	29780	broad.mit.edu	37	22	44532354	44532354	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44532354G>T	uc003ben.2	+	7	700	c.648G>T	c.(646-648)CTG>CTT	p.L216L	PARVB_uc003bem.2_Silent_p.L249L|PARVB_uc010gzn.2_Silent_p.L164L|PARVB_uc003beo.2_Silent_p.L179L	NM_013327	NP_037459	Q9HBI1	PARVB_HUMAN	parvin, beta isoform b	216					cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)				GGGAAGGCCTGCTGCATTCCA	0.562													17	20	---	---	---	---	PASS
FAM48B1	100130302	broad.mit.edu	37	X	24382817	24382817	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24382817A>G	uc011mjx.1	+	1	1940	c.1940A>G	c.(1939-1941)GAC>GGC	p.D647G		NM_001136234	NP_001129706			hypothetical protein LOC100130302											kidney(1)	1						AGTGGCAGTGACCTTCAGTCC	0.612													10	5	---	---	---	---	PASS
POLA1	5422	broad.mit.edu	37	X	24753605	24753605	+	Silent	SNP	G	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24753605G>T	uc004dbl.2	+	18	1928	c.1905G>T	c.(1903-1905)GTG>GTT	p.V635V		NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1	635					cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)	ATATCATTGTGGTGAGTAGAT	0.368													5	43	---	---	---	---	PASS
MAGEB6	158809	broad.mit.edu	37	X	26213027	26213027	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26213027A>G	uc004dbr.2	+	2	1213	c.1064A>G	c.(1063-1065)TAT>TGT	p.Y355C	MAGEB6_uc010ngc.1_Missense_Mutation_p.Y135C	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	355	MAGE.									ovary(3)	3						CCTCCATGCTATGAGTTCCTG	0.498													28	5	---	---	---	---	PASS
UBA1	7317	broad.mit.edu	37	X	47070573	47070573	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47070573G>C	uc004dhj.3	+	20	2564	c.2413G>C	c.(2413-2415)GTC>CTC	p.V805L	UBA1_uc004dhk.3_Missense_Mutation_p.V805L|UBA1_uc004dhm.2_Missense_Mutation_p.V253L	NM_153280	NP_695012	P22314	UBA1_HUMAN	ubiquitin-activating enzyme E1	805					cell death|protein modification process		ATP binding|ligase activity|protein binding|small protein activating enzyme activity			ovary(1)	1						CAAGTCTGGCGTCAAGATCCA	0.607													4	39	---	---	---	---	PASS
PHF8	23133	broad.mit.edu	37	X	53970684	53970684	+	Intron	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53970684G>A	uc004dsu.2	-						PHF8_uc004dst.2_Intron|PHF8_uc004dsv.2_Intron|PHF8_uc004dsw.2_Intron|PHF8_uc004dsx.2_Intron|PHF8_uc004dsy.2_Intron	NM_015107	NP_055922	Q9UPP1	PHF8_HUMAN	PHD finger protein 8						brain development|G1/S transition of mitotic cell cycle|negative regulation of chromatin silencing at rDNA|positive regulation of transcription from RNA polymerase I promoter|transcription, DNA-dependent	nucleolus	chromatin binding|histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(3)	3						GGGCTGCAAGGGAAACAGGAT	0.552													8	14	---	---	---	---	PASS
NKRF	55922	broad.mit.edu	37	X	118724197	118724197	+	Silent	SNP	A	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118724197A>G	uc004erq.2	-	2	1844	c.1191T>C	c.(1189-1191)AGT>AGC	p.S397S	NKRF_uc004err.2_Silent_p.S397S	NM_017544	NP_060014	O15226	NKRF_HUMAN	transcription factor NRF	397					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|double-stranded RNA binding			ovary(1)|central_nervous_system(1)	2						CTGCATGTTTACTTGTTTTCT	0.413													71	10	---	---	---	---	PASS
CXorf66	347487	broad.mit.edu	37	X	139038229	139038229	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139038229C>A	uc004fbb.2	-	3	934	c.912G>T	c.(910-912)AAG>AAT	p.K304N		NM_001013403	NP_001013421	Q5JRM2	CX066_HUMAN	hypothetical protein LOC347487 precursor	304	Cytoplasmic (Potential).					integral to membrane					0						TGGAAGAGGACTTGACTTTGC	0.378													15	35	---	---	---	---	PASS
UBE2NL	389898	broad.mit.edu	37	X	142967551	142967551	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142967551A>C	uc004fca.2	+	1	379	c.349A>C	c.(349-351)AAT>CAT	p.N117H		NM_001012989	NP_001013007	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like	117							acid-amino acid ligase activity				0	Acute lymphoblastic leukemia(192;6.56e-05)					AAATGCTCCCAATCCAGATGA	0.453													30	39	---	---	---	---	PASS
GDI1	2664	broad.mit.edu	37	X	153667172	153667172	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153667172G>A	uc004fli.3	+	3	557	c.215G>A	c.(214-216)TGG>TAG	p.W72*	GDI1_uc011mzo.1_Nonsense_Mutation_p.W72*	NM_001493	NP_001484	P31150	GDIA_HUMAN	GDP dissociation inhibitor 1	72					protein transport|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|midbody	GTPase activator activity|protein binding				0	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGCCGAGACTGGAATGTTGAC	0.572													86	11	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	2497662	2497662	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2497662delC								TNFRSF14 (2397 upstream) : C1orf93 (20587 downstream)																							CCTGTGTCCGCCCGCCTTGAC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	4072095	4072096	+	IGR	INS	-	T	T	rs139879026	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4072095_4072096insT								LOC100133612 (238218 upstream) : LOC284661 (400015 downstream)																							AAGATTTAAGATTTTTTTTTTA	0.099													1	5	---	---	---	---	
APITD1	378708	broad.mit.edu	37	1	10505400	10505400	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10505400delT	uc001arf.2	+						APITD1_uc001arg.2_Intron	NM_198544	NP_940946	Q8N2Z9	CENPS_HUMAN	apoptosis-inducing, TAF9-like domain 1 isoform						DNA repair|mitotic prometaphase|transcription initiation, DNA-dependent	chromosome, centromeric region|cytosol|Fanconi anaemia nuclear complex	chromatin binding|DNA binding|protein binding			ovary(1)	1	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.31e-07)|COAD - Colon adenocarcinoma(227;7.32e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		agttcaaggctttagtgaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	14498230	14498230	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14498230delA								PRDM2 (346658 upstream) : KAZ (426983 downstream)																							GATATGACTCATCTGGTATAT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18830355	18830356	+	IGR	INS	-	GGAG	GGAG	rs4920508	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18830355_18830356insGGAG								KLHDC7A (17816 upstream) : PAX7 (127144 downstream)																							gagggagggaaggagggaggga	0.040													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	19314266	19314277	+	IGR	DEL	GAAGGAAGGAAA	-	-	rs72498264		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19314266_19314277delGAAGGAAGGAAA								IFFO2 (31440 upstream) : UBR4 (84327 downstream)																							aggaaggaaggaaggaaggaaagaaggaagga	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20790002	20790002	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20790002delT								VWA5B1 (108615 upstream) : CAMK2N1 (18883 downstream)																							atcatcatcattaccaccacc	0.015													4	2	---	---	---	---	
EPB41	2035	broad.mit.edu	37	1	29379449	29379449	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29379449delC	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217	P11171	41_HUMAN	erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		GCTATCAGTTCCCTGGCAGAG	0.398													4	2	---	---	---	---	
LCK	3932	broad.mit.edu	37	1	32732188	32732190	+	Intron	DEL	TCC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32732188_32732190delTCC	uc001bux.2	+							NM_005356	NP_005347	P06239	LCK_HUMAN	lymphocyte-specific protein tyrosine kinase						activation of caspase activity|cellular zinc ion homeostasis|induction of apoptosis|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of T cell receptor signaling pathway|regulation of defense response to virus by virus|release of sequestered calcium ion into cytosol|response to drug|T cell costimulation|T cell differentiation|T cell receptor signaling pathway|viral reproduction	cytosol|Golgi apparatus|membrane raft|pericentriolar material|plasma membrane	ATP binding|ATPase binding|CD4 receptor binding|CD8 receptor binding|glycoprotein binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein kinase binding|protein serine/threonine phosphatase activity|SH2 domain binding			lung(3)|central_nervous_system(2)|ovary(1)	6		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)	cgcccTTtcttcctcctcctcct	0.005			T	TRB@	T-ALL								2	4	---	---	---	---	
ECHDC2	55268	broad.mit.edu	37	1	53373495	53373496	+	Intron	INS	-	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53373495_53373496insG	uc001cup.3	-						ECHDC2_uc001cun.2_Intron|ECHDC2_uc001cuo.3_Intron|ECHDC2_uc010onk.1_Intron|ECHDC2_uc010onl.1_Intron|ECHDC2_uc010onm.1_Intron|ECHDC2_uc010onn.1_Intron	NM_018281	NP_060751	Q86YB7	ECHD2_HUMAN	enoyl Coenzyme A hydratase domain containing 2						fatty acid metabolic process	mitochondrion	lyase activity			central_nervous_system(1)	1						TGTCATCGGCAGGGACCCCCAA	0.584													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56192003	56192004	+	Intron	INS	-	GGG	GGG	rs143957648	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56192003_56192004insGGG	uc001cyi.1	+											SubName: Full=cDNA FLJ45337 fis, clone BRHIP3007960;																		aatggggaaatgggggggaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	71123754	71123755	+	IGR	INS	-	TCCTTCCTTCCT	TCCTTCCTTCCT	rs143061057	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71123754_71123755insTCCTTCCTTCCT								CTH (218502 upstream) : PTGER3 (194281 downstream)																							tccttcctttctccttccttcc	0.079													3	3	---	---	---	---	
C1orf173	127254	broad.mit.edu	37	1	75115073	75115073	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75115073delC	uc001dgg.2	-							NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254											ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						TTTACTGTTTCCCCAAATAGT	0.269													4	8	---	---	---	---	
SLC44A5	204962	broad.mit.edu	37	1	75679783	75679795	+	Intron	DEL	AATTGTATTTGGC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75679783_75679795delAATTGTATTTGGC	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4						TCTTTGCTGAAATTGTATTTGGCAATTGTTTTG	0.333													6	3	---	---	---	---	
LPHN2	23266	broad.mit.edu	37	1	82306031	82306031	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82306031delT	uc001dit.3	+						LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Intron|LPHN2_uc001div.2_Intron|LPHN2_uc009wcd.2_Intron	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		CTTTTAGATCTTTTTTTTTCC	0.308													4	2	---	---	---	---	
PKN2	5586	broad.mit.edu	37	1	89188798	89188799	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89188798_89188799insT	uc001dmn.2	+						PKN2_uc001dmm.1_Intron|PKN2_uc010osp.1_Intron|PKN2_uc010osq.1_Intron|PKN2_uc009wcv.2_Intron	NM_006256	NP_006247	Q16513	PKN2_HUMAN	protein kinase N2						signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		AGCCAGGTATCttttttttttt	0.099													4	2	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120558407	120558410	+	Intron	DEL	GTCA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120558407_120558410delGTCA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTTAATTCTGTCACTCTGTGTAA	0.417			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	2	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120602929	120602932	+	Intron	DEL	GAGA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120602929_120602932delGAGA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		tcactgtaatgagagaggcatatt	0.034			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142626634	142626635	+	Intron	DEL	TT	-	-	rs141628095		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142626634_142626635delTT	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		ttgtttttcctttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143413594	143413594	+	IGR	DEL	G	-	-	rs112862668		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143413594delG								None (None upstream) : LOC100286793 (234045 downstream)																							tcagagccttggtctggactc	0.000													3	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144597983	144597991	+	Intron	DEL	CAGATAGAC	-	-	rs111294330		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144597983_144597991delCAGATAGAC	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc009wif.1_Intron|uc001ele.2_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						TATACGTGTACAGATAGACCAGATAGACC	0.282													7	4	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144852792	144852793	+	Intron	DEL	TT	-	-	rs72112087		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144852792_144852793delTT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCCAAATCACTTTGTCTCAGCA	0.515			T	PDGFRB	MPD								8	4	---	---	---	---	
SEC22B	9554	broad.mit.edu	37	1	145116327	145116328	+	3'UTR	INS	-	T	T	rs67374323		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145116327_145116328insT	uc001eml.1	+	7					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron	NM_004892	NP_004883	O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|melanosome	protein binding				0						ttgtttttttgttttttttGAC	0.307													3	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145190415	145190415	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145190415delC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						tgctctcactcccagcaccct	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	146859177	146859177	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146859177delT	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																		ggtataattgttttttttttt	0.000													4	2	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	147994684	147994685	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147994684_147994685insT	uc001eqf.2	-						LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						TTTTTTTGTTGTTTTTTTCCCC	0.371													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149027449	149027449	+	IGR	DEL	C	-	-	rs111702243		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149027449delC								LOC645166 (74395 upstream) : LOC388692 (252027 downstream)																							GATGTGTTTTCCCCTGTTTTT	0.373													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149030114	149030114	+	IGR	DEL	T	-	-	rs139349446		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149030114delT								LOC645166 (77060 upstream) : LOC388692 (249362 downstream)																							ccctcttttctttttgggatt	0.164													6	3	---	---	---	---	
RORC	6097	broad.mit.edu	37	1	151797724	151797725	+	Intron	DEL	CA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151797724_151797725delCA	uc001ezh.2	-						RORC_uc001ezg.2_Intron|RORC_uc010pdo.1_Intron|RORC_uc010pdp.1_Intron	NM_005060	NP_005051	P51449	RORG_HUMAN	RAR-related orphan receptor C isoform a						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CCTGGAGAACcacacacacaca	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	151840035	151840037	+	IGR	DEL	TTC	-	-	rs112825312		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151840035_151840037delTTC								THEM5 (13862 upstream) : THEM4 (6023 downstream)																							ttcttcttctttcttttcttcct	0.000													8	4	---	---	---	---	
DCAF8	50717	broad.mit.edu	37	1	160206237	160206238	+	Intron	DEL	TA	-	-	rs61341479		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160206237_160206238delTA	uc001fvo.2	-						DCAF8_uc001fvn.2_Intron|DCAF8_uc009wth.2_Intron|DCAF8_uc010pjb.1_Intron|DCAF8_uc010pjc.1_Intron	NM_015726	NP_056541	Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8							CUL4 RING ubiquitin ligase complex	protein binding			skin(2)	2						tgtgtgtgtgtatatatatata	0.114													4	2	---	---	---	---	
NOS1AP	9722	broad.mit.edu	37	1	162111835	162111837	+	Intron	DEL	ACA	-	-	rs67670247		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162111835_162111837delACA	uc001gbv.2	+						NOS1AP_uc010pkr.1_Intron|NOS1AP_uc010pks.1_Intron|NOS1AP_uc001gbw.2_Intron	NM_014697	NP_055512	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			tacagtggtgacaacaacagtta	0.133													4	3	---	---	---	---	
SH2D1B	117157	broad.mit.edu	37	1	162381975	162381975	+	5'Flank	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162381975delG	uc001gbz.1	-						SH2D1B_uc001gca.1_5'Flank	NM_053282	NP_444512	O14796	SH21B_HUMAN	SH2 domain containing 1B											pancreas(1)	1	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			GAAATGAGGAGGGCGGGGTGA	0.478													6	3	---	---	---	---	
MGST3	4259	broad.mit.edu	37	1	165606445	165606446	+	Intron	DEL	AG	-	-	rs71901812		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165606445_165606446delAG	uc001gdf.2	+						MGST3_uc001gdg.2_Intron	NM_004528	NP_004519	O14880	MGST3_HUMAN	microsomal glutathione S-transferase 3						leukotriene biosynthetic process|leukotriene production involved in inflammatory response|signal transduction|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glutathione peroxidase activity|glutathione transferase activity				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Glutathione(DB00143)	AAGAAAAAAAAGAGCAGTTGAG	0.356													3	4	---	---	---	---	
POU2F1	5451	broad.mit.edu	37	1	167258032	167258032	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167258032delT	uc001gec.2	+						POU2F1_uc010plg.1_Intron|POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5						AAGATCCTAATTTTTTGTGTT	0.269													4	3	---	---	---	---	
KIFAP3	22920	broad.mit.edu	37	1	170036510	170036511	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170036510_170036511insA	uc001ggv.2	-						KIFAP3_uc010ply.1_Intron|KIFAP3_uc001ggw.1_Intron	NM_014970	NP_055785	Q92845	KIFA3_HUMAN	kinesin-associated protein 3						blood coagulation|plus-end-directed vesicle transport along microtubule|protein complex assembly|signal transduction	centrosome|condensed nuclear chromosome|cytosol|endoplasmic reticulum|kinesin II complex|spindle microtubule	kinesin binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					aaaaacttggcaaaaaaaacct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	170605473	170605474	+	IGR	INS	-	T	T	rs79837650		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170605473_170605474insT								GORAB (82499 upstream) : PRRX1 (27839 downstream)																							GTTTTTGGTTGTTTTTTTTTTT	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	171783232	171783233	+	IGR	INS	-	G	G	rs140616184	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171783232_171783233insG								METTL13 (16377 upstream) : DNM3 (27388 downstream)																							GAAAAGAGCCTGGTTTGGGAAT	0.277													3	3	---	---	---	---	
RFWD2	64326	broad.mit.edu	37	1	176065482	176065483	+	Intron	INS	-	CAGGCT	CAGGCT	rs141964397	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176065482_176065483insCAGGCT	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|RFWD2_uc001gkt.1_Intron	NM_022457	NP_071902	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0						TTAAATGGCCACAGGCTCAGGC	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181178626	181178627	+	IGR	DEL	TC	-	-	rs36110765		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181178626_181178627delTC								IER5 (118649 upstream) : CACNA1E (274089 downstream)																							gcctcatgggtctctgtttctt	0.005													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	184328088	184328088	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184328088delC								TSEN15 (284747 upstream) : C1orf21 (28062 downstream)																							ctgcccttggccTCAGTGGAA	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	187156933	187156934	+	IGR	DEL	TG	-	-	rs59688723		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187156933_187156934delTG								PLA2G4A (198828 upstream) : None (None downstream)																							aaaaaggaaTtgtgtgtgtgtg	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	187548286	187548289	+	IGR	DEL	CACA	-	-	rs34046290		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187548286_187548289delCACA								PLA2G4A (590181 upstream) : None (None downstream)																							CTATAGCATGcacacacacacaca	0.294													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	188098339	188098339	+	IGR	DEL	A	-	-	rs146695083		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188098339delA								None (None upstream) : None (None downstream)																							gtagggaaagaaaaaagaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	191865153	191865153	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191865153delA								None (None upstream) : RGS18 (262439 downstream)																							aggctaagggaaaaggcttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192486795	192486795	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192486795delT								RGS21 (150383 upstream) : RGS1 (58062 downstream)																							GATGTGAGTCTTGCAGAAGGG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	205878592	205878593	+	IGR	INS	-	A	A	rs145774402	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205878592_205878593insA								PM20D1 (59347 upstream) : SLC26A9 (3586 downstream)																							ttgcaagggagaaaaaaaaaac	0.000													4	2	---	---	---	---	
IL24	11009	broad.mit.edu	37	1	207075769	207075769	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207075769delT	uc001hes.1	+						IL24_uc001het.1_Intron|IL24_uc001heu.1_Intron|IL24_uc001hev.1_Intron|IL24_uc001hew.1_Intron	NM_006850	NP_006841	Q13007	IL24_HUMAN	interleukin 24 isoform 1 precursor						apoptosis	extracellular space	cytokine activity				0	Breast(84;0.201)					cATACACATCTGCAGTATTTT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	210402047	210402047	+	IGR	DEL	T	-	-	rs112549505		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210402047delT								SYT14 (64416 upstream) : C1orf133 (2757 downstream)																							agtcaagaaattttttttttt	0.000													3	3	---	---	---	---	
HHAT	55733	broad.mit.edu	37	1	210512773	210512774	+	Intron	INS	-	CTC	CTC	rs150243770	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210512773_210512774insCTC	uc009xcx.2	+						HHAT_uc010psq.1_Intron|HHAT_uc001hhz.3_Intron|HHAT_uc010psr.1_Intron|HHAT_uc010pss.1_Intron|HHAT_uc009xcy.2_Intron|HHAT_uc010pst.1_Intron	NM_001122834	NP_001116306	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		tggtctgttttctcctccttga	0.059													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	211878259	211878259	+	IGR	DEL	T	-	-	rs111600811		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211878259delT								NEK2 (29292 upstream) : LPGAT1 (38541 downstream)																							ttctcttatcttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	220843726	220843726	+	IGR	DEL	A	-	-	rs10707161		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220843726delA								MARK1 (5928 upstream) : C1orf115 (19902 downstream)																							ATTGAACCAGAAAAAAAAAAA	0.030													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222188661	222188662	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222188661_222188662insT								DUSP10 (273200 upstream) : HHIPL2 (506940 downstream)																							tatggtaattcttttttttttt	0.000													4	2	---	---	---	---	
DNAH14	127602	broad.mit.edu	37	1	225196526	225196527	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225196526_225196527insT	uc001how.2	+						DNAH14_uc001hou.3_Intron|DNAH14_uc001hot.3_Intron	NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						atgatgagctgttttttttcat	0.000													4	2	---	---	---	---	
C1orf55	163859	broad.mit.edu	37	1	226180816	226180817	+	Intron	INS	-	T	T	rs66975923		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226180816_226180817insT	uc001hpu.3	-						C1orf55_uc001hpv.2_Intron	NM_152608	NP_689821	Q6IQ49	CA055_HUMAN	hypothetical protein LOC163859											lung(1)	1	Breast(184;0.197)					TACTTTCTTTCTTTTTTTTTTT	0.302													4	4	---	---	---	---	
SIPA1L2	57568	broad.mit.edu	37	1	232652281	232652281	+	5'Flank	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232652281delT	uc001hvg.2	-							NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				AGTATCTGACTACTCATTTTC	0.358													4	2	---	---	---	---	
PCNXL2	80003	broad.mit.edu	37	1	233366032	233366032	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233366032delG	uc001hvl.2	-						PCNXL2_uc009xfu.2_Intron|PCNXL2_uc009xfv.1_Intron|PCNXL2_uc001hvq.1_Intron	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				AAGGGGTCTTGGGCATTCCCT	0.453													4	2	---	---	---	---	
KIAA1804	84451	broad.mit.edu	37	1	233475217	233475219	+	Intron	DEL	CTT	-	-	rs12027653		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233475217_233475219delCTT	uc001hvt.3	+						KIAA1804_uc001hvs.1_Intron	NM_032435	NP_115811	Q5TCX8	M3KL4_HUMAN	mixed lineage kinase 4						activation of JUN kinase activity|protein autophosphorylation		ATP binding|MAP kinase kinase kinase activity|protein homodimerization activity			lung(5)|central_nervous_system(2)|skin(1)	8		all_cancers(173;0.000405)|all_epithelial(177;0.0345)|Prostate(94;0.122)				cctccttctccttcttcttcttc	0.000													3	5	---	---	---	---	
EDARADD	128178	broad.mit.edu	37	1	236596227	236596228	+	Intron	INS	-	A	A	rs75286128		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236596227_236596228insA	uc001hxu.1	+						EDARADD_uc001hxv.1_Intron	NM_145861	NP_665860	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain isoform A						cell differentiation|signal transduction	cytoplasm					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			gcaagactctcaaaaaaaaaaa	0.035													4	2	---	---	---	---	
SDCCAG8	10806	broad.mit.edu	37	1	243643777	243643778	+	Intron	INS	-	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243643777_243643778insG	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron|SDCCAG8_uc001hzx.2_Intron	NM_006642	NP_006633	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		gatggatggatggatggatgga	0.000													4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	245995836	245995836	+	Intron	DEL	A	-	-	rs10714784		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245995836delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron|SMYD3_uc001ibi.2_Intron|SMYD3_uc001ibj.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		gattataagtaatatagtttt	0.000													2	5	---	---	---	---	
OR2G2	81470	broad.mit.edu	37	1	247751925	247751926	+	Frame_Shift_Ins	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247751925_247751926insT	uc010pyy.1	+	1	264_265	c.264_265insT	c.(262-267)CTGTGGfs	p.L88fs		NM_001001915	NP_001001915	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G,	88_89	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TGGTAAACCTGTGGGAACCCAT	0.515													50	50	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	248577086	248577086	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248577086delA								OR2T1 (6682 upstream) : OR2T2 (39013 downstream)																							aagacagattataaataacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	248596633	248596634	+	IGR	INS	-	G	G	rs143082377	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248596633_248596634insG								OR2T1 (26229 upstream) : OR2T2 (19465 downstream)																							cactggcgtttgggacctttgc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	29006	29007	+	IGR	INS	-	GTTC	GTTC	rs142283068	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29006_29007insGTTC								None (None upstream) : FAM110C (12602 downstream)																							tggggtggcatTGAGGGCCCTC	0.292													1	6	---	---	---	---	
TPO	7173	broad.mit.edu	37	2	1535704	1535706	+	Intron	DEL	CCT	-	-	rs113202068		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1535704_1535706delCCT	uc002qww.2	+						TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Intron|TPO_uc002qwr.2_Intron|TPO_uc002qwx.2_Intron|TPO_uc010yio.1_Intron|TPO_uc010yip.1_Intron|TPO_uc002qwy.1_Intron|TPO_uc002qwz.2_Intron	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a						cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CTGTGTGCAACCTCCTCAAATCC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2910768	2910769	+	Intron	INS	-	T	T	rs142585959	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2910768_2910769insT	uc002qxh.1	-											Homo sapiens cDNA FLJ37991 fis, clone CTONG2011765.																		tccaccccctctcccCAGCCCA	0.050													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	9296378	9296378	+	IGR	DEL	A	-	-	rs112176637		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9296378delA								MBOAT2 (152502 upstream) : ASAP2 (50516 downstream)																							TATGCATAGCAAAAAAAAAAA	0.373													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10385206	10385207	+	IGR	INS	-	A	A	rs147814235	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10385206_10385207insA								C2orf48 (33350 upstream) : HPCAL1 (57833 downstream)																							gtggatgggggatggggacagg	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10676477	10676477	+	IGR	DEL	G	-	-	rs70948901		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10676477delG								ODC1 (88024 upstream) : NOL10 (34417 downstream)																							GGGGTGTTTCGGGGGATCCTG	0.547													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	11148720	11148720	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11148720delA								KCNF1 (94370 upstream) : C2orf50 (124459 downstream)																							gtgccgcaataaacatatgtg	0.214													6	3	---	---	---	---	
ROCK2	9475	broad.mit.edu	37	2	11362626	11362626	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11362626delA	uc002rbd.1	-							NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		CAATAACTTCAGGATATAAAC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12969635	12969635	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12969635delT								TRIB2 (86779 upstream) : None (None downstream)																							gtctttcttcttatgttcacc	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19470871	19470871	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19470871delT								NT5C1B (700033 upstream) : OSR1 (80376 downstream)																							CACTTTATAAttttttttttg	0.169													4	2	---	---	---	---	
GPR113	165082	broad.mit.edu	37	2	26535147	26535148	+	Intron	INS	-	T	T	rs72540404		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26535147_26535148insT	uc002rhe.3	-						GPR113_uc010yky.1_Intron|GPR113_uc002rhb.1_Intron|GPR113_uc010eyk.1_Intron|GPR113_uc002rhc.1_Intron|GPR113_uc002rhd.1_Intron	NM_001145168	NP_001138640	Q8IZF5	GP113_HUMAN	G-protein coupled receptor 113 isoform 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACCACCTGGGGCATCTTCAAG	0.574													4	2	---	---	---	---	
PREB	10113	broad.mit.edu	37	2	27358006	27358007	+	5'Flank	INS	-	A	A	rs144236213		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27358006_27358007insA	uc002rix.1	-						PREB_uc002riy.1_5'Flank|PREB_uc002riz.1_5'Flank|PREB_uc002rja.1_5'Flank	NM_013388	NP_037520	Q9HCU5	PREB_HUMAN	prolactin regulatory element binding protein						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|nucleus	DNA binding|guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					aactccgtctcaaaaaaaaaaa	0.015													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	27943044	27943045	+	IGR	INS	-	GT	GT	rs150064702	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27943044_27943045insGT								SLC4A1AP (25198 upstream) : MRPL33 (51539 downstream)																							CTGGTCTGTAGgtgtgtgtgtg	0.411													4	2	---	---	---	---	
TRMT61B	55006	broad.mit.edu	37	2	29082447	29082447	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29082447delC	uc002rmm.2	-						TRMT61B_uc002rmn.2_Intron|TRMT61B_uc010ezk.2_Intron	NM_017910	NP_060380	Q9BVS5	TR61B_HUMAN	tRNA methyltransferase 61 homolog B								tRNA (adenine-N1-)-methyltransferase activity				0						ATATAACTCTCCCCCAGCAGC	0.348													4	2	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29592200	29592201	+	Intron	INS	-	TGTGTA	TGTGTA	rs7602265	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29592200_29592201insTGTGTA	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	gtgtgtgtgtgtTGGTCTCCTA	0.238			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	30434016	30434016	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30434016delA								YPEL5 (50618 upstream) : LBH (20381 downstream)																							actccgtgtcaaaaaaaaaaa	0.045													4	2	---	---	---	---	
CAPN13	92291	broad.mit.edu	37	2	30982959	30982959	+	Intron	DEL	T	-	-	rs67222095		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30982959delT	uc002rnn.2	-						CAPN13_uc002rnp.1_Intron	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					ATTGTTGTGAttttttttgag	0.269													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38124931	38124931	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38124931delA								CDC42EP3 (225605 upstream) : FAM82A1 (27531 downstream)																							TTTGCCATATAAGGAAATTTG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38143524	38143524	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38143524delT								CDC42EP3 (244198 upstream) : FAM82A1 (8938 downstream)																							TTAAAACTTCTTTTTTTTTTG	0.299													4	2	---	---	---	---	
DHX57	90957	broad.mit.edu	37	2	39093226	39093226	+	Intron	DEL	G	-	-	rs71402256		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39093226delG	uc002rrf.2	-						DHX57_uc002rre.2_Intron|DHX57_uc002rrg.2_Intron	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				actgtccaaaggaaggagcac	0.075													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	39130558	39130559	+	IGR	INS	-	T	T	rs71402262		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39130558_39130559insT								MORN2 (20710 upstream) : ARHGEF33 (16030 downstream)																							AAAGGGATGGATTTTTTTTTTT	0.376													4	2	---	---	---	---	
TTC7A	57217	broad.mit.edu	37	2	47199061	47199062	+	Intron	INS	-	A	A	rs5830930		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47199061_47199062insA	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron	NM_020458	NP_065191	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			CTGCAAGTGACAAAAAAAAAAA	0.252													4	2	---	---	---	---	
EPCAM	4072	broad.mit.edu	37	2	47572147	47572147	+	5'Flank	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47572147delA	uc002rvw.2	+						uc002rvu.1_5'Flank	NM_002354	NP_002345	P16422	EPCAM_HUMAN	epithelial cell adhesion molecule precursor						positive regulation of cell proliferation	apical plasma membrane|basolateral plasma membrane|integral to membrane|lateral plasma membrane|tight junction	protein binding	p.?(1)		skin(1)	1						AAAGGAAATGAAAAAAAAAAA	0.498									Lynch_syndrome				7	4	---	---	---	---	
MSH2	4436	broad.mit.edu	37	2	47858707	47858707	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47858707delG	uc002rvz.2	+							NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ggtcagatgaggggggtggat	0.234			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				4	2	---	---	---	---	
KLRAQ1	129285	broad.mit.edu	37	2	48728949	48728949	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48728949delA	uc002rwm.2	+						KLRAQ1_uc002rwl.2_Intron|KLRAQ1_uc002rwk.2_Intron|KLRAQ1_uc010yok.1_Intron	NM_001135629	NP_001129101	Q6ZMI0	KLRAQ_HUMAN	KLRAQ motif containing 1 isoform 1											ovary(1)	1						ccttgactctaaaaaaaaaaa	0.139													3	3	---	---	---	---	
LHCGR	3973	broad.mit.edu	37	2	48936273	48936273	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48936273delG	uc002rwu.3	-						GTF2A1L_uc002rwt.2_Intron|LHCGR_uc002rwv.2_Intron	NM_000233	NP_000224	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor						male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|lung(2)|breast(2)|skin(1)	8		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	AGGGTTAAAAGGGGGAAAAAG	0.398									Familial_Male-Limited_Precocious_Puberty				3	9	---	---	---	---	
ACYP2	98	broad.mit.edu	37	2	54521892	54521893	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54521892_54521893insA	uc002rxq.3	+							NM_138448	NP_612457	P14621	ACYP2_HUMAN	acylphosphatase 2						phosphate metabolic process		acylphosphatase activity				0						tacaaaaaattaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SPTBN1	6711	broad.mit.edu	37	2	54779701	54779703	+	Intron	DEL	CTC	-	-	rs150663001		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54779701_54779703delCTC	uc002rxu.2	+						SPTBN1_uc002rxv.1_Intron	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)			tcaagcgattctcctgcctcagc	0.000													4	2	---	---	---	---	
PEX13	5194	broad.mit.edu	37	2	61250538	61250539	+	Intron	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61250538_61250539delAC	uc002sau.3	+							NM_002618	NP_002609	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13						cerebral cortex cell migration|fatty acid alpha-oxidation|locomotory behavior|microtubule-based peroxisome localization|neuron migration|protein import into peroxisome matrix, docking|suckling behavior	integral to peroxisomal membrane|membrane fraction	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			GAATATacagacacacacacac	0.178													4	4	---	---	---	---	
FAM161A	84140	broad.mit.edu	37	2	62070274	62070277	+	Intron	DEL	TTTG	-	-	rs67150109		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62070274_62070277delTTTG	uc010ypo.1	-						FAM161A_uc002sbm.3_Intron|FAM161A_uc002sbn.3_Intron|FAM161A_uc010fcm.1_Intron|FAM161A_uc010fcn.1_Intron	NM_032180	NP_115556	Q3B820	F161A_HUMAN	hypothetical protein LOC84140						response to stimulus|visual perception	centrosome				large_intestine(2)|ovary(1)	3						TTTCAgtttttttgtttgtttgtt	0.181													3	5	---	---	---	---	
COMMD1	150684	broad.mit.edu	37	2	62348874	62348874	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62348874delA	uc002sbp.2	+						uc002sbr.2_Intron	NM_152516	NP_689729	Q8N668	COMD1_HUMAN	MURR1						copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			actccgtctcaaaaaaaaaaa	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62562587	62562587	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62562587delT								B3GNT2 (110723 upstream) : TMEM17 (164769 downstream)																							AGTTGGtttcttttttttttt	0.284													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62887237	62887238	+	Intron	INS	-	TACTGT	TACTGT	rs59896743		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62887237_62887238insTACTGT	uc002sbw.1	-											Homo sapiens cDNA clone IMAGE:5271366.																		gctgctgctgctgctcctgctg	0.079													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66362335	66362335	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66362335delC								SPRED2 (702679 upstream) : MEIS1 (300197 downstream)																							TCTGGTGAAACCAGAGTCATA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66411405	66411406	+	IGR	INS	-	A	A	rs138103994	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66411405_66411406insA								SPRED2 (751749 upstream) : MEIS1 (251126 downstream)																							GAATCAGAGATAAAAGGGACCA	0.406													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66568596	66568596	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66568596delA								SPRED2 (908940 upstream) : MEIS1 (93936 downstream)																							TTCTATGAGCAAAAAAAAAAA	0.224													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67698665	67698666	+	IGR	INS	-	G	G	rs150454445	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67698665_67698666insG								ETAA1 (61132 upstream) : C1D (570667 downstream)																							cttcTTGTTTTTTTTTCCCCCT	0.262													2	4	---	---	---	---	
CNRIP1	25927	broad.mit.edu	37	2	68518426	68518427	+	Intron	INS	-	T	T	rs145243940	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68518426_68518427insT	uc002sej.3	-							NM_001111101	NP_001104571	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1								protein binding			liver(1)	1						ACACTTTCCCCTTTTTTTTTTA	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	70326558	70326558	+	IGR	DEL	T	-	-	rs112543834		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70326558delT								PCBP1 (10226 upstream) : LOC100133985 (24611 downstream)																							acctggccacttttttttttt	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	70367544	70367545	+	IGR	INS	-	T	T	rs113151345		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70367544_70367545insT								LOC100133985 (15096 upstream) : C2orf42 (9474 downstream)																							CAGGCAAGttgttttttttttt	0.168													4	2	---	---	---	---	
ZNF638	27332	broad.mit.edu	37	2	71540661	71540662	+	Intron	INS	-	TT	TT			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71540661_71540662insTT	uc010yqw.1	+						ZNF638_uc010fec.2_Intron	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638						RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4						tctcttctctcctctcctctcc	0.005													4	2	---	---	---	---	
EXOC6B	23233	broad.mit.edu	37	2	72464175	72464175	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72464175delA	uc010fep.2	-							NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						AGACTTGGGGAAAAAAAAAGG	0.363													4	2	---	---	---	---	
DGUOK	1716	broad.mit.edu	37	2	74160736	74160736	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74160736delT	uc002sjx.2	+						DGUOK_uc002sjy.2_Intron|DGUOK_uc002sjz.2_Intron	NM_080916	NP_550438	Q16854	DGUOK_HUMAN	deoxyguanosine kinase isoform a precursor						guanosine metabolic process|purine base metabolic process|purine deoxyribonucleoside metabolic process|purine-containing compound salvage	mitochondrial matrix	ATP binding|deoxyguanosine kinase activity|phosphotransferase activity, alcohol group as acceptor				0						ATTTTTTGCCTTTTTTTTTTC	0.368													4	2	---	---	---	---	
TET3	200424	broad.mit.edu	37	2	74292683	74292683	+	Intron	DEL	T	-	-	rs67114907		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74292683delT	uc002skb.3	+						TET3_uc010fez.1_Intron	NM_144993	NP_659430	O43151	TET3_HUMAN	tet oncogene family member 3								metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						cttttTTTTGTTTTTTTTTTT	0.050													3	3	---	---	---	---	
LRRTM4	80059	broad.mit.edu	37	2	77226576	77226576	+	Intron	DEL	A	-	-	rs112152010		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77226576delA	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		GAAACAAAACAAAAAAAAAAA	0.378													4	2	---	---	---	---	
LRRTM4	80059	broad.mit.edu	37	2	77687189	77687190	+	Intron	INS	-	T	T	rs143605014	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77687189_77687190insT	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		AGAATTCCATGCTGCATTCACC	0.347													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	78881033	78881034	+	IGR	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78881033_78881034delAC								SNAR-H (698881 upstream) : REG3G (371792 downstream)																							agacagacagacacacacacac	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	79002378	79002379	+	IGR	INS	-	A	A	rs71385234		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79002378_79002379insA								SNAR-H (820226 upstream) : REG3G (250447 downstream)																							TGGGAAAAAGGAAAAAAAAAAA	0.327													3	3	---	---	---	---	
KCMF1	56888	broad.mit.edu	37	2	85208315	85208315	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85208315delT	uc002sox.3	+							NM_020122	NP_064507	Q9P0J7	KCMF1_HUMAN	potassium channel modulatory factor 1							intracellular	ligase activity|zinc ion binding			ovary(2)	2						TTCTGTTGAAttttttttttt	0.109													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85701191	85701192	+	IGR	INS	-	AC	AC	rs148093783		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85701191_85701192insAC								SH2D6 (37041 upstream) : MAT2A (65096 downstream)																							AGCACATCTATacacacacaca	0.361													6	5	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87633666	87633666	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87633666delA	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						caagccagccaagccagccaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90417220	90417224	+	Intron	DEL	ATGAA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90417220_90417224delATGAA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		aaatgaaatgatgaaatgaaatggt	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90475133	90475134	+	IGR	DEL	TC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90475133_90475134delTC								None (None upstream) : None (None downstream)																							ccttcttttttctctttctttc	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90479314	90479315	+	IGR	DEL	TT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90479314_90479315delTT								None (None upstream) : None (None downstream)																							acccagctaatttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91658464	91658464	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91658464delT								None (None upstream) : LOC654342 (146728 downstream)																							cctttattccttggaacatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91683264	91683265	+	IGR	INS	-	A	A	rs143557730		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91683264_91683265insA								None (None upstream) : LOC654342 (121927 downstream)																							ccaatatggtgaaaccctgtct	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91738192	91738194	+	IGR	DEL	TCA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91738192_91738194delTCA								None (None upstream) : LOC654342 (66998 downstream)																							tcatttcatctcatcatttttca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96311188	96311189	+	IGR	INS	-	TG	TG	rs62155100		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96311188_96311189insTG								TRIM43 (45721 upstream) : LOC729234 (365110 downstream)																							gcatgtttgtatgtgtgtgtgt	0.015													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96730750	96730751	+	IGR	INS	-	CATC	CATC	rs147426996	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96730750_96730751insCATC								GPAT2 (29028 upstream) : ADRA2B (47875 downstream)																							atccatccattcatccatccat	0.000													13	7	---	---	---	---	
FER1L5	90342	broad.mit.edu	37	2	97370172	97370173	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97370172_97370173insA	uc010fia.2	+						FER1L5_uc002sws.3_Intron|FER1L5_uc002swt.3_Intron|FER1L5_uc010yus.1_Intron	NM_001113382	NP_001106853	A0AVI2	FR1L5_HUMAN	fer-1-like 5 isoform 2							integral to membrane				ovary(1)	1						TTCAGCTTGCCACCCCAGGCTA	0.495													74	101	---	---	---	---	
TSGA10	80705	broad.mit.edu	37	2	99744172	99744173	+	Intron	INS	-	AAC	AAC	rs139925710	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99744172_99744173insAAC	uc002szh.3	-						TSGA10_uc002szi.3_Intron|TSGA10_uc010fin.1_Intron|TSGA10_uc010yvn.1_Intron|TSGA10_uc002szj.1_Intron	NM_182911	NP_878915	Q9BZW7	TSG10_HUMAN	testis specific, 10						spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2						acacaaattaaaacactgagat	0.000													3	5	---	---	---	---	
MRPL30	51263	broad.mit.edu	37	2	99799633	99799634	+	Intron	INS	-	G	G	rs141137700	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99799633_99799634insG	uc002szu.2	+						MRPL30_uc002szl.1_Intron|MRPL30_uc002szr.2_Intron|MITD1_uc002szs.1_5'Flank|MRPL30_uc002szt.1_Intron|MRPL30_uc002szv.2_Intron	NM_145213	NP_660214	Q8TCC3	RM30_HUMAN	RecName: Full=39S ribosomal protein L30, mitochondrial;          Short=L30mt; AltName: Full=MRP-L30; AltName: Full=MRP-L28; Flags: Precursor;						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1						agatcaaacaaggggggcagca	0.000													4	2	---	---	---	---	
MRPL30	51263	broad.mit.edu	37	2	99853144	99853144	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99853144delA	uc002szl.1	+							NM_145213		Q8TCC3	RM30_HUMAN	Homo sapiens HSPC249 mRNA, complete cds.						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1						ataaaagttgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	100815095	100815095	+	IGR	DEL	T	-	-	rs71886887		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100815095delT								AFF3 (56058 upstream) : LONRF2 (74659 downstream)																							CCTCACCCCCTCCTCAAGAGG	0.612													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	100856654	100856654	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100856654delA	uc002taj.1	+											Homo sapiens cDNA FLJ32078 fis, clone OCBBF1000192.																		AATATTGTATAATAAATACTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	100885132	100885132	+	IGR	DEL	C	-	-	rs75522322		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100885132delC								AFF3 (126095 upstream) : LONRF2 (4622 downstream)																							atctccccttccccccagtgt	0.000													6	3	---	---	---	---	
PDCL3	79031	broad.mit.edu	37	2	101190127	101190128	+	Intron	INS	-	T	T	rs151130844	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101190127_101190128insT	uc002tao.2	+							NM_024065	NP_076970	Q9H2J4	PDCL3_HUMAN	phosducin-like 3						apoptosis|interspecies interaction between organisms	cytoplasm	protein binding				0						gagcgaaactctatctcaaaaa	0.119													4	2	---	---	---	---	
TBC1D8	11138	broad.mit.edu	37	2	101746998	101746998	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101746998delA	uc010fiv.2	-						TBC1D8_uc010yvw.1_Intron	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3						CAAAGGCCCTAACCCCCTTGA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102160218	102160218	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102160218delT								RFX8 (69053 upstream) : MAP4K4 (154270 downstream)																							taagcactcctttagctgaat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102289638	102289638	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102289638delT								RFX8 (198473 upstream) : MAP4K4 (24850 downstream)																							ctttttaaggttttttttttt	0.030													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103732330	103732331	+	IGR	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103732330_103732331delAC								TMEM182 (298194 upstream) : None (None downstream)																							TTGAATacaaacacacacacac	0.302													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105839937	105839938	+	IGR	INS	-	T	T	rs139028025	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105839937_105839938insT								MRPS9 (123520 upstream) : GPR45 (18262 downstream)																							GTCTTGTTGTGTTTTTTTTGTT	0.376													4	5	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109785806	109785807	+	Intron	INS	-	A	A	rs146590198	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109785806_109785807insA	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						CTGAGCCCACCAAGTTTCAGGA	0.455													9	5	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109907737	109907737	+	Intron	DEL	T	-	-	rs113796944		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109907737delT	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						GAGTAATCTCTTTTTTTTTTT	0.393													4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109951241	109951242	+	Intron	DEL	TT	-	-	rs10602685		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109951241_109951242delTT	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						CCTGCCTCTGTTTTTCTCTCTC	0.485													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122631845	122631845	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122631845delT								TSN (106419 upstream) : None (None downstream)																							GAATAGAAGATTTTTTTTTTT	0.289													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	125851177	125851178	+	IGR	INS	-	C	C	rs147876054	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125851177_125851178insC								CNTNAP5 (178316 upstream) : None (None downstream)																							CTCCATAACAACACCACTTTCA	0.391													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126288710	126288710	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126288710delT								CNTNAP5 (615849 upstream) : None (None downstream)																							TATTTGTCTCTTTTTTTTTTT	0.239													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130676092	130676095	+	IGR	DEL	AGGA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130676092_130676095delAGGA								None (None upstream) : LOC389033 (4340 downstream)																							aagagaaaagaggaaggaaggaag	0.020													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131427272	131427272	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131427272delC								LOC150527 (119801 upstream) : C2orf14 (10351 downstream)																							CTGGCATGCACAGGCCCCAGG	0.577													4	2	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	132974712	132974712	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132974712delG	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						tctttgtgatgtcagcattcc	0.000													5	3	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	132982828	132982828	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132982828delT	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						tttgaaacactttttttgtag	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133028237	133028238	+	IGR	INS	-	CAGG	CAGG	rs144924161		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133028237_133028238insCAGG								NCRNA00164 (12695 upstream) : GPR39 (145909 downstream)																							aaagggagggacagagaaagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133037217	133037217	+	IGR	DEL	G	-	-	rs112154397		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133037217delG								NCRNA00164 (21675 upstream) : GPR39 (136930 downstream)																							cacggggataggggggcactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133046453	133046454	+	IGR	INS	-	GACA	GACA	rs146739177		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133046453_133046454insGACA								NCRNA00164 (30911 upstream) : GPR39 (127693 downstream)																							CAAACCAATGTGACAGACAGAG	0.386													4	4	---	---	---	---	
TMEM163	81615	broad.mit.edu	37	2	135231107	135231107	+	Intron	DEL	A	-	-	rs78560345		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135231107delA	uc002ttx.2	-						TMEM163_uc002tty.2_Intron	NM_030923	NP_112185	Q8TC26	TM163_HUMAN	transmembrane protein 163							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)		actctgtctcaaaaaaaaaaa	0.000													3	4	---	---	---	---	
ZRANB3	84083	broad.mit.edu	37	2	136033114	136033114	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136033114delA	uc002tum.2	-						ZRANB3_uc002tuk.2_Intron|ZRANB3_uc002tul.2_Intron|ZRANB3_uc002tun.1_Intron	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3							intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)		TAAAGAAGACAAAAAACACCT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	140051269	140051270	+	IGR	INS	-	AC	AC	rs151159017	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140051269_140051270insAC								NXPH2 (513458 upstream) : LRP1B (937726 downstream)																							GGAATCTAGGGacacacacaca	0.297													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	140251056	140251057	+	IGR	DEL	AG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140251056_140251057delAG								NXPH2 (713245 upstream) : LRP1B (737939 downstream)																							agatagaggtagagagagagag	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	140829856	140829857	+	IGR	INS	-	CT	CT	rs143099725	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140829856_140829857insCT								None (None upstream) : LRP1B (159139 downstream)																							TCTGTCTGCCCCTCTCTCCTAT	0.455													0	8	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142231614	142231614	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142231614delT	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ccttccttcctttccttcctt	0.075										TSP Lung(27;0.18)			7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	143602073	143602073	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143602073delA								LRP1B (712803 upstream) : KYNU (33122 downstream)																							CTGACAGGCTAAAGTAAATTT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146137945	146137945	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146137945delA								ZEB2 (860014 upstream) : None (None downstream)																							TGGGGAGTTTAAAAAAAAAAA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151357091	151357092	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151357091_151357092insT								RND3 (12911 upstream) : RBM43 (747637 downstream)																							ccaatactgtattttttttttt	0.000													4	2	---	---	---	---	
RIF1	55183	broad.mit.edu	37	2	152278352	152278352	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152278352delT	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc010fnv.1_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_Intron|RIF1_uc010zby.1_Intron	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)		ACATATATAAttttttttttt	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	159695548	159695548	+	IGR	DEL	C	-	-	rs66490023		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159695548delC								DAPL1 (23054 upstream) : TANC1 (129598 downstream)																							caggagagagccccccgacac	0.134													2	4	---	---	---	---	
LY75	4065	broad.mit.edu	37	2	160642188	160642189	+	Intron	INS	-	A	A	rs140068875	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160642188_160642189insA	uc002ubb.3	-						LY75_uc010fos.2_Intron|CD302_uc002uba.2_Intron|CD302_uc010zco.1_Intron	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		CACCTTCTTTGAAAATCTGGCC	0.262													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	161883727	161883727	+	IGR	DEL	A	-	-	rs10754967	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161883727delA								RBMS1 (533409 upstream) : TANK (109739 downstream)																							aaagccccccatttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181421783	181421783	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181421783delA								CWC22 (549943 upstream) : UBE2E3 (423329 downstream)																							aaaatgaaggaaaaaaaaaat	0.000													4	2	---	---	---	---	
UBE2E3	10477	broad.mit.edu	37	2	181883326	181883330	+	Intron	DEL	TTTTT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181883326_181883330delTTTTT	uc002unq.1	+						UBE2E3_uc002unr.1_Intron|UBE2E3_uc010fri.1_Intron	NM_182678	NP_872619	Q969T4	UB2E3_HUMAN	ubiquitin-conjugating enzyme E2E 3						protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|regulation of growth	cytoplasm|nucleolus	ATP binding|protein binding|ubiquitin-protein ligase activity			ovary(1)	1						AATTTCTGTGTTTTTTTTTTTTTTT	0.385													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	189483731	189483731	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189483731delT								GULP1 (23081 upstream) : DIRC1 (114734 downstream)																							tgtttttgtgtttttttttaa	0.000													1	6	---	---	---	---	
ANKAR	150709	broad.mit.edu	37	2	190541843	190541843	+	Intron	DEL	T	-	-	rs67184798		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190541843delT	uc002uqw.1	+						ANKAR_uc002uqu.2_Intron|ANKAR_uc002uqv.1_Intron	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing							integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			ACTTCTTAAATtttttttttt	0.169													8	5	---	---	---	---	
GTF3C3	9330	broad.mit.edu	37	2	197666397	197666397	+	5'Flank	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197666397delT	uc002uts.2	-						GTF3C3_uc010zgu.1_5'Flank|GTF3C3_uc002utu.2_5'Flank	NM_012086	NP_036218	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide							transcription factor TFIIIC complex	DNA binding|protein binding			ovary(3)|breast(3)|pancreas(1)	7						TGGTTTTTTGTTTTTTTTTGG	0.348													4	2	---	---	---	---	
MPP4	58538	broad.mit.edu	37	2	202546544	202546544	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202546544delC	uc002uyk.3	-						MPP4_uc010ftj.2_Intron|MPP4_uc010zhq.1_Intron|MPP4_uc010zhr.1_Intron|MPP4_uc010zhs.1_Intron|MPP4_uc002uyj.3_Intron|MPP4_uc010zht.1_Intron|MPP4_uc002uyl.3_Intron|MPP4_uc010ftk.2_Intron|MPP4_uc002uym.1_Intron|MPP4_uc002uyn.2_Intron	NM_033066	NP_149055	Q96JB8	MPP4_HUMAN	membrane protein, palmitoylated 4							cytoplasm	protein binding				0						CTTCCAGGGACCCCCCCCCAC	0.562													4	2	---	---	---	---	
ALS2	57679	broad.mit.edu	37	2	202637001	202637002	+	Intron	INS	-	AAC	AAC	rs143278825	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202637001_202637002insAAC	uc002uyo.2	-						ALS2_uc002uyp.3_Intron|ALS2_uc002uyq.2_Intron|ALS2_uc002uyr.2_Intron	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1						cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						gaagtgcccttaacaacaacaa	0.035													6	4	---	---	---	---	
NBEAL1	65065	broad.mit.edu	37	2	203911961	203911962	+	Intron	INS	-	A	A	rs79054448		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203911961_203911962insA	uc002uzt.3	+						NBEAL1_uc002uzq.3_Intron|NBEAL1_uc010zid.1_Intron|NBEAL1_uc010zie.1_Intron	NM_001114132	NP_001107604	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1 isoform 3								binding			ovary(1)|skin(1)	2						aactccatctcaaaaaaaaaaa	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	204906988	204906988	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204906988delC								ICOS (80692 upstream) : PARD3B (503528 downstream)																							ttggggagggcgggggggcaa	0.000													0	6	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	206428375	206428376	+	Intron	INS	-	A	A	rs138577270		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206428375_206428376insA	uc002var.1	+						PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		CTACGGGTTGTAAAAAAAAAAA	0.297													4	2	---	---	---	---	
ABCA12	26154	broad.mit.edu	37	2	215823928	215823928	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215823928delT	uc002vew.2	-						ABCA12_uc002vev.2_Intron|ABCA12_uc010zjn.1_Intron	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12						cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TTGGGGGACCTTTTTTTTTTA	0.284													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	218656665	218656665	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218656665delA								DIRC3 (35349 upstream) : TNS1 (7847 downstream)																							AGACAAAAACAAATGGCCACA	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	219243401	219243402	+	IGR	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219243401_219243402insA								C2orf62 (10585 upstream) : SLC11A1 (3350 downstream)																							gactctgtctcaaaaaaaaaaT	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	225988203	225988204	+	IGR	INS	-	T	T	rs149086129	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225988203_225988204insT								DOCK10 (80873 upstream) : KIAA1486 (277398 downstream)																							cttttcctcagtttttttcctc	0.030													2	8	---	---	---	---	
KIAA1486	57624	broad.mit.edu	37	2	226436922	226436922	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226436922delC	uc002voe.2	+						KIAA1486_uc010fxa.1_Intron	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624											ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)		ccaaactgttccaacctctgc	0.000													4	2	---	---	---	---	
DNER	92737	broad.mit.edu	37	2	230506672	230506672	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230506672delG	uc002vpv.2	-							NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		TATAACATTAGGGTGTCAGGA	0.433													4	2	---	---	---	---	
SPATA3	130560	broad.mit.edu	37	2	231869849	231869851	+	Intron	DEL	CAC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231869849_231869851delCAC	uc010zmd.1	+						SPATA3_uc002vri.3_Intron|SPATA3_uc002vrk.2_Intron	NM_139073	NP_620712	Q8NHX4	SPTA3_HUMAN	testis and spermatogenesis cell apoptosis						apoptosis|spermatogenesis						0						ccatcatcatcaccaccaccacc	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	233207636	233207636	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233207636delG								DIS3L2 (5729 upstream) : ALPP (35712 downstream)																							AGCCCTTGCTGGGCACAGATC	0.592													4	2	---	---	---	---	
RAMP1	10267	broad.mit.edu	37	2	238816195	238816196	+	Intron	INS	-	AT	AT	rs143970299	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238816195_238816196insAT	uc002vxj.2	+							NM_005855	NP_005846	O60894	RAMP1_HUMAN	receptor activity-modifying protein 1 precursor						intracellular protein transport|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane	protein transporter activity				0		Breast(86;0.000596)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;9.56e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.49e-11)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.49e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00013)|Lung(119;0.0119)|LUSC - Lung squamous cell carcinoma(224;0.0288)	Pramlintide(DB01278)	tttctactgacatcttcaattt	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239377775	239377775	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239377775delT								ASB1 (16885 upstream) : TWIST2 (378898 downstream)																							tcagtctgtattttttttctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	1032547	1032550	+	IGR	DEL	TGGA	-	-	rs67893316		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1032547_1032550delTGGA								CHL1 (581452 upstream) : CNTN6 (102070 downstream)																							gatggatggttggatggatggatg	0.000													2	4	---	---	---	---	
LOH3CR2A	29931	broad.mit.edu	37	3	8612637	8612637	+	5'Flank	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8612637delC	uc010hci.2	+							NR_024065				Homo sapiens NAG-7 protein (NAG-7) mRNA, complete cds.												0						GCCTGCAATTCCCCACACTGT	0.488													4	2	---	---	---	---	
ATP2B2	491	broad.mit.edu	37	3	10752533	10752534	+	5'Flank	DEL	GT	-	-	rs139716916		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10752533_10752534delGT	uc003bvw.2	-							NM_001683	NP_001674	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 2						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6						gtgtgtgtgcgtgtgtgtgtgt	0.267													4	3	---	---	---	---	
MRPS25	64432	broad.mit.edu	37	3	15099205	15099205	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15099205delT	uc003bzl.2	-						MRPS25_uc011avl.1_Intron|MRPS25_uc011avm.1_Intron	NM_022497	NP_071942	P82663	RT25_HUMAN	mitochondrial ribosomal protein S25						translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome				0						tacgtaagtgtacaGGTATAT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	28673033	28673033	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28673033delA								ZCWPW2 (106403 upstream) : RBMS3 (649910 downstream)																							TGTTAAAAGCAAAAAGGCCTA	0.493													4	2	---	---	---	---	
CMTM8	152189	broad.mit.edu	37	3	32314622	32314625	+	Intron	DEL	TGTG	-	-	rs72236328		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32314622_32314625delTGTG	uc003cex.2	+						CMTM8_uc010hfu.2_Intron	NM_178868	NP_849199	Q8IZV2	CKLF8_HUMAN	CKLF-like MARVEL transmembrane domain containing						chemotaxis	extracellular space|integral to membrane	cytokine activity				0						ttggaacaaatgtgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	35644539	35644540	+	IGR	DEL	TG	-	-	rs113443536		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35644539_35644540delTG								None (None upstream) : ARPP21 (36541 downstream)																							AGATGAAAAAtgtgtgtgtgtg	0.262													4	2	---	---	---	---	
SLC25A38	54977	broad.mit.edu	37	3	39430727	39430727	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39430727delT	uc003cjo.2	+							NM_017875	NP_060345	Q96DW6	S2538_HUMAN	solute carrier family 25, member 38						erythrocyte differentiation|heme biosynthetic process|transport	integral to membrane|mitochondrial inner membrane					0				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		ATGGAAATAGTTTTGCTCCCA	0.393													4	2	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54744030	54744030	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54744030delT	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		AAGTCTTTTGTTTTCACACAC	0.279													4	2	---	---	---	---	
ARF4	378	broad.mit.edu	37	3	57586077	57586080	+	5'Flank	DEL	TTTC	-	-	rs112082137		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57586077_57586080delTTTC	uc003dix.3	-						ARF4_uc003diy.3_5'Flank|ARF4_uc010hnd.2_5'Flank|ARF4_uc003diz.3_5'Flank	NM_001660	NP_001651	P18085	ARF4_HUMAN	ADP-ribosylation factor 4						protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	Golgi apparatus	GTP binding|GTPase activity			upper_aerodigestive_tract(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0449)|Kidney(284;0.0561)		ctcttttctttttctttctttcct	0.000													0	6	---	---	---	---	
CADM2	253559	broad.mit.edu	37	3	86109374	86109375	+	Intron	INS	-	A	A	rs149153880	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86109374_86109375insA	uc003dqj.2	+						CADM2_uc003dqk.2_Intron|CADM2_uc003dql.2_Intron	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		GTTTTAATGTCAAAAAAAAAAG	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	86197561	86197561	+	IGR	DEL	A	-	-	rs142393073		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86197561delA								CADM2 (79613 upstream) : VGLL3 (789564 downstream)																							acacatggacaaaaaaaaaaa	0.000													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	86393754	86393755	+	IGR	DEL	TT	-	-	rs113598819		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86393754_86393755delTT								CADM2 (275806 upstream) : VGLL3 (593370 downstream)																							gccctgctaatttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	86487290	86487290	+	IGR	DEL	T	-	-	rs71617991		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86487290delT								CADM2 (369342 upstream) : VGLL3 (499835 downstream)																							tctttgtctgttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	86792691	86792691	+	IGR	DEL	T	-	-	rs113926145		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86792691delT								CADM2 (674743 upstream) : VGLL3 (194434 downstream)																							agtttctggattttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	87543796	87543799	+	IGR	DEL	GAAG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87543796_87543799delGAAG								POU1F1 (218059 upstream) : HTR1F (487927 downstream)																							gaaggagagagaaggaaggaagga	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	87545211	87545212	+	IGR	INS	-	T	T	rs140873826	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87545211_87545212insT								POU1F1 (219474 upstream) : HTR1F (486514 downstream)																							caacgcccaccttttttctttg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90499140	90499141	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90499140_90499141insT								EPHA3 (967858 upstream) : None (None downstream)																							cctcagagctgccaaatatcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	94347033	94347036	+	IGR	DEL	CTTC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94347033_94347036delCTTC								NSUN3 (501403 upstream) : LOC255025 (310071 downstream)																							tcccttccttcttccttccttcct	0.000													3	7	---	---	---	---	
EPHA6	285220	broad.mit.edu	37	3	96725371	96725372	+	Intron	INS	-	T	T	rs141081001	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96725371_96725372insT	uc010how.1	+						EPHA6_uc003drp.1_Intron	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						ctagcagtctatttttttttta	0.000													1	6	---	---	---	---	
EPHA6	285220	broad.mit.edu	37	3	96845742	96845742	+	Intron	DEL	A	-	-	rs68000143		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96845742delA	uc010how.1	+						EPHA6_uc003drp.1_Intron	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						GGAGAAGGTGAAAAAAAAAAA	0.284													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	104408450	104408451	+	IGR	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104408450_104408451insA								None (None upstream) : ALCAM (677262 downstream)																							gtgcccataagaaaaaaaaaaa	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112309292	112309293	+	IGR	INS	-	TG	TG	rs147314041	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112309292_112309293insTG								SLC35A5 (6290 upstream) : CCDC80 (14118 downstream)																							tttgttgagaatgtgtgtgtgt	0.064													2	4	---	---	---	---	
KIAA1407	57577	broad.mit.edu	37	3	113732668	113732668	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113732668delT	uc003eax.2	-						KIAA1407_uc011bin.1_Intron|KIAA1407_uc011bio.1_Intron|KIAA1407_uc011bip.1_Intron	NM_020817	NP_065868	Q8NCU4	K1407_HUMAN	hypothetical protein LOC57577											ovary(2)	2						GTTTTGGAACTTACAAGTCAG	0.219													4	2	---	---	---	---	
RABL3	285282	broad.mit.edu	37	3	120436131	120436131	+	Intron	DEL	A	-	-	rs11349554		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120436131delA	uc003edx.2	-							NM_173825	NP_776186	Q5HYI8	RABL3_HUMAN	RAB, member of RAS oncogene family-like 3						small GTPase mediated signal transduction		GTP binding				0				GBM - Glioblastoma multiforme(114;0.151)		aaaaaacaacaaaaaaaaaaa	0.164													3	3	---	---	---	---	
STXBP5L	9515	broad.mit.edu	37	3	120960224	120960231	+	Intron	DEL	ACACACAC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120960224_120960231delACACACAC	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		acacacacatacacacacacacacacac	0.000													3	3	---	---	---	---	
IQCB1	9657	broad.mit.edu	37	3	121499712	121499713	+	Intron	DEL	TG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121499712_121499713delTG	uc010hre.1	-						IQCB1_uc003eek.2_Intron|IQCB1_uc010hrf.1_Intron	NM_001023570	NP_001018864	Q15051	IQCB1_HUMAN	IQ motif containing B1 isoform a						cilium assembly|maintenance of organ identity|photoreceptor cell maintenance	centrosome|photoreceptor connecting cilium	calmodulin binding				0				GBM - Glioblastoma multiforme(114;0.0983)		tgtgtgtgtatgtgtgtgtgtg	0.312													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	123608541	123608541	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123608541delC								MYLK (5392 upstream) : CCDC14 (23735 downstream)																							ggtggatctaccattctgggg	0.000													4	2	---	---	---	---	
MUC13	56667	broad.mit.edu	37	3	124641091	124641092	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124641091_124641092delTC	uc003ehq.1	-	4	717_718	c.693_694delGA	c.(691-696)GAGAAAfs	p.E231fs		NM_033049	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, epithelial transmembrane	231_232	SEA.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane					0						ATGGAATGTTTCTCTTCTGGGT	0.361													22	55	---	---	---	---	
ZNF148	7707	broad.mit.edu	37	3	125076785	125076785	+	Intron	DEL	T	-	-	rs77538994		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125076785delT	uc003ehx.3	-						ZNF148_uc003ehz.3_Intron|ZNF148_uc010hsa.2_Intron|ZNF148_uc003eia.3_Intron|ZNF148_uc003ehy.2_Intron	NM_021964	NP_068799	Q9UQR1	ZN148_HUMAN	zinc finger protein 148						cellular defense response|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4						CTTGCCTTGCTTGTTTTATAT	0.328													0	8	---	---	---	---	
CHCHD6	84303	broad.mit.edu	37	3	126479678	126479678	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126479678delT	uc003ejf.1	+						CHCHD6_uc010hsj.1_Intron	NM_032343	NP_115719	Q9BRQ6	CHCH6_HUMAN	coiled-coil-helix-coiled-coil-helix domain												0						ctttcaattcttttttttttc	0.000													3	3	---	---	---	---	
TMCC1	23023	broad.mit.edu	37	3	129585951	129585951	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129585951delA	uc003emz.3	-						TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1						CCTATGAGTTAAAAAAAAAAA	0.368													3	3	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131436722	131436723	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131436722_131436723insT	uc003eok.2	-						CPNE4_uc011blq.1_Intron|CPNE4_uc003eol.2_Intron|CPNE4_uc003eom.2_Intron	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						tctttcttttctttctttcttt	0.035													6	3	---	---	---	---	
RAB6B	51560	broad.mit.edu	37	3	133554513	133554513	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133554513delA	uc003epy.2	-						RAB6B_uc011blu.1_Intron	NM_016577	NP_057661	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family						protein transport|retrograde vesicle-mediated transport, Golgi to ER|small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle|Golgi membrane	GTP binding|GTPase activity|protein binding			pancreas(1)	1						atgttgaaacagaatctccaa	0.134													4	2	---	---	---	---	
PPP2R3A	5523	broad.mit.edu	37	3	135766747	135766747	+	Intron	DEL	A	-	-	rs75344101		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135766747delA	uc003eqv.1	+						PPP2R3A_uc011blz.1_Intron|PPP2R3A_uc003eqw.1_Intron|PPP2R3A_uc011bma.1_Intron	NM_002718	NP_002709	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'',						protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(3)|pancreas(1)|lung(1)|breast(1)|skin(1)	7						actccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
IL20RB	53833	broad.mit.edu	37	3	136725528	136725528	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136725528delT	uc003eri.1	+						IL20RB_uc003erj.1_Intron|IL20RB_uc010hud.1_Intron	NM_144717	NP_653318	Q6UXL0	I20RB_HUMAN	interleukin 20 receptor beta precursor							integral to membrane	receptor activity			ovary(1)	1						tttttcaaggtttttagctta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137224814	137224815	+	IGR	INS	-	T	T	rs141465878	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137224814_137224815insT								IL20RB (494894 upstream) : SOX14 (258764 downstream)																							tgatatctttcttttttagttc	0.015													0	7	---	---	---	---	
RBP2	5948	broad.mit.edu	37	3	139180381	139180381	+	Intron	DEL	T	-	-	rs10709555		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139180381delT	uc003eth.2	-							NM_004164	NP_004155	P50120	RET2_HUMAN	retinol binding protein 2, cellular						epidermis development|retinoid metabolic process|steroid metabolic process|vitamin A metabolic process	cytosol	retinal binding|retinol binding|transporter activity			skin(1)	1					Vitamin A(DB00162)	AACCTACTGATTTTTTTTTTT	0.328													3	4	---	---	---	---	
TFDP2	7029	broad.mit.edu	37	3	141866890	141866890	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141866890delA	uc003eun.3	-						TFDP2_uc003eum.3_Intron|TFDP2_uc003euo.2_Intron	NM_006286	NP_006277	Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1						TCACGAGCTGAAAAAAAAAAC	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147500899	147500900	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147500899_147500900insT								ZIC1 (366395 upstream) : AGTR1 (914758 downstream)																							tttgttttttgttttgtttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147929868	147929868	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147929868delC								ZIC1 (795364 upstream) : AGTR1 (485790 downstream)																							ATTACAGTGACCCAAACTAGG	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151383299	151383304	+	IGR	DEL	CTCTTT	-	-	rs75825638		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151383299_151383304delCTCTTT								IGSF10 (206802 upstream) : AADACL2 (68400 downstream)																							ctgtttcttcctctttctctttctct	0.000													5	3	---	---	---	---	
RSRC1	51319	broad.mit.edu	37	3	158103715	158103715	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158103715delT	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			TAGAAAACTCTTTGACTAATG	0.318													4	2	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	158971400	158971401	+	Intron	DEL	AC	-	-	rs72144224		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158971400_158971401delAC	uc003fcq.1	+						SCHIP1_uc003fcr.1_Intron|IQCJ_uc003fco.2_Intron|IQCJ_uc010hvy.1_Intron|IQCJ_uc003fcp.1_Intron	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			TCCCTcacaaacacacacacac	0.322													5	5	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	158991480	158991481	+	5'Flank	DEL	GT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158991480_158991481delGT	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_5'Flank	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			CACTTATTTAGTGTGTGTTATA	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	159812176	159812177	+	Intron	INS	-	TT	TT	rs112372359		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159812176_159812177insTT	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		TTCAGTTAGTCttttttttttt	0.252													2	4	---	---	---	---	
NMD3	51068	broad.mit.edu	37	3	160949061	160949061	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160949061delA	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron	NM_015938	NP_057022	Q96D46	NMD3_HUMAN	NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			gaactagaggaaataagctgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162685249	162685249	+	Intron	DEL	A	-	-	rs142802955		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162685249delA	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																		agctggtaccattccttctga	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163406137	163406138	+	IGR	INS	-	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163406137_163406138insG								None (None upstream) : MIR1263 (483121 downstream)																							tgtgtgtgtgtgtgtgtgtgtg	0.203													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163618818	163618818	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163618818delG								None (None upstream) : MIR1263 (270441 downstream)																							CAGTAGTTATGGAGACATGAC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166195343	166195344	+	IGR	DEL	TG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166195343_166195344delTG								BCHE (640090 upstream) : ZBBX (762737 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166457863	166457864	+	IGR	INS	-	TGTG	TGTG	rs146797645	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166457863_166457864insTGTG								BCHE (902610 upstream) : ZBBX (500217 downstream)																							AAATATACATATGTGTGTGTGT	0.173													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166670693	166670694	+	IGR	INS	-	T	T	rs140029392	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166670693_166670694insT								None (None upstream) : ZBBX (287387 downstream)																							tttactgagtctttttttttgc	0.000													4	5	---	---	---	---	
PHC3	80012	broad.mit.edu	37	3	169885973	169885974	+	Intron	INS	-	CAAAGG	CAAAGG	rs147945976	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169885973_169885974insCAAAGG	uc010hws.1	-						PHC3_uc003fgl.2_Intron|PHC3_uc011bpq.1_Intron|PHC3_uc011bpr.1_Intron|PHC3_uc003fgm.2_Intron|PHC3_uc003fgo.1_Intron	NM_024947	NP_079223	Q8NDX5	PHC3_HUMAN	polyhomeotic like 3						multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			aaaggcaaagtcaaagggaaag	0.104													1	7	---	---	---	---	
PRKCI	5584	broad.mit.edu	37	3	169992507	169992507	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169992507delT	uc003fgs.2	+							NM_002740	NP_002731	P41743	KPCI_HUMAN	protein kinase C, iota						anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			ATGCAGGCTCTTTTTTTTTTG	0.368													4	2	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170565611	170565613	+	Intron	DEL	GTG	-	-	rs146069344		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170565611_170565613delGTG	uc011bpt.1	+							NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			TTTGTTTTTTgtggtggtggtgg	0.059													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	170669197	170669197	+	IGR	DEL	A	-	-	rs111637819		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170669197delA								EIF5A2 (42771 upstream) : SLC2A2 (44940 downstream)																							GCaaaaaaagaaaaaaaaaaa	0.388													4	2	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	170969852	170969853	+	Intron	INS	-	GT	GT	rs146267125	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170969852_170969853insGT	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			ATCTGgtatgcgtgtgtgtgtg	0.292													8	6	---	---	---	---	
TMEM212	389177	broad.mit.edu	37	3	171569995	171569996	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171569995_171569996insT	uc003fhw.1	+									A6NML5	TM212_HUMAN	RecName: Full=Transmembrane protein 212;							integral to membrane					0						GTTTTAAAAGAttttttttttt	0.139													4	2	---	---	---	---	
GHSR	2693	broad.mit.edu	37	3	172165178	172165179	+	Intron	DEL	GA	-	-	rs141566941		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172165178_172165179delGA	uc003fib.1	-							NM_198407	NP_940799	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor isoform 1a						actin polymerization or depolymerization|adult feeding behavior|decidualization|growth hormone secretion|hormone-mediated signaling pathway|negative regulation of inflammatory response|negative regulation of interleukin-1 beta production|negative regulation of interleukin-6 biosynthetic process|negative regulation of tumor necrosis factor biosynthetic process|positive regulation of appetite|positive regulation of multicellular organism growth	cell surface|integral to membrane|membrane raft|neuron projection|plasma membrane	growth hormone secretagogue receptor activity|growth hormone-releasing hormone receptor activity			lung(3)|ovary(1)|central_nervous_system(1)	5	Ovarian(172;0.00143)|Breast(254;0.197)		Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			aaagggggaggagagagagaga	0.158													7	18	---	---	---	---	
NCEH1	57552	broad.mit.edu	37	3	172369354	172369354	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172369354delT	uc011bpx.1	-						NCEH1_uc003fig.2_Intron|NCEH1_uc011bpw.1_Intron|NCEH1_uc011bpy.1_Intron	NM_001146276	NP_001139748	Q6PIU2	NCEH1_HUMAN	arylacetamide deacetylase-like 1 isoform a						lipid catabolic process	endoplasmic reticulum|integral to membrane|microsome	carboxylesterase activity				0						TTGGAGAATCttttttttttt	0.179													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	174428021	174428021	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174428021delT	uc003fir.2	+						uc003fis.2_Intron|uc010hwx.1_Intron					Homo sapiens NAALADL2 gene, partial 5'UTR, variant 1.																		atgagcctccttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	175535131	175535131	+	IGR	DEL	A	-	-	rs111457778		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175535131delA								NAALADL2 (11705 upstream) : None (None downstream)																							actccatctcaaaaaaaaaaa	0.070													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176133194	176133194	+	IGR	DEL	T	-	-	rs73041506	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176133194delT								NAALADL2 (609768 upstream) : TBL1XR1 (605349 downstream)																							ACTGCTTTCCTTTTTTTTTTC	0.308													4	2	---	---	---	---	
TBL1XR1	79718	broad.mit.edu	37	3	176914530	176914531	+	5'Flank	INS	-	T	T	rs148467145	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176914530_176914531insT	uc003fiw.3	-						TBL1XR1_uc003fix.3_Intron|TBL1XR1_uc011bpz.1_Intron|TBL1XR1_uc003fiy.2_Intron	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)			GCCTCCCCCCCCAAACACACAC	0.505													2	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176937838	176937839	+	IGR	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176937838_176937839delAC								TBL1XR1 (22790 upstream) : None (None downstream)																							AATCAACAGTacacacacacac	0.198													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177143178	177143178	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177143178delT								TBL1XR1 (228130 upstream) : None (None downstream)																							tttttctttcttttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177547466	177547469	+	Intron	DEL	AAAC	-	-	rs72448079		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177547466_177547469delAAAC	uc003fiz.1	+											Homo sapiens cDNA FLJ31690 fis, clone NT2RI2005621.																		ctccatctcaaaacaaacaaacaa	0.152													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177652580	177652583	+	IGR	DEL	TGTG	-	-	rs148978131		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177652580_177652583delTGTG								TBL1XR1 (737532 upstream) : KCNMB2 (601641 downstream)																							TGGGGGGATAtgtgtgtgtgtgtg	0.368													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177765823	177765828	+	IGR	DEL	TGTGTG	-	-	rs76951388		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177765823_177765828delTGTGTG								TBL1XR1 (850775 upstream) : KCNMB2 (488396 downstream)																							AAGGCTCATCtgtgtgtgtgtgtgtg	0.340													5	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	178026716	178026716	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178026716delT								None (None upstream) : KCNMB2 (227508 downstream)																							TGACTTATTCTTTTTTTTTTT	0.244													6	4	---	---	---	---	
KCNMB2	10242	broad.mit.edu	37	3	178367290	178367290	+	Intron	DEL	T	-	-	rs10711859		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178367290delT	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron|KCNMB2_uc003fje.2_Intron|KCNMB2_uc003fjf.2_Intron	NM_181361	NP_852006	Q9Y691	KCMB2_HUMAN	calcium-activated potassium channel beta 2						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of vasoconstriction	voltage-gated potassium channel complex	calcium-activated potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(1)	1	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)			agtcctgggcttttttttttg	0.000													1	7	---	---	---	---	
ACTL6A	86	broad.mit.edu	37	3	179289209	179289221	+	Intron	DEL	AAAAAAAAAAACA	-	-	rs150813047		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179289209_179289221delAAAAAAAAAAACA	uc003fjw.2	+						ACTL6A_uc003fjx.2_Intron|ACTL6A_uc003fjy.2_Intron	NM_004301	NP_004292	O96019	ACL6A_HUMAN	actin-like 6A isoform 1						chromatin remodeling|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|nervous system development|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	Ino80 complex|npBAF complex|NuA4 histone acetyltransferase complex|plasma membrane|SWI/SNF complex	ATP binding|chromatin binding			ovary(1)	1	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			actctgtctcaaaaaaaaaaacaaaaaaaaaaa	0.014													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	179514027	179514028	+	IGR	INS	-	TTG	TTG	rs142387204	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179514027_179514028insTTG								USP13 (6840 upstream) : PEX5L (4022 downstream)																							GAACTGCCTAATTGTTGTTGTT	0.411													9	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	179978414	179978418	+	IGR	DEL	AAAGA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179978414_179978418delAAAGA								PEX5L (223897 upstream) : TTC14 (341500 downstream)																							cagaaatgagaaagaaaagaaaaga	0.024													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180472829	180472835	+	Intron	DEL	CCCACGC	-	-	rs7620497	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180472829_180472835delCCCACGC	uc003fko.2	-											Homo sapiens mRNA; cDNA DKFZp434A128 (from clone DKFZp434A128).																		TAACAGTTGGCCCACGCCCAAACAAAA	0.232													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180472851	180472852	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180472851_180472852insA	uc003fko.2	-											Homo sapiens mRNA; cDNA DKFZp434A128 (from clone DKFZp434A128).																		CAAAACAAACTAAAAAAAATAA	0.193													7	4	---	---	---	---	
FXR1	8087	broad.mit.edu	37	3	180636163	180636164	+	Intron	INS	-	AAT	AAT	rs140415451	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180636163_180636164insAAT	uc003fkq.2	+						FXR1_uc003fkp.2_Intron|FXR1_uc003fkr.2_Intron|FXR1_uc011bqj.1_Intron|FXR1_uc003fks.2_Intron|FXR1_uc011bqk.1_Intron|FXR1_uc011bql.1_Intron	NM_005087	NP_005078	P51114	FXR1_HUMAN	fragile X mental retardation-related protein 1						apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			tggtctcaagcaatactcccat	0.059													9	6	---	---	---	---	
SOX2OT	347689	broad.mit.edu	37	3	181412205	181412205	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181412205delG	uc003fkv.2	+						SOX2OT_uc003fkw.3_Intron					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0						ACTACGTACTGGTAATTACAA	0.353													4	2	---	---	---	---	
MCF2L2	23101	broad.mit.edu	37	3	183098114	183098115	+	Intron	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183098114_183098115delAC	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc003flp.1_Intron	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			tttgagggaaacacagtgacag	0.000													1	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	183791569	183791569	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183791569delC								HTR3C (13110 upstream) : HTR3E (23283 downstream)																							ctgtagttttccactgacttt	0.000													0	14	---	---	---	---	
LIPH	200879	broad.mit.edu	37	3	185266202	185266202	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185266202delA	uc003fpm.2	-						LIPH_uc010hyh.2_Intron	NM_139248	NP_640341	Q8WWY8	LIPH_HUMAN	lipase, member H precursor						lipid catabolic process	extracellular space|plasma membrane	heparin binding|phospholipase activity			ovary(1)|pancreas(1)	2	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			acataaaaggaaaaaaaaaac	0.020													6	3	---	---	---	---	
IGF2BP2	10644	broad.mit.edu	37	3	185431949	185431950	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185431949_185431950insT	uc003fpo.2	-						IGF2BP2_uc010hyi.2_Intron|IGF2BP2_uc010hyj.2_Intron|IGF2BP2_uc010hyk.2_Intron|IGF2BP2_uc010hyl.2_Intron|IGF2BP2_uc003fpp.2_Intron|IGF2BP2_uc003fpq.2_Intron|C3orf65_uc003fpr.2_Intron|C3orf65_uc003fps.3_Intron	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			GAATACATTCCTTTTTTTTTTT	0.262													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	185749893	185749894	+	IGR	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185749893_185749894insA								TRA2B (93969 upstream) : ETV5 (14214 downstream)																							gactccgtctcaaaaaaaaaaa	0.000													5	3	---	---	---	---	
DGKG	1608	broad.mit.edu	37	3	185951268	185951270	+	Intron	DEL	GTT	-	-	rs146286671		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185951268_185951270delGTT	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	cgtttttgtcgttgttgttgttg	0.000													5	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186820058	186820058	+	IGR	DEL	T	-	-	rs140744682		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186820058delT								ST6GAL1 (23719 upstream) : RPL39L (18683 downstream)																							tctttgtgggttttttttttt	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187052110	187052111	+	IGR	INS	-	AGAGGAGAGG	AGAGGAGAGG	rs146337933	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187052110_187052111insAGAGGAGAGG								MASP1 (42358 upstream) : RTP4 (34057 downstream)																							TCTACTCTCAAAGAGGAGAGGA	0.480													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187203099	187203100	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187203099_187203100insT								RTP4 (113732 upstream) : SST (183596 downstream)																							CAAAAGCATTCTTTTTTTTTTT	0.332													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189132415	189132416	+	IGR	INS	-	ACACAC	ACACAC	rs142344575	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189132415_189132416insACACAC								TPRG1 (91145 upstream) : TP63 (216800 downstream)																							aaatttGCTAAacacacacaca	0.114													6	3	---	---	---	---	
TP63	8626	broad.mit.edu	37	3	189402421	189402422	+	Intron	INS	-	T	T	rs72446129		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189402421_189402422insT	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		ttctttctttcttttttttttt	0.149									Hay-Wells_syndrome	HNSCC(45;0.13)			4	3	---	---	---	---	
TMEM207	131920	broad.mit.edu	37	3	190147698	190147698	+	Intron	DEL	G	-	-	rs5855335		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190147698delG	uc003fsj.2	-							NM_207316	NP_997199	Q6UWW9	TM207_HUMAN	transmembrane protein 207 precursor							integral to membrane					0	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)		AGTCACCACAGGGGGGAAAAA	0.363													6	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190424837	190424838	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190424837_190424838insT								IL1RAP (48994 upstream) : LOC647309 (145688 downstream)																							atgcctggctattttttttttc	0.000													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190645236	190645236	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190645236delT								SNAR-I (49397 upstream) : OSTN (285086 downstream)																							TTATTATGGCttttttttttt	0.129													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190862312	190862312	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190862312delA								SNAR-I (266473 upstream) : OSTN (68010 downstream)																							GATAGCCACTAAATTTTCAAG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191417477	191417480	+	IGR	DEL	AAAG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191417477_191417480delAAAG								PYDC2 (238234 upstream) : FGF12 (442204 downstream)																							aaagaaagaaaaagaaaggaaaga	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191452022	191452023	+	IGR	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191452022_191452023insA								PYDC2 (272779 upstream) : FGF12 (407661 downstream)																							tcaggcaagataaaaaaaaaaa	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	192649578	192649578	+	IGR	DEL	A	-	-	rs63199260		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192649578delA								C3orf59 (13628 upstream) : HRASLS (309340 downstream)																							aaactctgtcaaaaaaaaaaa	0.179													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193731918	193731919	+	IGR	DEL	CA	-	-	rs66514639		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193731918_193731919delCA								LOC100128023 (19891 upstream) : HES1 (122015 downstream)																							TTCACTCTATcacacacacaca	0.351													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193814111	193814112	+	IGR	INS	-	TAAAC	TAAAC	rs139407398	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193814111_193814112insTAAAC								LOC100128023 (102084 upstream) : HES1 (39822 downstream)																							gaactggcgtttgagactaaga	0.015													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195424068	195424068	+	5'Flank	DEL	T	-	-	rs66848246		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195424068delT	uc011btd.1	+						uc003fux.1_5'Flank|MIR570_hsa-mir-570|MI0003577_5'Flank					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		tttcccattcttttttttttt	0.264													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195431864	195431864	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195431864delA	uc011btd.1	+						uc003fux.1_Intron					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		gtggctttccaacgtttctgg	0.219													10	5	---	---	---	---	
TCTEX1D2	255758	broad.mit.edu	37	3	196020518	196020518	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196020518delT	uc003fwi.2	-							NM_152773	NP_689986	Q8WW35	TC1D2_HUMAN	Tctex1 domain containing 2								protein binding			ovary(1)|breast(1)	2	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		acaaGATGCAttttttttttt	0.015													4	2	---	---	---	---	
PAK2	5062	broad.mit.edu	37	3	196493802	196493803	+	Intron	INS	-	GTGT	GTGT	rs71621297		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196493802_196493803insGTGT	uc003fwy.3	+							NM_002577	NP_002568	Q13177	PAK2_HUMAN	p21-activated kinase 2						axon guidance|cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of apoptosis|regulation of defense response to virus by virus|regulation of growth|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|nucleus|perinuclear region of cytoplasm|plasma membrane	ATP binding|identical protein binding|protein kinase binding|protein serine/threonine kinase activity|protein tyrosine kinase activator activity			ovary(1)|lung(1)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		AAGTACACCCCgtgtgtgtgtg	0.099													4	2	---	---	---	---	
KIAA0226	9711	broad.mit.edu	37	3	197468787	197468787	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197468787delG	uc003fyd.3	-						KIAA0226_uc003fyf.2_Intron	NM_001145642	NP_001139114	Q92622	RUBIC_HUMAN	hypothetical protein LOC9711 isoform 1						autophagy|endocytosis|negative regulation of autophagy|negative regulation of endocytosis	early endosome|late endosome|lysosome	protein binding				0	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		ctttttttttgagacggagtc	0.129													4	2	---	---	---	---	
LRCH3	84859	broad.mit.edu	37	3	197601797	197601798	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197601797_197601798insT	uc011bul.1	+						LRCH3_uc011bum.1_Intron|LRCH3_uc011bun.1_Intron|LRCH3_uc003fyk.2_Intron	NM_032773	NP_116162	Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH)							extracellular region				ovary(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		tgcaacagttcttttttttttt	0.000													5	5	---	---	---	---	
ZFYVE28	57732	broad.mit.edu	37	4	2400735	2400736	+	Intron	INS	-	GGT	GGT			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2400735_2400736insGGT	uc003gex.1	-						ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						GCACAAGGAGGGGCGAGATCTA	0.614													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3609800	3609800	+	IGR	DEL	G	-	-	rs67423032		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3609800delG								LRPAP1 (75576 upstream) : ADRA2C (158275 downstream)																							GCAGAGCCCAGGGCCCGCCCT	0.652													2	4	---	---	---	---	
MAN2B2	23324	broad.mit.edu	37	4	6584046	6584048	+	Intron	DEL	GTT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6584046_6584048delGTT	uc003gjf.1	+						MAN2B2_uc003gje.1_Intron|MAN2B2_uc011bwf.1_Intron	NM_015274	NP_056089	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2						mannose metabolic process	extracellular region	alpha-mannosidase activity|carbohydrate binding|zinc ion binding			ovary(2)	2						GCAGTATTTAgttgttgttgttg	0.261													4	2	---	---	---	---	
LGI2	55203	broad.mit.edu	37	4	25007888	25007888	+	Intron	DEL	C	-	-	rs34706304		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25007888delC	uc003grf.2	-							NM_018176	NP_060646	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2							extracellular region					0		Breast(46;0.173)				CACCCAGATGCCCCCCAGACC	0.517													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	27196306	27196309	+	IGR	DEL	CCTG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27196306_27196309delCCTG								STIM2 (170498 upstream) : None (None downstream)																							tccttccttccctgcttccttcct	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	37795519	37795520	+	IGR	DEL	AA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37795519_37795520delAA								RELL1 (107520 upstream) : PGM2 (32762 downstream)																							AAAAATTTAGAAAGAGAGAGAG	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49155208	49155209	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49155208_49155209insT								CWH43 (91115 upstream) : None (None downstream)																							attccattccattcattccatt	0.000													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49217676	49217677	+	IGR	INS	-	C	C	rs146012723	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49217676_49217677insC								CWH43 (153583 upstream) : None (None downstream)																							TTTTCCTTCCACCCaaccccct	0.109													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49519809	49519811	+	IGR	DEL	TTT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49519809_49519811delTTT								CWH43 (455716 upstream) : None (None downstream)																							gcgtggcttgttttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49645273	49645273	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49645273delT								CWH43 (581180 upstream) : None (None downstream)																							tggaatggaatcaacccgatt	0.000													12	7	---	---	---	---	
RASL11B	65997	broad.mit.edu	37	4	53730433	53730433	+	Intron	DEL	A	-	-	rs148367785		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53730433delA	uc003gzt.2	+							NM_023940	NP_076429	Q9BPW5	RSLBB_HUMAN	RAS-like family 11 member B						small GTPase mediated signal transduction	membrane	GTP binding|GTPase activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0302)			AAAAACTTGCAAACTTTGCCC	0.303													3	3	---	---	---	---	
BMPR1B	658	broad.mit.edu	37	4	95750478	95750479	+	Intron	INS	-	T	T	rs76146174		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95750478_95750479insT	uc003htm.3	+							NM_001203	NP_001194	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB						BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity			lung(4)|skin(2)|stomach(1)|breast(1)	8		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		TTTTATTTTCCTTTTTTTTTTT	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	96796492	96796492	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96796492delA								PDHA2 (33868 upstream) : None (None downstream)																							tgtgaggaggaaaataatcca	0.000													4	2	---	---	---	---	
NHEDC1	150159	broad.mit.edu	37	4	103826510	103826511	+	Intron	DEL	CA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103826510_103826511delCA	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		cctgagtagccaggaCTGGTTA	0.119													3	3	---	---	---	---	
TET2	54790	broad.mit.edu	37	4	106176103	106176103	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106176103delC	uc003hxk.2	+						TET2_uc011cez.1_Intron|TET2_uc003hxj.2_Intron	NM_001127208	NP_001120680	Q6N021	TET2_HUMAN	tet oncogene family member 2 isoform a						cell cycle|myeloid cell differentiation		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			haematopoietic_and_lymphoid_tissue(732)|pancreas(1)	733		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ttcagattttcctatcccaac	0.000			Mis N|F		MDS								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	157465089	157465090	+	IGR	INS	-	A	A	rs111862243		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157465089_157465090insA								CTSO (590041 upstream) : PDGFC (217674 downstream)																							gcaaggaacagaaaaaaaaaac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188103723	188103723	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188103723delA								FAT1 (455873 upstream) : ZFP42 (813202 downstream)																							CACCAATCCTAAAAAAAAAAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190558519	190558526	+	IGR	DEL	AGGAAGGA	-	-	rs36214844		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190558519_190558526delAGGAAGGA								None (None upstream) : FRG1 (303448 downstream)																							gaaggaagggaggaaggaaggaaggaag	0.111													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190840895	190840895	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190840895delG	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		tttttgcattgaaaaggagaa	0.085													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190842429	190842430	+	Intron	INS	-	G	G	rs139006224		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190842429_190842430insG	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		atcaagtagaagaaaaaaacag	0.000													4	2	---	---	---	---	
SLC12A7	10723	broad.mit.edu	37	5	1080185	1080185	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1080185delC	uc003jbu.2	-							NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride						potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GCCTGAAGCACCCATTGCTCG	0.672													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2145692	2145693	+	IGR	INS	-	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2145692_2145693insC								IRX4 (262812 upstream) : IRX2 (600588 downstream)																							CCTAATCACTTCCAGATCCTCC	0.525													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2787622	2787635	+	IGR	DEL	TCTTTTAGATCAGC	-	-	rs35813681	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2787622_2787635delTCTTTTAGATCAGC								C5orf38 (32110 upstream) : IRX1 (808533 downstream)																							ATCAGTAACTTCTTTTAGATCAGCTGGTTTCCAT	0.355													17	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3161039	3161040	+	IGR	DEL	TG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3161039_3161040delTG								C5orf38 (405527 upstream) : IRX1 (435128 downstream)																							tctgtgtctctgtgtgtgtgtg	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3725571	3725571	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3725571delG								IRX1 (124055 upstream) : None (None downstream)																							TGGGACACCAGGGCTGCAGGG	0.388													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4977980	4977981	+	IGR	DEL	TG	-	-	rs35730416		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4977980_4977981delTG								None (None upstream) : LOC340094 (56491 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6231531	6231532	+	IGR	INS	-	CACA	CACA			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6231531_6231532insCACA								KIAA0947 (741194 upstream) : FLJ33360 (79022 downstream)																							acacacacacacacacacacac	0.183													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8780467	8780468	+	IGR	INS	-	TAT	TAT	rs149316972	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8780467_8780468insTAT								MTRR (879234 upstream) : SEMA5A (254670 downstream)																							AGTAAAGAAGATGAATTTAGAA	0.163													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	12386817	12386817	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12386817delT								CTNND2 (482707 upstream) : None (None downstream)																							cattggattctttcatataat	0.000													4	2	---	---	---	---	
DNAH5	1767	broad.mit.edu	37	5	13899333	13899333	+	Intron	DEL	C	-	-	rs71600032		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13899333delC	uc003jfd.2	-							NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					agccaccgtgcccggccatcc	0.000									Kartagener_syndrome				5	3	---	---	---	---	
FBXL7	23194	broad.mit.edu	37	5	15821704	15821706	+	Intron	DEL	TGG	-	-	rs145146063		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15821704_15821706delTGG	uc003jfn.1	+							NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3						AGGACTTGCTTGGTGGTTATCAG	0.266													4	2	---	---	---	---	
LOC285696	285696	broad.mit.edu	37	5	17212948	17212949	+	Intron	DEL	AA	-	-	rs71601728		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17212948_17212949delAA	uc003jfw.2	-							NR_027253				Homo sapiens cDNA FLJ34047 fis, clone FCBBF3000001.												0						atctctacttaaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	18142791	18142791	+	IGR	DEL	T	-	-	rs112240090		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18142791delT								BASP1 (865856 upstream) : None (None downstream)																							AATTACATTGTTTTTTTAGTA	0.154													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20653013	20653013	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20653013delA	uc003jge.1	+											Homo sapiens cDNA FLJ36043 fis, clone TESTI2017582.																		gcctggacataatgccacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	21012416	21012417	+	IGR	INS	-	T	T	rs149340721	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21012416_21012417insT								None (None upstream) : GUSBP1 (329525 downstream)																							TCCTGGTTAGATTTTTTGTTTT	0.337													4	2	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21460642	21460642	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21460642delT	uc010iub.2	+						GUSBP1_uc011cnn.1_Intron|GUSBP1_uc003jgh.3_Intron|GUSBP1_uc003jgf.3_Intron|GUSBP1_uc003jgg.3_Intron	NR_027028				SubName: Full=Putative uncharacterized protein GUSBL2;												0						tttctattcattttttttttt	0.159													4	2	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21529382	21529383	+	Intron	DEL	TG	-	-	rs149059727		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21529382_21529383delTG	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						tggcttcttttgtgtctttaag	0.153													4	3	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22258746	22258746	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22258746delG	uc003jgk.2	-							NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						caggctccatggatgataggt	0.010										HNSCC(59;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28466748	28466751	+	IGR	DEL	TCCA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28466748_28466751delTCCA								None (None upstream) : None (None downstream)																							catccatccgtccatccatccatc	0.137													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28609441	28609441	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28609441delA								None (None upstream) : None (None downstream)																							tctgcaggctaaacaggaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	31578544	31578546	+	IGR	DEL	AGG	-	-	rs13165278	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31578544_31578546delAGG								C5orf22 (23380 upstream) : PDZD2 (60971 downstream)																							aagaagaagaaggagaaggagaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36577863	36577866	+	IGR	DEL	CAGA	-	-	rs148869339		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36577863_36577866delCAGA								RANBP3L (275852 upstream) : SLC1A3 (28591 downstream)																							gagacagaggcagacagacaggga	0.029													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36796836	36796837	+	IGR	DEL	GA	-	-	rs112033128		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36796836_36796837delGA								SLC1A3 (108402 upstream) : NIPBL (80024 downstream)																							tcacatgttggagagagagaga	0.000													4	2	---	---	---	---	
WDR70	55100	broad.mit.edu	37	5	37586768	37586768	+	Intron	DEL	C	-	-	rs78823996		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37586768delC	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504	Q9NW82	WDR70_HUMAN	WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			cacacaccttctttttaaaag	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38251126	38251127	+	IGR	DEL	TG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38251126_38251127delTG								GDNF (411344 upstream) : EGFLAM (7406 downstream)																							gtgtgtgtgttgtgtgtgtgtg	0.272													4	2	---	---	---	---	
C9	735	broad.mit.edu	37	5	39367330	39367330	+	5'Flank	DEL	A	-	-	rs113099454		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39367330delA	uc003jlv.3	-							NM_001737	NP_001728	P02748	CO9_HUMAN	complement component 9 precursor						complement activation, alternative pathway|complement activation, classical pathway|cytolysis|hemolysis by symbiont of host erythrocytes	extracellular region|membrane attack complex					0	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)			actccgtctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
GHR	2690	broad.mit.edu	37	5	42610768	42610769	+	Intron	INS	-	A	A	rs112288959		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42610768_42610769insA	uc003jmt.2	+						GHR_uc011cpq.1_Intron	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor						2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	aatcccagtggaaaaaaaaaaa	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43029239	43029240	+	IGR	DEL	AC	-	-	rs34330161		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43029239_43029240delAC								SEPP1 (203241 upstream) : C5orf39 (9943 downstream)																							CCTGGAATAAACACAGAGTTAG	0.376													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	46327887	46327887	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46327887delA								HCN1 (631667 upstream) : None (None downstream)																							gcttctgtgtagtttttctgt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	50557085	50557088	+	IGR	DEL	ATTT	-	-	rs147913802		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50557085_50557088delATTT								PARP8 (418916 upstream) : ISL1 (121870 downstream)																							ttatccattcatttgtcaatggac	0.000													1	6	---	---	---	---	
NDUFAF2	91942	broad.mit.edu	37	5	60265784	60265784	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60265784delC	uc003jsp.3	+						NDUFAF2_uc003jso.3_Intron	NM_174889	NP_777549	Q8N183	MIMIT_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha							membrane|mitochondrion	electron carrier activity|NADH dehydrogenase (ubiquinone) activity				0		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)				tccagtttttccagcaccatt	0.000													4	2	---	---	---	---	
CWC27	10283	broad.mit.edu	37	5	64082402	64082402	+	Frame_Shift_Del	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64082402delA	uc003jtn.1	+	6	766	c.547delA	c.(547-549)AAAfs	p.K183fs	CWC27_uc003jtl.2_Frame_Shift_Del_p.K183fs|CWC27_uc003jtm.2_Frame_Shift_Del_p.K183fs|CWC27_uc010iwt.1_Frame_Shift_Del_p.K183fs	NM_005869	NP_005860	Q6UX04	CWC27_HUMAN	serologically defined colon cancer antigen 10	183					protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0						TAAAAGGCTGAAAAAAGAGAA	0.308													10	26	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	97450862	97450863	+	IGR	INS	-	A	A	rs144895410	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97450862_97450863insA								RIOK2 (931857 upstream) : RGMB (654136 downstream)																							tgaaatgaaggaaaaaatgtta	0.000													2	4	---	---	---	---	
EFNA5	1946	broad.mit.edu	37	5	106723289	106723290	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106723289_106723290insA	uc003kol.2	-							NM_001962	NP_001953	P52803	EFNA5_HUMAN	ephrin-A5 precursor						cell-cell signaling	anchored to plasma membrane|caveola|extracellular space	ephrin receptor binding				0		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		TGTTGATATACAAAACAGATAC	0.356													14	17	---	---	---	---	
FER	2241	broad.mit.edu	37	5	108509881	108509881	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108509881delG	uc003kop.1	+						FER_uc011cvg.1_Intron	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		AGGTCGCAAAGGGAAGAGAAG	0.443													4	2	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111501747	111501747	+	Intron	DEL	A	-	-	rs73787786	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111501747delA	uc003kpv.1	-						EPB41L4A_uc003kpp.1_Intron|EPB41L4A_uc003kpu.1_Intron	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		GAATTACCAGAAAAAAAGTGC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	112951965	112951965	+	IGR	DEL	T	-	-	rs78516249		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112951965delT								YTHDC2 (20986 upstream) : KCNN2 (746051 downstream)																							gtcttcgacattttttttttt	0.000													4	2	---	---	---	---	
ECSCR	641700	broad.mit.edu	37	5	138785585	138785585	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138785585delT	uc011cze.1	-						ECSCR_uc011czd.1_5'Flank	NM_001077693	NP_001071161	Q19T08	ECSCR_HUMAN	endothelial cell-specific chemotaxis regulator						angiogenesis|cell differentiation|chemotaxis	integral to membrane|plasma membrane					0						aaAGCCTCAAttttttttttt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139985757	139985757	+	IGR	DEL	T	-	-	rs113836014		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139985757delT								SLC35A4 (37074 upstream) : CD14 (25560 downstream)																							ttctttcctcttttttttttt	0.015													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	156313050	156313051	+	IGR	DEL	AA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156313050_156313051delAA								PPP1R2P3 (33511 upstream) : TIMD4 (33242 downstream)																							TGCTACGTTTAAGCCACTGGCA	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	158964366	158964366	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158964366delG								LOC285627 (71082 upstream) : ADRA1B (379374 downstream)																							taacatggctgggaattgtgt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	161656060	161656060	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161656060delA								GABRG2 (73516 upstream) : None (None downstream)																							GGAACACAGGAAAAAAAAAAA	0.398													4	2	---	---	---	---	
MAML1	9794	broad.mit.edu	37	5	179211886	179211886	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179211886delA	uc003mkn.1	+							NM_014757	NP_055572	Q92585	MAML1_HUMAN	mastermind-like 1						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	peptide antigen binding|protein kinase binding|transcription coactivator activity			lung(4)|ovary(2)	6	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TAACTGGATTAAAATTGTTTG	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	10331422	10331422	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10331422delA								None (None upstream) : TFAP2A (65495 downstream)																							ctgtctcattaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14353231	14353231	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14353231delT								CD83 (216085 upstream) : JARID2 (892503 downstream)																							ATTGTATGGATTTTCAGGGAC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18079337	18079337	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18079337delA								KIF13A (91538 upstream) : NHLRC1 (41381 downstream)																							ctggcgtgataaccacagagg	0.000													4	2	---	---	---	---	
KIAA0319	9856	broad.mit.edu	37	6	24605693	24605693	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24605693delT	uc011djo.1	-						KIAA0319_uc011djp.1_Intron|KIAA0319_uc003neh.1_Intron|KIAA0319_uc011djq.1_Intron|KIAA0319_uc011djr.1_Intron	NM_014809	NP_055624	Q5VV43	K0319_HUMAN	KIAA0319 precursor						negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2						GCTGCTTGCCTTTTGCCCACC	0.393													4	2	---	---	---	---	
ZSCAN23	222696	broad.mit.edu	37	6	28402480	28402480	+	Frame_Shift_Del	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28402480delC	uc003nli.3	-	4	1113	c.932delG	c.(931-933)GGCfs	p.G311fs	ZSCAN23_uc003nlh.2_RNA|ZSCAN23_uc010jrf.1_RNA|ZSCAN23_uc011dli.1_3'UTR	NM_001012455	NP_001012458	Q3MJ62	ZSC23_HUMAN	zinc finger protein 390	311	C2H2-type 3.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GAAGGCTTTGCCACAAACACT	0.532													7	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	40839945	40839945	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40839945delG								LRFN2 (284819 upstream) : UNC5CL (154827 downstream)																							ctgagaacttgctggcctccc	0.139													4	2	---	---	---	---	
CCND3	896	broad.mit.edu	37	6	41955242	41955273	+	Intron	DEL	TCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTG	-	-	rs71544258	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41955242_41955273delTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTG	uc003orp.2	-						CCND3_uc011duk.1_Intron|CCND3_uc011dum.1_Intron	NM_001136017	NP_001129489	P30281	CCND3_HUMAN	cyclin D3 isoform 1						cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding				0	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			tctctctctctctctctctctctctgtgtgtgtgtgtgtgtgtgtgtgtgtg	0.203			T	IGH@	MM								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	43705900	43705901	+	IGR	INS	-	TCTGT	TCTGT			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43705900_43705901insTCTGT								MRPS18A (50372 upstream) : VEGFA (32052 downstream)																							gtgtgtgtgtggtgtgtgtggt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	43950444	43950444	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43950444delA								LOC100132354 (44501 upstream) : C6orf223 (17895 downstream)																							ctatggctgcaaaacaaacta	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	44042334	44042335	+	RNA	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44042334_44042335delAC	uc003owm.1	-	1		c.55_56delGT								Homo sapiens cDNA: FLJ21083 fis, clone CAS03150.																		CAGTTTCATTACACACACAGAC	0.574											OREG0017461	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
RUNX2	860	broad.mit.edu	37	6	45367507	45367510	+	Intron	DEL	GGAG	-	-	rs77744169	byFrequency	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45367507_45367510delGGAG	uc011dvx.1	+						RUNX2_uc011dvy.1_Intron	NM_001024630	NP_001019801	Q13950	RUNX2_HUMAN	runt-related transcription factor 2 isoform a						negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3						aaggaaggaaggagggagggaggg	0.020													4	2	---	---	---	---	
CD2AP	23607	broad.mit.edu	37	6	47465057	47465058	+	Intron	INS	-	TTTCCTTTCA	TTTCCTTTCA	rs139822478	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47465057_47465058insTTTCCTTTCA	uc003oyw.2	+							NM_012120	NP_036252	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein						cell division|mitosis|protein complex assembly|signal transduction|substrate-dependent cell migration, cell extension	cytoplasm|filamentous actin|nucleolus|plasma membrane|ruffle	SH3 domain binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			ctttcctttcctttcctttcct	0.025													3	3	---	---	---	---	
GLYATL3	389396	broad.mit.edu	37	6	49483578	49483579	+	Intron	INS	-	CTAT	CTAT	rs145419942	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49483578_49483579insCTAT	uc003ozi.2	+							NM_001010904	NP_001010904	Q5SZD4	GLYL3_HUMAN	glycine N-acyltransferase-like protein 3							mitochondrion	glycine N-acyltransferase activity				0						AGCTTACAACACTGTTTCACCA	0.188													3	3	---	---	---	---	
DST	667	broad.mit.edu	37	6	56344323	56344324	+	Intron	DEL	AA	-	-	rs113615614		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56344323_56344324delAA	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			gaaccaatataagtgtccatca	0.000													5	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57250114	57250114	+	Intron	DEL	T	-	-	rs145906273		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57250114delT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ATTCTTCCCCTTCCAAACATA	0.259													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57257973	57257974	+	Intron	INS	-	GTG	GTG	rs140385725	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57257973_57257974insGTG	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		gatacccagtagtgttgctgga	0.000													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57324548	57324550	+	Intron	DEL	CTT	-	-	rs142446807		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57324548_57324550delCTT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ggcagaattccttcttcttcaaa	0.000													5	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57325208	57325209	+	Intron	INS	-	T	T	rs139197745	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57325208_57325209insT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CTTTACTAGGATTTAGGAATAT	0.396													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57358075	57358076	+	Intron	INS	-	TC	TC	rs147835952	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57358075_57358076insTC	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ccaaaaaATCATGTCTTGACCT	0.203													1	6	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57397342	57397342	+	Intron	DEL	G	-	-	rs5876596		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57397342delG	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		tggaaaactagttagtaataa	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57402022	57402023	+	Intron	INS	-	G	G	rs144916181		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57402022_57402023insG	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		actttgttaatttttttttctc	0.000													5	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57415142	57415142	+	Intron	DEL	A	-	-	rs11346545		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57415142delA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CTTTTCATTTAAAAAGTATAA	0.338													3	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57431455	57431456	+	Intron	INS	-	CTA	CTA	rs142026445		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57431455_57431456insCTA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ATGTGTTTTCGCTTTTATATAC	0.228													5	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57436347	57436348	+	Intron	DEL	CT	-	-	rs5876618		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57436347_57436348delCT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ggattacaggcttgagccacca	0.134													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57438940	57438941	+	Intron	INS	-	AATTT	AATTT	rs111656065		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57438940_57438941insAATTT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CATACCTGTGGAATTTATAGTT	0.381													8	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57441568	57441568	+	Intron	DEL	T	-	-	rs11301075		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57441568delT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AAGATCCATCTTTTTCTCTCT	0.318													5	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57466685	57466686	+	Intron	INS	-	T	T	rs150786912		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57466685_57466686insT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AGTAGAATGGGTAGATATGGGA	0.252													3	6	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57481478	57481480	+	Intron	DEL	TAA	-	-	rs112552854		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57481478_57481480delTAA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		gcgtctctactaataatacaaaa	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57493368	57493369	+	Intron	INS	-	AA	AA	rs141060212		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57493368_57493369insAA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TTGTCTTACAGAAAAAATATCA	0.312													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57515927	57515928	+	IGR	DEL	TT	-	-	rs10575067		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57515927_57515928delTT								PRIM2 (2552 upstream) : GUSBL2 (730231 downstream)																							GAGTCTACTCTTTGCAAATTTA	0.361													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57524861	57524861	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57524861delT								PRIM2 (11486 upstream) : GUSBL2 (721298 downstream)																							atatagggtatttttttctag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57557438	57557439	+	IGR	INS	-	C	C	rs140134047		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57557438_57557439insC								PRIM2 (44063 upstream) : GUSBL2 (688720 downstream)																							GGTATgctccacccccaggtaa	0.025													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57558058	57558058	+	IGR	DEL	T	-	-	rs74318708		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57558058delT								PRIM2 (44683 upstream) : GUSBL2 (688101 downstream)																							tatgacaaagttctaatatcc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57561144	57561144	+	IGR	DEL	T	-	-	rs143809920		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57561144delT								PRIM2 (47769 upstream) : GUSBL2 (685015 downstream)																							gagATGAAAGTCCCCttatac	0.104													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57566383	57566383	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57566383delG								PRIM2 (53008 upstream) : GUSBL2 (679776 downstream)																							gttcgagtcaggggggagagt	0.000													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57582258	57582259	+	IGR	INS	-	A	A	rs141383306	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57582258_57582259insA								PRIM2 (68883 upstream) : GUSBL2 (663900 downstream)																							caaggagatagaaaaagaagct	0.272													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	63939602	63939603	+	IGR	INS	-	G	G	rs148844302	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63939602_63939603insG								KHDRBS2 (943502 upstream) : LGSN (46254 downstream)																							GCCAAGCTGTTGAGGTGGACAT	0.564													8	8	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65548511	65548512	+	Intron	DEL	AC	-	-	rs71887288		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65548511_65548512delAC	uc011dxu.1	-							NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						CTGTTTCTCTacacacacacac	0.198													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	78801858	78801858	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78801858delT								HTR1B (628738 upstream) : IRAK1BP1 (775331 downstream)																							tcttctctccttccttccttc	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	87274198	87274198	+	IGR	DEL	C	-	-	rs147112048	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87274198delC								SNHG5 (885747 upstream) : HTR1E (372826 downstream)																							tttgtttttgctttttgctta	0.000													4	2	---	---	---	---	
BACH2	60468	broad.mit.edu	37	6	90707477	90707477	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90707477delT	uc011eab.1	-						BACH2_uc003pnw.2_Intron|BACH2_uc010kch.2_Intron	NM_021813	NP_068585	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper							nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		TGGATAGATCTTCAAAGTGAC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	91873717	91873718	+	IGR	INS	-	A	A	rs139905192	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91873717_91873718insA								MAP3K7 (576810 upstream) : None (None downstream)																							aatgtaagaataaaaaaaaaac	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	99252339	99252339	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99252339delA								MIR2113 (779842 upstream) : POU3F2 (30241 downstream)																							CATGCTTGGGAGGAAGCTCAC	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	101800262	101800262	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101800262delA								ASCC3 (471038 upstream) : GRIK2 (46643 downstream)																							ATGGACTTGGAAAAAAAAAAA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	106140580	106140580	+	IGR	DEL	T	-	-	rs72026456		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106140580delT								PREP (289611 upstream) : PRDM1 (393615 downstream)																							TCTGAAACTCTTTTTTTTTTT	0.378													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	110401834	110401835	+	IGR	INS	-	CTGGCTGGCCCTAG	CTGGCTGGCCCTAG	rs146606235	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110401834_110401835insCTGGCTGGCCCTAG								GPR6 (99913 upstream) : WASF1 (19187 downstream)																							CCCTCCCACCCCTGGTGATTCT	0.307													4	3	---	---	---	---	
C6orf204	387119	broad.mit.edu	37	6	118791292	118791293	+	Intron	DEL	AA	-	-	rs145365888		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118791292_118791293delAA	uc003pxz.1	-							NM_001042475	NP_001035940	Q5SZL2	CF204_HUMAN	chromosome 6 open reading frame 204 isoform a							centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)		AAAGAAGAAGAAAAAAAGAAAA	0.287													4	2	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	125060242	125060242	+	Intron	DEL	T	-	-	rs11318224		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125060242delT	uc003pzo.2	+						NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		TTAAGCCAACTGTTCAATATA	0.239													2	4	---	---	---	---	
ARHGAP18	93663	broad.mit.edu	37	6	129920087	129920088	+	Intron	DEL	GT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129920087_129920088delGT	uc003qbr.2	-						ARHGAP18_uc011ebw.1_Intron	NM_033515	NP_277050	Q8N392	RHG18_HUMAN	Rho GTPase activating protein 18						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		GGGTGTAGGGgtgtgtgtgtgt	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	130932352	130932354	+	IGR	DEL	TTG	-	-	rs68144412		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130932352_130932354delTTG								TMEM200A (168144 upstream) : LOC285733 (215970 downstream)																							AGAGTGAGTCTTGTTGTATATGT	0.360													3	3	---	---	---	---	
RGS17	26575	broad.mit.edu	37	6	153440870	153440870	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153440870delT	uc003qpm.2	-							NM_012419	NP_036551	Q9UGC6	RGS17_HUMAN	regulator of G-protein signalling 17						negative regulation of signal transduction	cytoplasm|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			pancreas(1)	1		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)		TGGCAACATCTTTGTGATACA	0.139									Lung_Cancer_Familial_Clustering_of				4	2	---	---	---	---	
IPCEF1	26034	broad.mit.edu	37	6	154617002	154617003	+	Intron	DEL	CA	-	-	rs67910940		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154617002_154617003delCA	uc003qpx.2	-						IPCEF1_uc003qpw.2_Intron|IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368	Q8WWN9	ICEF1_HUMAN	phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0						tgtgcacacgcacacacacaca	0.307													3	3	---	---	---	---	
PACRG	135138	broad.mit.edu	37	6	163697000	163697000	+	Intron	DEL	T	-	-	rs79000543		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163697000delT	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		AGAGTATTGCTTTTTTTTTTT	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164561598	164561598	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164561598delT								QKI (566706 upstream) : None (None downstream)																							catggagaggttgtcacttgt	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164785788	164785789	+	IGR	DEL	AA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164785788_164785789delAA								QKI (790896 upstream) : C6orf118 (907366 downstream)																							tggtcatgagaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170529464	170529464	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170529464delG								C6orf208 (326495 upstream) : LOC154449 (33958 downstream)																							GACTCCATACGGGGAGTCAGT	0.587													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1320135	1320136	+	IGR	INS	-	GGAG	GGAG			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1320135_1320136insGGAG								UNCX (43523 upstream) : MICALL2 (153860 downstream)																							ggaaggaggaagaagaaggaag	0.000													4	3	---	---	---	---	
INTS1	26173	broad.mit.edu	37	7	1546840	1546840	+	5'Flank	DEL	T	-	-	rs111819550		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1546840delT	uc003skn.2	-						INTS1_uc003skq.2_5'Flank	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1						snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GTCAttattcttttttttttt	0.269													5	4	---	---	---	---	
THSD7A	221981	broad.mit.edu	37	7	11446726	11446726	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11446726delT	uc003ssf.3	-							NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TATGTTATGGTTTTGCAAGCA	0.408										HNSCC(18;0.044)			11	11	---	---	---	---	
TWISTNB	221830	broad.mit.edu	37	7	19737345	19737346	+	3'UTR	DEL	AA	-	-	rs76513523		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19737345_19737346delAA	uc003sup.1	-	4						NM_001002926	NP_001002926	Q3B726	RPA43_HUMAN	TWIST neighbor							microtubule cytoskeleton|nucleolus	DNA-directed RNA polymerase activity			ovary(1)	1						GAAAGAAAAGAAAATAATGAAT	0.391													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	30259219	30259219	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30259219delA								C7orf41 (56838 upstream) : ZNRF2 (64704 downstream)																							gttagtatacaaaagtcaatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	31484775	31484776	+	IGR	INS	-	A	A	rs142020873	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31484775_31484776insA								NEUROD6 (104237 upstream) : CCDC129 (68909 downstream)																							TTCACCCCAATAAAAAAACTCT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	33683012	33683012	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33683012delA								BBS9 (37332 upstream) : BMPER (262100 downstream)																							gttttttaataatggcatttt	0.000													4	2	---	---	---	---	
ELMO1	9844	broad.mit.edu	37	7	36907954	36907954	+	Intron	DEL	T	-	-	rs71553092		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36907954delT	uc003tfk.1	-						ELMO1_uc003tfi.1_Intron|ELMO1_uc003tfj.1_Intron|ELMO1_uc011kbb.1_Intron|ELMO1_uc011kbc.1_Intron|ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						cttcttcttcttttttttttt	0.000													4	2	---	---	---	---	
VPS41	27072	broad.mit.edu	37	7	38894450	38894451	+	Intron	INS	-	G	G	rs146739395	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38894450_38894451insG	uc003tgy.2	-						VPS41_uc003tgz.2_Intron|VPS41_uc010kxn.2_Intron	NM_014396	NP_055211	P49754	VPS41_HUMAN	vacuolar protein sorting 41 isoform 1						Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4						CAAGAAGTGGAGAAAAAAAAAA	0.168													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46258763	46258764	+	IGR	INS	-	A	A	rs143138942		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46258763_46258764insA								IGFBP3 (297892 upstream) : None (None downstream)																							ACATTGCACTTAAAAAAAAACA	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	49282483	49282483	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49282483delT								CDC14C (315434 upstream) : VWC2 (530774 downstream)																							ctttttctcattttctttcct	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56354226	56354226	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56354226delC								PSPH (170136 upstream) : DKFZp434L192 (209690 downstream)																							acctgatctgccccaaaatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57736605	57736606	+	IGR	INS	-	AAAT	AAAT	rs147219220		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57736605_57736606insAAAT								ZNF716 (203340 upstream) : None (None downstream)																							cttaaagaaaaaaaaataaaaG	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	58009857	58009857	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:58009857delA								ZNF716 (476592 upstream) : None (None downstream)																							agagtttttcaaaactgctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61739627	61739631	+	IGR	DEL	AATTC	-	-	rs140005492		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61739627_61739631delAATTC								None (None upstream) : None (None downstream)																							aatggaatggaattcaatggaactg	0.180													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61754578	61754578	+	IGR	DEL	C	-	-	rs36188794		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61754578delC								None (None upstream) : LOC643955 (997094 downstream)																							caaaaggaaacgtcaaatgga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61788485	61788485	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61788485delG								None (None upstream) : LOC643955 (963187 downstream)																							ccatcaaaaagaatcgaagta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62028590	62028591	+	IGR	INS	-	C	C	rs144731645		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62028590_62028591insC								None (None upstream) : LOC643955 (723081 downstream)																							aaagagtgtttcaaactgctga	0.000													6	4	---	---	---	---	
ZNF273	10793	broad.mit.edu	37	7	64379342	64379343	+	Intron	DEL	CA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64379342_64379343delCA	uc003tto.2	+						ZNF273_uc003ttl.2_Intron|ZNF273_uc003ttm.1_Intron|ZNF273_uc003ttn.2_Intron|ZNF273_uc003ttp.1_Intron	NM_021148	NP_066971	Q14593	ZN273_HUMAN	zinc finger protein 273						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AACTATTTTTCATGTTCTCTTT	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65480180	65480181	+	IGR	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65480180_65480181insA								GUSB (32934 upstream) : ASL (60595 downstream)																							gactccgtctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	70255577	70255579	+	In_Frame_Del	DEL	CCA	-	-	rs35604576		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70255577_70255579delCCA	uc003tvw.3	+	19	4118_4120	c.3375_3377delCCA	c.(3373-3378)AGCCAC>AGC	p.H1133del	AUTS2_uc003tvx.3_In_Frame_Del_p.H1109del|AUTS2_uc011keg.1_In_Frame_Del_p.H585del	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1	1133	His-rich.									ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		ACGACTACAGccaccaccaccac	0.591													4	2	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71464505	71464505	+	Intron	DEL	T	-	-	rs34318737		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71464505delT	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				agcatatgcattttttttttt	0.000													6	3	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	77842491	77842495	+	Intron	DEL	TTTGC	-	-	rs67730737		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77842491_77842495delTTTGC	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				agCAAGAGCATTTGCTTTGGGATTT	0.063													3	3	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78237408	78237408	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78237408delA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GCTCAAGCCCAAGCATGGCCT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	79272014	79272014	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79272014delT								MAGI2 (189124 upstream) : GNAI1 (492126 downstream)																							tgagccttgattgcctcactg	0.035													4	2	---	---	---	---	
CD36	948	broad.mit.edu	37	7	80073554	80073555	+	Intron	INS	-	T	T	rs148169716	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80073554_80073555insT	uc003uhc.2	+							NM_001127444	NP_001120916	P16671	CD36_HUMAN	CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1						TTTTCTTCAAATCCCTTCCCCT	0.262													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	89758535	89758536	+	IGR	INS	-	T	T	rs111376342		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89758535_89758536insT								DPY19L2P4 (3621 upstream) : STEAP1 (25153 downstream)																							acgtgatctcatttttttatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	93031802	93031803	+	IGR	DEL	GT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93031802_93031803delGT								CCDC132 (43465 upstream) : CALCR (21996 downstream)																							gtgtgtgtgagtgtgtgtgtgt	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98408891	98408893	+	IGR	DEL	TAG	-	-	rs140739561	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98408891_98408893delTAG								NPTX2 (149710 upstream) : TMEM130 (35219 downstream)																							gtggtggtgatagtggtggtggt	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100111252	100111252	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100111252delA								C7orf51 (18830 upstream) : AGFG2 (25582 downstream)																							agaccttgtcaaaaaaaaaaa	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100611516	100611517	+	5'Flank	INS	-	T	T	rs146675456	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100611516_100611517insT	uc003uxm.1	-						uc003uxn.1_5'Flank					Homo sapiens cDNA FLJ32697 fis, clone TESTI2000372.																		ACTCTGAGCCCTGAAATCCTCA	0.327													4	3	---	---	---	---	
CDHR3	222256	broad.mit.edu	37	7	105522955	105522956	+	Intron	DEL	TT	-	-	rs67021019		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105522955_105522956delTT	uc003vdk.2	+						uc003vdj.1_Intron			Q6ZTQ4	CDHR3_HUMAN	RecName: Full=Cadherin-like protein 28; Flags: Precursor;						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1						attaaaccggtttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	108928021	108928021	+	IGR	DEL	T	-	-	rs35001349		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108928021delT								C7orf66 (403384 upstream) : EIF3IP1 (671263 downstream)																							ccagcctttgtctttgtaccc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	115441188	115441189	+	IGR	DEL	GT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115441188_115441189delGT								MDFIC (781925 upstream) : TFEC (134013 downstream)																							gatATAGAAGgtgtgtgtgtgt	0.124													3	3	---	---	---	---	
ST7	7982	broad.mit.edu	37	7	116824112	116824113	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116824112_116824113insA	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron|ST7_uc011knn.1_Intron|ST7_uc003vix.1_Intron|ST7OT3_uc003viy.1_Intron	NM_021908	NP_068708	Q9NRC1	ST7_HUMAN	suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		AACTTTTAATGAAAGGCTTTCA	0.188													4	2	---	---	---	---	
KCND2	3751	broad.mit.edu	37	7	120199047	120199048	+	Intron	INS	-	TG	TG	rs141390565	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120199047_120199048insTG	uc003vjj.1	+							NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)					TCACAAAGTACtgtgtgtgtgt	0.238													0	7	---	---	---	---	
C7orf58	79974	broad.mit.edu	37	7	120698938	120698938	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120698938delT	uc003vjq.3	+						C7orf58_uc003vjr.1_Intron|C7orf58_uc003vjs.3_Intron	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1							endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)					GTCAATAACCTTATAATGAAC	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124582792	124582792	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124582792delT	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																		tccaacgtggttttgaaccta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	125163778	125163778	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125163778delA								POT1 (593741 upstream) : GRM8 (914874 downstream)																							cctggaattgaaaaggcacag	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128861742	128861743	+	IGR	DEL	GT	-	-	rs78089998		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128861742_128861743delGT								SMO (8359 upstream) : AHCYL2 (3121 downstream)																							actgtacctggtgtccctcagC	0.228													3	3	---	---	---	---	
AHCYL2	23382	broad.mit.edu	37	7	128975912	128975913	+	Intron	INS	-	T	T	rs11384557		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128975912_128975913insT	uc011kov.1	+						AHCYL2_uc003vot.2_Intron	NM_015328	NP_056143	Q96HN2	SAHH3_HUMAN	S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2						cttttctttccttttttttttt	0.089													4	3	---	---	---	---	
DGKI	9162	broad.mit.edu	37	7	137506397	137506398	+	Intron	DEL	AA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137506397_137506398delAA	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3						catacatcagaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
KIAA1549	57670	broad.mit.edu	37	7	138635176	138635178	+	Intron	DEL	AGA	-	-	rs141992427		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138635176_138635178delAGA	uc011kql.1	-						KIAA1549_uc011kqj.1_Intron	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1							integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						TCAAGAAAGGAGAAGGAGTTGAG	0.448			O	BRAF	pilocytic astrocytoma								3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141229767	141229767	+	IGR	DEL	A	-	-	rs34117157		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141229767delA								MRPS33 (514986 upstream) : AGK (21311 downstream)																							actccatctcaaaaaaaaaaa	0.154													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142109108	142109109	+	Intron	INS	-	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142109108_142109109insG	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		aaagaacaaaaagaagagactc	0.000													3	3	---	---	---	---	
OR2A9P	441295	broad.mit.edu	37	7	143997734	143997734	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143997734delC	uc003wec.1	-						OR2A9P_uc003weg.1_3'UTR|OR2A9P_uc003weh.1_RNA					SubName: Full=Seven transmembrane helix receptor;												0						tgtgtccccacccaaatctca	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	145582312	145582312	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145582312delG								None (None upstream) : CNTNAP2 (231141 downstream)																							ATAGGTTGAAGGAACATTCAG	0.388													3	3	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146989342	146989342	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146989342delT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			cttctctgtatttatccagtt	0.000										HNSCC(39;0.1)			4	2	---	---	---	---	
C7orf33	202865	broad.mit.edu	37	7	148294822	148294823	+	Intron	INS	-	TTTGT	TTTGT	rs71529622		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148294822_148294823insTTTGT	uc003wew.2	+							NM_145304	NP_660347	Q8WU49	CG033_HUMAN	hypothetical protein LOC202865											central_nervous_system(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			cttcctctgcatttgttttgtt	0.054													4	2	---	---	---	---	
CUL1	8454	broad.mit.edu	37	7	148494795	148494795	+	Intron	DEL	T	-	-	rs72007939		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148494795delT	uc010lpg.2	+						CUL1_uc003wey.2_Intron|CUL1_uc003wez.2_Intron|CUL1_uc003wfa.2_Intron	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			TTTTGGGTGattttttttttt	0.343													7	4	---	---	---	---	
EZH2	2146	broad.mit.edu	37	7	148542051	148542051	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148542051delA	uc003wfd.1	-						EZH2_uc011kug.1_Intron|EZH2_uc003wfb.1_Intron|EZH2_uc003wfc.1_Intron|EZH2_uc011kuh.1_Intron|EZH2_uc011kui.1_Intron|EZH2_uc011kuj.1_Intron	NM_004456	NP_004447	Q15910	EZH2_HUMAN	enhancer of zeste 2 isoform a						negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding			haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1)	183	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			tgcctggattaaaaaaaaaaa	0.164			Mis		DLBCL								4	2	---	---	---	---	
ZNF767	79970	broad.mit.edu	37	7	149308536	149308537	+	Intron	INS	-	AAAC	AAAC	rs142406965	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149308536_149308537insAAAC	uc003wfy.3	-						ZNF767_uc003wfx.2_Intron|ZNF767_uc011kuq.1_Intron	NR_027789				Homo sapiens cDNA FLJ12700 fis, clone NT2RP1000721.											central_nervous_system(1)	1	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00434)			actctgtctcaaaacaaacaaa	0.203													4	2	---	---	---	---	
RHEB	6009	broad.mit.edu	37	7	151171273	151171273	+	Intron	DEL	T	-	-	rs5888440		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151171273delT	uc003wkh.1	-							NM_005614	NP_005605	Q15382	RHEB_HUMAN	Ras homolog enriched in brain precursor						cell cycle arrest|insulin receptor signaling pathway|positive regulation of TOR signaling cascade|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity|metal ion binding|protein binding			large_intestine(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00306)	UCEC - Uterine corpus endometrioid carcinoma (81;0.174)		TGtttttttgttttttttttg	0.100													2	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151975797	151975801	+	Intron	DEL	TAAAC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151975797_151975801delTAAAC	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						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)		aaatagaatttaaactaaaaagcag	0.020			N		medulloblastoma								4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152103179	152103179	+	Intron	DEL	T	-	-	rs5888468		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152103179delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						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)		GACAAAATAGTTTTTAAAAAA	0.199			N		medulloblastoma								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153058176	153058177	+	IGR	INS	-	T	T	rs150995824		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153058176_153058177insT								ACTR3B (505713 upstream) : DPP6 (526242 downstream)																							TTTTTCCACCATTTTTTTTTTT	0.342													4	3	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153978444	153978444	+	Intron	DEL	G	-	-	rs112929088		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153978444delG	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TAAATAAAATGGGTGCATCCT	0.254													4	3	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154570725	154570726	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154570725_154570726insA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			ccaccagcaccccaccatcacc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	31077819	31077820	+	IGR	DEL	TA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31077819_31077820delTA								WRN (46543 upstream) : NRG1 (419448 downstream)																							TCCTCAAAATTACACAGTTTCA	0.436													9	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	36514336	36514337	+	IGR	INS	-	T	T	rs139717221	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36514336_36514337insT								UNC5D (862156 upstream) : KCNU1 (127505 downstream)																							ccattttctcctttttttttct	0.257													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	40017621	40017622	+	IGR	INS	-	C	C	rs143869941	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40017621_40017622insC								C8orf4 (4800 upstream) : ZMAT4 (370494 downstream)																							gtttcctgaggccccccccagc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43824491	43824492	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43824491_43824492insT								POTEA (606163 upstream) : None (None downstream)																							tatgctgaaaaaggaaatatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	47506770	47506771	+	IGR	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47506770_47506771insA								None (None upstream) : BEYLA (245737 downstream)																							GGCTGTCTTCCATGCCAATTAC	0.460													6	13	---	---	---	---	
SNTG1	54212	broad.mit.edu	37	8	51680705	51680705	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51680705delC	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				TGCCCCAAGTCCCCACCATCT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	60827438	60827438	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60827438delA								TOX (795671 upstream) : CA8 (273985 downstream)																							gtaaaaaaagaaaaaaaaaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	62963302	62963303	+	IGR	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62963302_62963303insA								ASPH (336103 upstream) : NKAIN3 (198198 downstream)																							aaactctgtctaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	66353009	66353009	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66353009delT								CYP7B1 (641661 upstream) : ARMC1 (162063 downstream)																							gcccagcgccttgaagatccc	0.080													4	2	---	---	---	---	
VCPIP1	80124	broad.mit.edu	37	8	67574246	67574246	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67574246delC	uc003xwn.2	-							NM_025054	NP_079330	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex						protein ubiquitination	endoplasmic reticulum|Golgi stack	ubiquitin-specific protease activity			lung(2)|ovary(2)|central_nervous_system(1)|breast(1)|skin(1)|kidney(1)	8		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			tcgtgatctgcccgcctcagc	0.070													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	72729278	72729281	+	IGR	DEL	ACAG	-	-	rs66499372		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72729278_72729281delACAG								EYA1 (454811 upstream) : MSC (24496 downstream)																							ATCAGAATTCACAGATAGAGAGCG	0.387													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81142303	81142303	+	IGR	DEL	A	-	-	rs75958353		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81142303delA								TPD52 (58467 upstream) : ZBTB10 (255551 downstream)																							aaactccgtcaaaaaaaaaaa	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	93149819	93149819	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93149819delA								RUNX1T1 (42113 upstream) : C8orf83 (746046 downstream)																							CAGGTATGTTAACACTCAACT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	93251990	93251990	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93251990delT								RUNX1T1 (144284 upstream) : C8orf83 (643875 downstream)																							gattgccttctcctgctataa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94492916	94492917	+	IGR	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94492916_94492917insA								C8orf83 (463015 upstream) : FAM92A1 (219856 downstream)																							aagtataaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
MATN2	4147	broad.mit.edu	37	8	98935356	98935356	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98935356delT	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TTGCATGCCCTTTTTTTTTTC	0.378													3	3	---	---	---	---	
MATN2	4147	broad.mit.edu	37	8	98967410	98967412	+	Intron	DEL	ATT	-	-	rs10615745		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98967410_98967412delATT	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron|MATN2_uc010mbi.1_Intron	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			tgaccatcacattagagtttttg	0.000													0	7	---	---	---	---	
ZFPM2	23414	broad.mit.edu	37	8	106332485	106332486	+	Intron	DEL	TG	-	-	rs71577970		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106332485_106332486delTG	uc003ymd.2	+							NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2						blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			TTCAGATCTTtgtgtgtgtgtg	0.248													4	2	---	---	---	---	
OXR1	55074	broad.mit.edu	37	8	107442256	107442257	+	Intron	DEL	TG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107442256_107442257delTG	uc003ymf.2	+							NM_018002	NP_060472	Q8N573	OXR1_HUMAN	oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TTCTGTAGCCtgtgtgtgtgtg	0.262													5	3	---	---	---	---	
ANGPT1	284	broad.mit.edu	37	8	108267211	108267211	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108267211delA	uc003ymn.2	-						ANGPT1_uc011lhv.1_Intron|ANGPT1_uc003ymo.2_Intron	NM_001146	NP_001137	Q15389	ANGP1_HUMAN	angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			GTGACAGCTTAAAAAAAAAAA	0.328													4	2	---	---	---	---	
TRPS1	7227	broad.mit.edu	37	8	116555847	116555849	+	Intron	DEL	TTC	-	-	rs5894273		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116555847_116555849delTTC	uc003ynz.2	-						TRPS1_uc011lhy.1_Intron|TRPS1_uc003yny.2_Intron|TRPS1_uc010mcy.2_Intron	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1						negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			TCCTCATTTTTTCTTCTTCATAC	0.286									Langer-Giedion_syndrome				1	5	---	---	---	---	
DEPDC6	64798	broad.mit.edu	37	8	120963313	120963314	+	Intron	DEL	AC	-	-	rs35455263		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120963313_120963314delAC	uc003yow.3	+						DEPDC6_uc011lid.1_Intron	NM_022783	NP_073620	Q8TB45	DPTOR_HUMAN	DEP domain containing 6						intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis	intracellular	protein binding				0	Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			acacacacaaacacacacacac	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124682455	124682456	+	IGR	DEL	CT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124682455_124682456delCT								KLHL38 (17265 upstream) : ANXA13 (10579 downstream)																							tcctccccaccttcctcctcct	0.144													4	2	---	---	---	---	
SQLE	6713	broad.mit.edu	37	8	126029927	126029927	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126029927delC	uc011liq.1	+							NM_003129	NP_003120	Q14534	ERG1_HUMAN	squalene epoxidase						cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome	flavin adenine dinucleotide binding|squalene monooxygenase activity			ovary(1)|breast(1)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)	GGGGGATGATCGCCAGAGGAC	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129343328	129343328	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129343328delT								MIR1208 (180894 upstream) : None (None downstream)																							GGGCTGGACCTTTTTTTCAGA	0.592													4	2	---	---	---	---	
FAM49B	51571	broad.mit.edu	37	8	131024448	131024449	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131024448_131024449insA	uc003ysw.2	-						FAM49B_uc003ysx.2_Intron|FAM49B_uc003ysy.1_Intron	NM_016623	NP_057707	Q9NUQ9	FA49B_HUMAN	hypothetical protein LOC51571												0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			CCAAAAGAAGGAAAAAAAAAAT	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	132072826	132072827	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132072826_132072827insT								ADCY8 (19991 upstream) : EFR3A (843532 downstream)																							ttttctttttgttttttttttt	0.213													4	2	---	---	---	---	
TG	7038	broad.mit.edu	37	8	133922839	133922840	+	Intron	INS	-	C	C	rs138496927	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133922839_133922840insC	uc003ytw.2	+						TG_uc010mdw.2_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		tataaaagagacccagagagat	0.000													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	135480413	135480414	+	IGR	INS	-	T	T	rs146901216	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135480413_135480414insT								ST3GAL1 (896230 upstream) : ZFAT (9619 downstream)																							ctgtccctgcctggcgcctgta	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136143882	136143882	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136143882delC								MIR30D (326694 upstream) : LOC286094 (102492 downstream)																							TAATCTACTACCCCATACACA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137545059	137545059	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137545059delT								KHDRBS3 (885213 upstream) : None (None downstream)																							cagagataggtaagactgagg	0.154													4	2	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139890382	139890382	+	Frame_Shift_Del	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139890382delA	uc003yvd.2	-	3	716	c.269delT	c.(268-270)TTCfs	p.F90fs		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	90	VWFA.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TCCCAACTCGAAGGCCGTGGT	0.701										HNSCC(7;0.00092)			4	2	---	---	---	---	
EIF2C2	27161	broad.mit.edu	37	8	141591619	141591619	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141591619delA	uc003yvn.2	-						EIF2C2_uc010men.2_Intron|EIF2C2_uc010meo.2_Intron	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1						mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)			tcctgtctctaaaaaaaaaaa	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142606919	142606922	+	IGR	DEL	CCCT	-	-	rs72236536		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142606919_142606922delCCCT								FLJ43860 (89589 upstream) : MIR1302-7 (260681 downstream)																							CCTGAtctccccctccctccctcc	0.426													2	4	---	---	---	---	
ARC	23237	broad.mit.edu	37	8	143694528	143694528	+	Frame_Shift_Del	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143694528delG	uc003ywn.1	-	1	1306	c.1105delC	c.(1105-1107)CACfs	p.H369fs		NM_015193	NP_056008	Q7LC44	ARC_HUMAN	activity-regulated cytoskeleton-associated	369					endocytosis	acrosomal vesicle|cell junction|dendritic spine|endosome|postsynaptic density|postsynaptic membrane				breast(1)	1	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				ACCGGGAGGTGGGGGCCGGCC	0.711													2	4	---	---	---	---	
C9orf46	55848	broad.mit.edu	37	9	5589994	5589994	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5589994delC	uc003zjd.2	-							NM_018465	NP_060935	Q9HBL7	CI046_HUMAN	hypothetical protein LOC55848							integral to membrane				ovary(1)	1	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.00106)|Lung(218;0.125)		AAGTTGCCTACCAGGTTAATA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	34158282	34158283	+	IGR	INS	-	T	T	rs72731252		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34158282_34158283insT								DCAF12 (31511 upstream) : UBAP1 (20728 downstream)																							ctctctctctcttttttttttt	0.000													4	4	---	---	---	---	
C9orf25	203259	broad.mit.edu	37	9	34434811	34434814	+	Intron	DEL	TTTC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34434811_34434814delTTTC	uc011lok.1	-						C9orf25_uc003zuj.2_Intron|C9orf25_uc003zuk.2_Intron|C9orf25_uc011lol.1_Intron|C9orf25_uc003zul.2_Intron	NM_147202	NP_671735	Q8IW50	CI025_HUMAN	hypothetical protein LOC203259												0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.0858)		TGTTGATGGTtttctttctttctt	0.211													9	6	---	---	---	---	
MELK	9833	broad.mit.edu	37	9	36627521	36627522	+	Intron	INS	-	T	T	rs150933274		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36627521_36627522insT	uc003zzn.2	+						MELK_uc011lpm.1_Intron|MELK_uc011lpn.1_Intron|MELK_uc011lpo.1_Intron|MELK_uc010mll.2_Intron|MELK_uc011lpp.1_Intron|MELK_uc010mlm.2_Intron|MELK_uc011lpq.1_Intron|MELK_uc011lpr.1_Intron|MELK_uc011lps.1_Intron	NM_014791	NP_055606	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase							cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			CTCTCTCTCTCttttttttttt	0.163													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	36735068	36735069	+	IGR	INS	-	CTCTG	CTCTG	rs143959655	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36735068_36735069insCTCTG								MELK (57390 upstream) : PAX5 (103462 downstream)																							CATCCACCCGACTCTGTTGGTC	0.411													9	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	36764523	36764526	+	IGR	DEL	GTGT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36764523_36764526delGTGT								MELK (86845 upstream) : PAX5 (74005 downstream)																							ggtgtgtgtggtgtgtgtgagtgg	0.000													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66460611	66460611	+	5'Flank	DEL	T	-	-	rs149679567		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66460611delT	uc004aeb.2	-						uc004aec.2_Intron					Homo sapiens cDNA clone IMAGE:3941306, partial cds.																		tttgtaaatattttttcctca	0.000													4	2	---	---	---	---	
AQP7P1	375719	broad.mit.edu	37	9	67284101	67284101	+	5'Flank	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67284101delG	uc004aem.1	-						AQP7P1_uc004aen.1_Intron|AQP7P1_uc004aeo.1_Intron|AQP7P1_uc004aep.1_Intron					Homo sapiens aquaporin 7 pseudogene 1, mRNA (cDNA clone IMAGE:6191443).												0						GGAGTTGGATGGGGGCCAGTG	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68375418	68375419	+	IGR	INS	-	AC	AC	rs138387266		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68375418_68375419insAC								FAM27B (581229 upstream) : MIR1299 (626820 downstream)																							aaaacaaacaaaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68402587	68402587	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68402587delA								FAM27B (608398 upstream) : MIR1299 (599652 downstream)																							TGTAAAATTTAGGCAGAATTT	0.289													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69818412	69818412	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69818412delT								LOC100133920 (153463 upstream) : FOXD4L5 (357297 downstream)																							gttctaagtgtttgtccctca	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	72294347	72294348	+	IGR	DEL	AC	-	-	rs34118635		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72294347_72294348delAC								APBA1 (7072 upstream) : PTAR1 (30091 downstream)																							acacacacaaacacacacacac	0.262													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	72978460	72978460	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72978460delA								SMC5 (8671 upstream) : KLF9 (21055 downstream)																							TATCCCCTATAAGGTGACATT	0.144													4	2	---	---	---	---	
TRPM3	80036	broad.mit.edu	37	9	73287621	73287622	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73287621_73287622insT	uc004aid.2	-						TRPM3_uc004ahu.2_Intron|TRPM3_uc004ahv.2_Intron|TRPM3_uc004ahw.2_Intron|TRPM3_uc004ahx.2_Intron|TRPM3_uc004ahy.2_Intron|TRPM3_uc004ahz.2_Intron|TRPM3_uc004aia.2_Intron|TRPM3_uc004aib.2_Intron|TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9						TATTGGTTTTCTTTTTTTTTCC	0.168													4	2	---	---	---	---	
GDA	9615	broad.mit.edu	37	9	74737419	74737420	+	Intron	DEL	CT	-	-	rs35484246		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74737419_74737420delCT	uc011lse.1	+							NM_004293	NP_004284	Q9Y2T3	GUAD_HUMAN	guanine deaminase						nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		AATATTGTAACTCTGCAACTTT	0.188													4	3	---	---	---	---	
PRUNE2	158471	broad.mit.edu	37	9	79517223	79517223	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79517223delC	uc010mpk.2	-						PRUNE2_uc004akn.2_Intron	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2						apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						TCCCTACACTCCTTCAACTTC	0.418													4	2	---	---	---	---	
VPS13A	23230	broad.mit.edu	37	9	79906139	79906152	+	Intron	DEL	GTTGCATGCTCCTT	-	-	rs112918253		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79906139_79906152delGTTGCATGCTCCTT	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron|VPS13A_uc010mpo.1_5'Flank	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10						caggatctaggttgcatgctccttgtgagaatct	0.000													4	2	---	---	---	---	
GNAQ	2776	broad.mit.edu	37	9	80645804	80645807	+	Intron	DEL	TGTG	-	-	rs71503297		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80645804_80645807delTGTG	uc004akw.2	-							NM_002072	NP_002063	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity			eye(136)|skin(44)|meninges(11)|ovary(1)|kidney(1)	193						tgtgtgtcgctgtgtgtgtgtgtg	0.407			Mis		uveal melanoma								3	3	---	---	---	---	
NTRK2	4915	broad.mit.edu	37	9	87570121	87570121	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87570121delG	uc004aoa.1	+						NTRK2_uc004any.1_Intron|NTRK2_uc004anz.1_Intron	NM_001018064	NP_001018074	Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16						CAAGAGGGACGGGGAGGGGCA	0.592										TSP Lung(25;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	88484708	88484708	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88484708delA								AGTPBP1 (127764 upstream) : NAA35 (71349 downstream)																							actttttgtcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91256181	91256182	+	IGR	DEL	GT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91256181_91256182delGT								NXNL2 (65478 upstream) : LOC286238 (5912 downstream)																							tctgcagaacgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91326753	91326754	+	IGR	INS	-	TGA	TGA	rs113293491		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91326753_91326754insTGA								LOC286238 (59678 upstream) : C9orf47 (279024 downstream)																							ggtgatgatggtggtgatgatg	0.173													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91378437	91378438	+	IGR	DEL	AG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91378437_91378438delAG								LOC286238 (111362 upstream) : C9orf47 (227340 downstream)																							aggcaggcaaagagagagagag	0.000													5	5	---	---	---	---	
ROR2	4920	broad.mit.edu	37	9	94526842	94526843	+	Intron	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94526842_94526843delAC	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20						ATAATCACTTacacacacacac	0.252													3	3	---	---	---	---	
HIATL2	84278	broad.mit.edu	37	9	99766056	99766056	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99766056delA	uc004aws.2	-							NR_002894				RecName: Full=Hippocampus abundant transcript-like protein 2;												0						ccatgtctccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	105113008	105113010	+	IGR	DEL	TGT	-	-	rs66988467		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105113008_105113010delTGT								GRIN3A (612146 upstream) : CYLC2 (644583 downstream)																							attcctataatgttgttatttgt	0.005													1	5	---	---	---	---	
C9orf5	23731	broad.mit.edu	37	9	111777517	111777520	+	3'UTR	DEL	TAGC	-	-	rs16401		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111777517_111777520delTAGC	uc004bdt.3	-	18					C9orf5_uc004bds.3_RNA|C9orf5_uc004bdr.3_3'UTR|CTNNAL1_uc004bdo.1_5'Flank|CTNNAL1_uc010mtt.1_5'Flank|CTNNAL1_uc004bdp.1_5'Flank	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		CAAAGCAAGTTAGCTAAGAAACAG	0.309													0	6	---	---	---	---	
LPAR1	1902	broad.mit.edu	37	9	113774750	113774751	+	Intron	DEL	CA	-	-	rs35289856		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113774750_113774751delCA	uc011lwo.1	-						LPAR1_uc004bfb.2_Intron|LPAR1_uc004bfc.2_Intron|LPAR1_uc011lwn.1_Intron|LPAR1_uc010mub.2_Intron	NM_057159	NP_476500	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2						cgcacgcgcgcacacacacaca	0.208													4	3	---	---	---	---	
C9orf80	58493	broad.mit.edu	37	9	115455309	115455309	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115455309delA	uc004bgg.2	-						C9orf80_uc010muk.2_Intron	NM_021218	NP_067041	Q9NRY2	SOSSC_HUMAN	SOSSC protein						DNA repair|response to ionizing radiation	SOSS complex	protein binding				0						accctgtctcaaaaaaaaaaa	0.109													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119908771	119908771	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119908771delC	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						aaaaaaaaaacaagaataaaa	0.124													4	2	---	---	---	---	
C5	727	broad.mit.edu	37	9	123771999	123771999	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123771999delT	uc004bkv.2	-						C5_uc010mvm.1_Intron	NM_001735	NP_001726	P01031	CO5_HUMAN	complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)	cagtacctggttttgacttta	0.000													4	2	---	---	---	---	
TTLL11	158135	broad.mit.edu	37	9	124628938	124628939	+	Intron	INS	-	A	A	rs10656322		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124628938_124628939insA	uc011lyl.1	-						TTLL11_uc004blr.2_Intron	NM_001139442	NP_001132914	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11						protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0						gactccatctcaaaaaaaaaaa	0.050													2	4	---	---	---	---	
PRRX2	51450	broad.mit.edu	37	9	132446707	132446710	+	Intron	DEL	ACAC	-	-	rs145311338		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132446707_132446710delACAC	uc004byh.2	+							NM_016307	NP_057391	Q99811	PRRX2_HUMAN	paired related homeobox 2							nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)	1		Ovarian(14;0.00556)				cacagatacaacacacacacacac	0.020													3	3	---	---	---	---	
ASS1	445	broad.mit.edu	37	9	133364331	133364331	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133364331delG	uc004bzm.2	+						ASS1_uc004bzn.2_Intron|ASS1_uc010mza.2_Intron|ASS1_uc004bzo.2_Intron|ASS1_uc010mzb.2_Intron|ASS1_uc004bzp.2_Intron|ASS1_uc010mzc.2_Intron	NM_000050	NP_000041	P00966	ASSY_HUMAN	argininosuccinate synthetase 1						arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	CTGGCTCCCTGGTGGAAGGGA	0.602													4	2	---	---	---	---	
SNAPC4	6621	broad.mit.edu	37	9	139277995	139277997	+	In_Frame_Del	DEL	GCT	-	-	rs35266724		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139277995_139277997delGCT	uc004chh.2	-	15	1633_1635	c.1624_1626delAGC	c.(1624-1626)AGCdel	p.S542del		NM_003086	NP_003077	Q5SXM2	SNPC4_HUMAN	small nuclear RNA activating complex,	542					snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter	snRNA-activating protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		CGTCCTCCTCgctgctgctgctg	0.473													7	6	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140563828	140563829	+	Intron	INS	-	CAC	CAC	rs55818410		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140563828_140563829insCAC	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GCACGTGCACTGGACTCCACCC	0.653													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3690919	3690919	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3690919delC	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																		cacacacatacCCATGTGTGC	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3994294	3994294	+	IGR	DEL	C	-	-	rs60125473		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3994294delC								KLF6 (166821 upstream) : LOC100216001 (627150 downstream)																							AACTCTCTAACTCTACCACGG	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	5348627	5348634	+	IGR	DEL	GACATGCT	-	-	rs61072920		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5348627_5348634delGACATGCT								AKR1C4 (87717 upstream) : UCN3 (58342 downstream)																							TGTAACTGTGGACATGCTGAGCTCGAAG	0.288													4	2	---	---	---	---	
TAF3	83860	broad.mit.edu	37	10	7877292	7877293	+	Intron	INS	-	G	G	rs140987167	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7877292_7877293insG	uc010qbd.1	+							NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140						maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						ggctgtgggttgacaagcttgC	0.203													3	3	---	---	---	---	
SEPHS1	22929	broad.mit.edu	37	10	13368551	13368551	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13368551delT	uc001imk.2	-						SEPHS1_uc001imh.2_Intron|SEPHS1_uc010qbs.1_Intron|SEPHS1_uc001imi.2_Intron|SEPHS1_uc001imj.2_Intron|SEPHS1_uc010qbt.1_Intron	NM_012247	NP_036379	P49903	SPS1_HUMAN	selenophosphate synthetase 1						protein modification process		ATP binding|GTP binding|selenide, water dikinase activity			skin(1)	1						gatctatAACttttttttttt	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	21060570	21060570	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21060570delT								PLXDC2 (491455 upstream) : NEBL (8335 downstream)																							tgtgactatatttggagatac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	25414896	25414896	+	IGR	DEL	A	-	-	rs72468077		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25414896delA								ENKUR (63688 upstream) : LOC100128811 (32105 downstream)																							CCCCCCAACCAAAAAAAAAAA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29070221	29070221	+	IGR	DEL	G	-	-	rs36093774		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29070221delG								BAMBI (98353 upstream) : LYZL1 (507769 downstream)																							ccttccttttgtaaggaccct	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30792135	30792135	+	IGR	DEL	T	-	-	rs146806991		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30792135delT								MAP3K8 (41374 upstream) : LYZL2 (108574 downstream)																							CCAGTAAttcttttttttttt	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30978028	30978029	+	IGR	DEL	TG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30978028_30978029delTG								LYZL2 (59381 upstream) : ZNF438 (155538 downstream)																							ACGTGTGAAATGTGTGTGTGTG	0.470													3	3	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	35058401	35058401	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35058401delT	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				ATTACTGTAATTTTTTTTTTC	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37070263	37070265	+	IGR	DEL	TTG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37070263_37070265delTTG								None (None upstream) : ANKRD30A (344520 downstream)																							ATTAAGAAAtttgtttttttttt	0.138													2	5	---	---	---	---	
ANKRD30A	91074	broad.mit.edu	37	10	37418691	37418693	+	Intron	DEL	AGG	-	-	rs72246787		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37418691_37418693delAGG	uc001iza.1	+							NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						TACTTTCTTCAGGAGAATATTAA	0.241													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	39151351	39151360	+	IGR	DEL	AGAATGGAAT	-	-	rs148944743		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39151351_39151360delAGAATGGAAT								LOC399744 (410271 upstream) : None (None downstream)																							tgaatggaacagaatggaatggaatggaat	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42747512	42747513	+	IGR	INS	-	A	A	rs143876906		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42747512_42747513insA								None (None upstream) : LOC441666 (79802 downstream)																							ttcttttatttttttttttttt	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44853208	44853209	+	IGR	INS	-	T	T	rs146673492	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44853208_44853209insT								HNRNPA3P1 (567343 upstream) : CXCL12 (12398 downstream)																							CTTTTACTAGATTTTTTTTTTC	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46977838	46977839	+	IGR	INS	-	A	A	rs146963725		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46977838_46977839insA								SYT15 (7237 upstream) : GPRIN2 (15707 downstream)																							aagggaacaagaaaagggatgc	0.000													4	3	---	---	---	---	
PPYR1	5540	broad.mit.edu	37	10	47083740	47083740	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47083740delA	uc001jee.2	+						ANXA8_uc001jed.3_Intron|PPYR1_uc009xna.2_Intron	NM_005972	NP_005963	P50391	NPY4R_HUMAN	pancreatic polypeptide receptor 1						blood circulation|digestion|feeding behavior	integral to plasma membrane				ovary(1)|skin(1)	2						CCAAGGAGGTAAGGGGTGCAT	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	47590582	47590582	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47590582delT								FAM35B2 (169346 upstream) : ANTXRL (67652 downstream)																							TCAATGTTCCTTTTAGATCAC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	55099101	55099101	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55099101delA								MBL2 (567641 upstream) : PCDH15 (463434 downstream)																							ttgtgcttccaaatcctcctg	0.000													3	3	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	55763858	55763859	+	Intron	INS	-	AAAAACCC	AAAAACCC	rs138414279	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55763858_55763859insAAAAACCC	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				tctttcatgataaaaaccctca	0.000										HNSCC(58;0.16)			3	3	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	55951777	55951777	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55951777delA	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				agagagaaagaaaaaaataat	0.005										HNSCC(58;0.16)			1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	61144632	61144633	+	IGR	DEL	TG	-	-	rs71745331		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61144632_61144633delTG								FAM13C (21971 upstream) : SLC16A9 (265889 downstream)																							ccactgtgtatgtgtgtgtgtg	0.000													5	3	---	---	---	---	
SLC16A9	220963	broad.mit.edu	37	10	61432365	61432366	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61432365_61432366insT	uc010qig.1	-							NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid						urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						CACTGGGCAGGTTTTTTTCACT	0.371													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	63266539	63266539	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63266539delA								TMEM26 (53331 upstream) : C10orf107 (156180 downstream)																							acttaaaattaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65265706	65265706	+	IGR	DEL	A	-	-	rs35048644		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65265706delA								LOC84989 (39386 upstream) : REEP3 (15417 downstream)																							TCCCCCTGCCAAAATTTAGTC	0.408													4	2	---	---	---	---	
NODAL	4838	broad.mit.edu	37	10	72194640	72194642	+	Intron	DEL	AGA	-	-	rs3838763		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72194640_72194642delAGA	uc001jrc.2	-							NM_018055	NP_060525	Q96S42	NODAL_HUMAN	nodal precursor						growth	extracellular space	cytokine activity|growth factor activity			large_intestine(1)|kidney(1)	2						gaagcttgagagaataagcaacc	0.000													3	4	---	---	---	---	
ADAMTS14	140766	broad.mit.edu	37	10	72474729	72474729	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72474729delG	uc001jrh.2	+						ADAMTS14_uc001jrg.2_Intron	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6						aaaaaaaaaagaaaCAAAACC	0.199													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85320982	85320983	+	IGR	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85320982_85320983delAC								NRG3 (574047 upstream) : GHITM (578202 downstream)																							CATCTCTAAAACACACACACAC	0.436													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85585254	85585254	+	IGR	DEL	G	-	-	rs5786624		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85585254delG								NRG3 (838319 upstream) : GHITM (313931 downstream)																							GAAGCAAAGTGGGGCTGGCAC	0.532													1	5	---	---	---	---	
KIF20B	9585	broad.mit.edu	37	10	91469973	91469973	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91469973delT	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						CGTATTGCTGttttttttttt	0.144													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	105010823	105010831	+	Intron	DEL	CACCACGAT	-	-	rs140015106	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105010823_105010831delCACCACGAT	uc001kwr.2	-											Homo sapiens, clone IMAGE:5199023, mRNA.																		tcaccacctccaccacgatcaccaccacc	0.000													4	2	---	---	---	---	
SORCS1	114815	broad.mit.edu	37	10	108756378	108756379	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108756378_108756379insA	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TTCGTCGTACCAAAAAAATCAG	0.411													4	2	---	---	---	---	
TACC2	10579	broad.mit.edu	37	10	123911190	123911191	+	Intron	INS	-	T	T	rs146685929	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123911190_123911191insT	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron|TACC2_uc001lfx.2_Intron|TACC2_uc001lfy.2_Intron	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing							microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				gaggaggagggtgggtggagga	0.069													2	6	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127592169	127592170	+	Intron	INS	-	G	G	rs74316414		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127592169_127592170insG	uc001ljh.3	+						FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				gaagctgaggcggggggactgc	0.198													5	3	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127615446	127615447	+	Intron	INS	-	C	C	rs148348150		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127615446_127615447insC	uc001ljh.3	+						FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				CTCATACTTAATTTtttttatt	0.050													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134329523	134329523	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134329523delG	uc001lln.2	-											Homo sapiens full length insert cDNA clone ZB55F04.																		TGCTTGCAAAGGGGACAGTGC	0.632													4	2	---	---	---	---	
ODF3	113746	broad.mit.edu	37	11	194745	194746	+	5'Flank	INS	-	CTCG	CTCG	rs143574295		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:194745_194746insCTCG	uc001lob.2	+						ODF3_uc010qvk.1_5'Flank|ODF3_uc001loc.2_5'Flank	NM_053280	NP_444510	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm				ovary(1)	1		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCAGGAACACAGGGCCACAGCC	0.559													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	3510578	3510578	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3510578delT								LOC650368 (80200 upstream) : TRPC2 (127884 downstream)																							ACAGTACTGCTTTTTTTTTTT	0.443													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	18953243	18953243	+	IGR	DEL	A	-	-	rs71443724		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18953243delA								PTPN5 (139854 upstream) : MRGPRX1 (2118 downstream)																							ggtagaagagaaagaggtgag	0.214													1	5	---	---	---	---	
TSPAN18	90139	broad.mit.edu	37	11	44933580	44933580	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44933580delT	uc001mye.3	+						TP53I11_uc001myf.1_Intron|TSPAN18_uc001myg.2_Intron	NM_130783	NP_570139	Q96SJ8	TSN18_HUMAN	tetraspanin 18 isoform 2							integral to membrane					0						atctctgtccttttttttttc	0.070													4	2	---	---	---	---	
SLC35C1	55343	broad.mit.edu	37	11	45832809	45832810	+	Frame_Shift_Ins	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45832809_45832810insT	uc001nbp.2	+	2	1730_1731	c.1018_1019insT	c.(1018-1020)GTCfs	p.V340fs	SLC35C1_uc001nbo.2_Frame_Shift_Ins_p.V327fs|SLC35C1_uc010rgm.1_Frame_Shift_Ins_p.V327fs	NM_018389	NP_060859	Q96A29	FUCT1_HUMAN	GDP-fucose transporter 1 isoform a	340						Golgi membrane|integral to membrane	GDP-fucose transmembrane transporter activity				0				GBM - Glioblastoma multiforme(35;0.227)		CTACACCTGGGTCAGGGGCTGG	0.634													2	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48765264	48765264	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48765264delT								OR4A47 (253992 upstream) : FOLH1 (402924 downstream)																							caaaagaaagtttcaactctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50779833	50779833	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50779833delG								LOC646813 (400030 upstream) : OR4A5 (631615 downstream)																							gtggacatttggagtgctttg	0.000													4	2	---	---	---	---	
SSRP1	6749	broad.mit.edu	37	11	57094048	57094049	+	Intron	INS	-	CAGCGC	CAGCGC			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57094048_57094049insCAGCGC	uc001njt.2	-						TNKS1BP1_uc001njs.2_5'Flank|TNKS1BP1_uc009ymd.1_5'Flank	NM_003146	NP_003137	Q08945	SSRP1_HUMAN	structure specific recognition protein 1						DNA repair|DNA replication|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|cytoplasm|nucleoplasm	DNA binding|protein binding			ovary(2)	2						GCCCCCAACTACAGCACCCCCC	0.559													5	7	---	---	---	---	
MS4A10	341116	broad.mit.edu	37	11	60563177	60563177	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60563177delG	uc001npz.1	+							NM_206893	NP_996776	Q96PG2	M4A10_HUMAN	membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity			ovary(1)|skin(1)	2						GACAAAAAATGGGGGCATGAG	0.522													8	4	---	---	---	---	
FEN1	2237	broad.mit.edu	37	11	61560188	61560188	+	5'UTR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61560188delC	uc001nsg.2	+	1					C11orf10_uc001nsf.2_5'Flank|MIR611_hsa-mir-611|MI0003624_5'Flank	NM_004111	NP_004102	P39748	FEN1_HUMAN	flap structure-specific endonuclease 1						base-excision repair|DNA replication, removal of RNA primer|double-strand break repair|phosphatidylinositol-mediated signaling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|UV protection	mitochondrion|nucleolus|nucleoplasm	5'-3' exonuclease activity|5'-flap endonuclease activity|damaged DNA binding|double-stranded DNA binding|double-stranded DNA specific exodeoxyribonuclease activity|metal ion binding|protein binding|ribonuclease H activity			ovary(1)	1						CAGGGGCCTGCGGGGACCTGG	0.622								Direct_reversal_of_damage|Editing_and_processing_nucleases					4	2	---	---	---	---	
RTN3	10313	broad.mit.edu	37	11	63523791	63523791	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63523791delT	uc001nxq.2	+						RTN3_uc001nxo.2_Intron|RTN3_uc001nxm.2_Intron|RTN3_uc001nxn.2_Intron|RTN3_uc001nxp.2_Intron|RTN3_uc009yov.2_Intron|RTN3_uc010rmt.1_Intron|RTN3_uc010rmu.1_Intron	NM_201428	NP_958831	O95197	RTN3_HUMAN	reticulon 3 isoform b						apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1						CTAAAAATTATTATAGCTGCT	0.254													4	2	---	---	---	---	
CTSF	8722	broad.mit.edu	37	11	66337389	66337389	+	5'Flank	DEL	A	-	-	rs11344495		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66337389delA	uc001oip.2	-							NM_003793	NP_003784	Q9UBX1	CATF_HUMAN	cathepsin F precursor						proteolysis	lysosome	cysteine-type endopeptidase activity				0						actccatctcaaaaaaaaaaa	0.000													2	4	---	---	---	---	
CORO1B	57175	broad.mit.edu	37	11	67207355	67207355	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67207355delC	uc001olj.1	-						PTPRCAP_uc001oli.1_5'Flank|CORO1B_uc009yrs.1_Intron|CORO1B_uc001olk.1_Intron|CORO1B_uc009yrt.1_Intron|CORO1B_uc009yru.1_Intron|CORO1B_uc001oll.1_Intron	NM_020441	NP_065174	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm	actin filament binding			large_intestine(1)|ovary(1)	2			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			ACCCTCACCGCCCCCCCCACC	0.637													4	2	---	---	---	---	
CORO1B	57175	broad.mit.edu	37	11	67209168	67209169	+	Intron	DEL	GG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67209168_67209169delGG	uc001olj.1	-						CORO1B_uc009yrs.1_Intron|CORO1B_uc001olk.1_Intron|CORO1B_uc009yrt.1_Intron|CORO1B_uc009yru.1_Intron|CORO1B_uc001oll.1_Intron|CORO1B_uc010rps.1_Intron|CORO1B_uc009yrv.1_Frame_Shift_Del_p.P163fs	NM_020441	NP_065174	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm	actin filament binding			large_intestine(1)|ovary(1)	2			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			AGGGGTCCGTGGGGGGGGGGAG	0.475													4	2	---	---	---	---	
MRPL48	51642	broad.mit.edu	37	11	73542264	73542264	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73542264delG	uc001ouh.3	+						MRPL48_uc009ytt.2_Intron|MRPL48_uc010rri.1_Intron|MRPL48_uc009ytu.2_Intron	NM_016055	NP_057139	Q96GC5	RM48_HUMAN	mitochondrial ribosomal protein L48 precursor						translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0						CCTTGTCCTTGATGCTTTTTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	87130233	87130234	+	IGR	INS	-	A	A	rs36107308		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87130233_87130234insA								TMEM135 (95665 upstream) : RAB38 (716197 downstream)																							gactccgtctcaaaaaaaaaaa	0.158													4	2	---	---	---	---	
GUCY1A2	2977	broad.mit.edu	37	11	106849403	106849403	+	Frame_Shift_Del	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106849403delG	uc001pjg.1	-	3	819	c.429delC	c.(427-429)TCCfs	p.S143fs	GUCY1A2_uc010rvo.1_Frame_Shift_Del_p.S143fs|GUCY1A2_uc009yxn.1_Frame_Shift_Del_p.S143fs	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	143					intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)		CTTCTTTGTTGGAGTGGTCTG	0.323													10	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107085891	107085892	+	IGR	INS	-	CACACA	CACACA	rs11212084		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107085891_107085892insCACACA								GUCY1A2 (196720 upstream) : CWF19L2 (111182 downstream)																							acacacacattcacacacacac	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	122860408	122860409	+	IGR	INS	-	TGATGA	TGATGA	rs143836978	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122860408_122860409insTGATGA								BSX (8029 upstream) : LOC341056 (27865 downstream)																							gatgatggtggtggtggtgatg	0.054													4	2	---	---	---	---	
B4GALNT3	283358	broad.mit.edu	37	12	640476	640486	+	Intron	DEL	CCACTGCTGGC	-	-	rs11267447		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:640476_640486delCCACTGCTGGC	uc001qii.1	+							NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			TGCCATACTGccactgctggcccactgctgg	0.246													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4063135	4063135	+	IGR	DEL	T	-	-	rs68033519		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4063135delT								PARP11 (80527 upstream) : CCND2 (319767 downstream)																							tttctttttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	10392018	10392021	+	IGR	DEL	TCCA	-	-	rs36153976	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10392018_10392021delTCCA								GABARAPL1 (16296 upstream) : KLRD1 (65029 downstream)																							cttccttctttccatccttccttc	0.191													4	2	---	---	---	---	
ETV6	2120	broad.mit.edu	37	12	11835084	11835084	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11835084delC	uc001qzz.2	+							NM_001987	NP_001978	P41212	ETV6_HUMAN	ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				gccgcactgtccacaatggtt	0.000			T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								4	3	---	---	---	---	
STRAP	11171	broad.mit.edu	37	12	16050648	16050648	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16050648delT	uc001rdc.3	+						STRAP_uc010shw.1_Intron|STRAP_uc001rdd.3_Intron	NM_007178	NP_009109	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated						mRNA processing|RNA splicing	cell junction|mitochondrion|spliceosomal complex	identical protein binding			skin(1)	1		Hepatocellular(102;0.121)				ATCCATTTGATTTTTTTTTTT	0.338													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	17102215	17102216	+	IGR	DEL	AC	-	-	rs10547834		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17102215_17102216delAC								LMO3 (339457 upstream) : None (None downstream)																							GCACTTacatacacacacacac	0.272													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	20007152	20007153	+	IGR	INS	-	A	A	rs140488761	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20007152_20007153insA								AEBP2 (331979 upstream) : PDE3A (515044 downstream)																							GAAAAAGATTGAAAAATCACTA	0.297													2	4	---	---	---	---	
SLCO1A2	6579	broad.mit.edu	37	12	21500594	21500595	+	Intron	INS	-	GAAA	GAAA	rs68101904		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21500594_21500595insGAAA	uc001res.2	-						SLCO1A2_uc010siq.1_Intron	NM_134431	NP_602307	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A						bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						aaggaaagaagaaagaaagaaa	0.050													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	21569291	21569292	+	IGR	DEL	CA	-	-	rs143508542		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21569291_21569292delCA								SLCO1A2 (20920 upstream) : PYROXD1 (21246 downstream)																							GAATCTCGGGcacacacacaca	0.312													4	2	---	---	---	---	
H3F3C	440093	broad.mit.edu	37	12	31945016	31945016	+	Frame_Shift_Del	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31945016delT	uc001rkr.2	-	1	160	c.85delA	c.(85-87)AGCfs	p.S29fs		NM_001013699	NP_001013721	Q6NXT2	H3C_HUMAN	histone H3-like	29					nucleosome assembly	nucleosome|nucleus	DNA binding				0						GAGGGGGTGCTTTTCCTGGCA	0.587										HNSCC(67;0.2)			32	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34346529	34346530	+	IGR	DEL	TG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34346529_34346530delTG								ALG10 (165295 upstream) : None (None downstream)																							agtgtgtgcatgtgtgtgtgtg	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34464839	34464840	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34464839_34464840insT								ALG10 (283605 upstream) : None (None downstream)																							gttccacgccgttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	43262768	43262769	+	IGR	DEL	GA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43262768_43262769delGA								PRICKLE1 (279196 upstream) : ADAMTS20 (485244 downstream)																							GTTCGAAACTGagagagagaga	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	43719460	43719461	+	IGR	INS	-	A	A	rs150696919	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43719460_43719461insA								PRICKLE1 (735888 upstream) : ADAMTS20 (28552 downstream)																							tcaacaatttcgatggctcagt	0.223													3	3	---	---	---	---	
KRT8	3856	broad.mit.edu	37	12	53320721	53320724	+	Intron	DEL	TGAA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53320721_53320724delTGAA	uc009zml.1	-						KRT8_uc009zmk.1_5'Flank|KRT8_uc009zmm.1_Intron	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8						cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TTTGATTCACtgaatgaatgaatg	0.368													4	2	---	---	---	---	
KRT8	3856	broad.mit.edu	37	12	53331472	53331472	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53331472delA	uc009zml.1	-						KRT8_uc009zmm.1_Intron	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8						cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	actctgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
ATF7	11016	broad.mit.edu	37	12	53903826	53903827	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53903826_53903827insT	uc010sok.1	-						NPFF_uc001sdw.1_5'Flank	NM_001130059		P17544	ATF7_HUMAN	activating transcription factor 7 isoform 1						interspecies interaction between organisms	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2						GTAGttttatcttttttttttt	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	59036722	59036723	+	Intron	INS	-	A	A	rs143347658	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59036722_59036723insA	uc001sqq.1	-											Homo sapiens cDNA FLJ35805 fis, clone TESTI2005982.																		aaacaaacaacaaaaaaacttt	0.064													4	2	---	---	---	---	
FAM19A2	338811	broad.mit.edu	37	12	62254402	62254403	+	Intron	INS	-	T	T	rs138037715	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62254402_62254403insT	uc001sqw.2	-						FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		ttgctctctgctctccagtcac	0.045													4	4	---	---	---	---	
MON2	23041	broad.mit.edu	37	12	62909269	62909269	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62909269delA	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srf.2_Intron	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		agttagtgttaagtgggtata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	66733084	66733084	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66733084delT								HELB (1092 upstream) : GRIP1 (8140 downstream)																							attttagaacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68639449	68639450	+	IGR	INS	-	C	C	rs148561529	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68639449_68639450insC								IL26 (19878 upstream) : IL22 (2575 downstream)																							agcaccccagacttcacagtgt	0.000													4	2	---	---	---	---	
TSPAN8	7103	broad.mit.edu	37	12	71572816	71572816	+	Intron	DEL	A	-	-	rs35903658		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71572816delA	uc001swk.1	-							NM_004616	NP_004607	P19075	TSN8_HUMAN	transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)			actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76991648	76991648	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76991648delA								OSBPL8 (38059 upstream) : ZDHHC17 (166206 downstream)																							TCTGAAGATCAAAGTGTGGAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92880120	92880120	+	IGR	DEL	A	-	-	rs72469951		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92880120delA								CLLU1 (2664 upstream) : C12orf74 (216720 downstream)																							AATGCAAGGGAAAAAAAAAAA	0.318													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	94030790	94030791	+	IGR	DEL	TC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94030790_94030791delTC								SOCS2 (60812 upstream) : CRADD (40360 downstream)																							TTTTGTTTTTTCTCTTTGGGCT	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	95749358	95749359	+	IGR	DEL	AG	-	-	rs112156933		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95749358_95749359delAG								MIR331 (47069 upstream) : METAP2 (118463 downstream)																							agaaaaagaaagagaaagaaag	0.094													5	3	---	---	---	---	
USP44	84101	broad.mit.edu	37	12	95929038	95929038	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95929038delG	uc001teg.2	-						USP44_uc001teh.2_Intron|USP44_uc009zte.2_Intron	NM_001042403	NP_001035862	Q9H0E7	UBP44_HUMAN	ubiquitin thiolesterase 44						anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)|breast(1)|central_nervous_system(1)	3						tctgacacatggtaaatggta	0.095													4	2	---	---	---	---	
ANO4	121601	broad.mit.edu	37	12	101382052	101382053	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101382052_101382053insA	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.2_Intron|ANO4_uc001thx.2_Intron	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						TGAGGAACTGCAAAAATGAAAG	0.470										HNSCC(74;0.22)	OREG0022059	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
KIAA1033	23325	broad.mit.edu	37	12	105540161	105540162	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105540161_105540162insT	uc001tld.2	+						KIAA1033_uc010swr.1_Intron|KIAA1033_uc010sws.1_Intron	NM_015275	NP_056090	Q2M389	WAHS7_HUMAN	hypothetical protein LOC23325						endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2						ATAAGTCATTATGCTGATACAA	0.238													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106591995	106591996	+	IGR	DEL	GC	-	-	rs150260747		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106591995_106591996delGC								NUAK1 (58184 upstream) : CKAP4 (39664 downstream)																							ggaaagggaaGcacacacacac	0.144													3	4	---	---	---	---	
POLR3B	55703	broad.mit.edu	37	12	106799317	106799318	+	Intron	INS	-	AC	AC	rs72438243		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106799317_106799318insAC	uc001tlp.2	+						POLR3B_uc001tlq.2_Intron	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2						gctatatgtctacacacacaca	0.035													3	3	---	---	---	---	
CUX2	23316	broad.mit.edu	37	12	111499019	111499020	+	Intron	INS	-	AA	AA			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111499019_111499020insAA	uc001tsa.1	+							NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						cacacacacacaGCAAGGAGGA	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112367439	112367440	+	IGR	INS	-	G	G	rs10161310	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112367439_112367440insG								MAPKAPK5 (36212 upstream) : TMEM116 (1663 downstream)																							aaggaaagaaagaaggaaggaa	0.035													4	2	---	---	---	---	
C12orf51	283450	broad.mit.edu	37	12	112685781	112685782	+	Intron	INS	-	AC	AC	rs151176253	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112685781_112685782insAC	uc009zwc.2	-							NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						TTATTTTACCTacacacacaca	0.272													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119387284	119387286	+	IGR	DEL	TTG	-	-	rs71683399		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119387284_119387286delTTG								SUDS3 (531445 upstream) : SRRM4 (32110 downstream)																							cacttctcttttgttgttgttgt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	122082592	122082595	+	IGR	DEL	ACTG	-	-	rs34759476		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122082592_122082595delACTG								ORAI1 (2646 upstream) : MORN3 (6699 downstream)																							AGTCACAGACACTGACTGAAGACT	0.201													3	3	---	---	---	---	
TMEM120B	144404	broad.mit.edu	37	12	122172072	122172073	+	Intron	DEL	TG	-	-	rs63043063		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122172072_122172073delTG	uc001ubc.3	+						TMEM120B_uc009zxh.2_Intron	NM_001080825	NP_001074294	A0PK00	T120B_HUMAN	transmembrane protein 120B							integral to membrane					0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		gaggcctgactgtgctctgtga	0.045													3	4	---	---	---	---	
DIABLO	56616	broad.mit.edu	37	12	122699267	122699267	+	Intron	DEL	T	-	-	rs112840220		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122699267delT	uc010tab.1	-						DIABLO_uc010taa.1_Intron|DIABLO_uc010tac.1_Intron|DIABLO_uc010tad.1_Intron|VPS33A_uc001ucc.2_Intron	NM_019887	NP_063940	Q9NR28	DBLOH_HUMAN	diablo isoform 1 precursor						activation of caspase activity by cytochrome c|induction of apoptosis via death domain receptors	CD40 receptor complex|cytosol|internal side of plasma membrane|mitochondrial intermembrane space	protein binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000302)|Epithelial(86;0.00051)|BRCA - Breast invasive adenocarcinoma(302;0.223)		TCCCAGtttcttttttttttc	0.104													4	2	---	---	---	---	
KNTC1	9735	broad.mit.edu	37	12	123028598	123028598	+	Intron	DEL	A	-	-	rs72319360		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123028598delA	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		ctctgtctccaaaaaaaaaaa	0.090													4	4	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	125001339	125001340	+	Intron	INS	-	C	C	rs141032737	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125001339_125001340insC	uc010tay.1	-						NCOR2_uc010taz.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_006312	NP_006303	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 1						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		AATCCCAGGGGCCCCCCACCCT	0.351													3	3	---	---	---	---	
RIMBP2	23504	broad.mit.edu	37	12	131151339	131151350	+	Intron	DEL	GGAGGGAGGAAG	-	-	rs148423387		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131151339_131151350delGGAGGGAGGAAG	uc001uim.2	-									O15034	RIMB2_HUMAN	RecName: Full=RIMS-binding protein 2;          Short=RIM-BP2;							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		agggagggatggagggaggaagggagggagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131962092	131962093	+	IGR	INS	-	ATA	ATA			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131962092_131962093insATA								LOC116437 (264617 upstream) : SFRS8 (233542 downstream)																							tggtaatggtggtggtgatggt	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19276693	19276694	+	IGR	INS	-	A	A	rs144229434	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19276693_19276694insA								None (None upstream) : LOC284232 (131849 downstream)																							CTTAATTCTGCAAAAAAAAAAT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	24042574	24042574	+	5'Flank	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24042574delT	uc001uos.2	+											Homo sapiens mRNA; cDNA DKFZp313E1940 (from clone DKFZp313E1940).																		tccaaaatgattttgatatag	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31984362	31984364	+	IGR	DEL	GGA	-	-	rs5802603		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31984362_31984364delGGA								B3GALTL (77953 upstream) : RXFP2 (329315 downstream)																							caatttcttgggaggaggaggag	0.000													3	3	---	---	---	---	
FRY	10129	broad.mit.edu	37	13	32614858	32614859	+	Intron	INS	-	ACAT	ACAT			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32614858_32614859insACAT	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CTCCAATATGAAGTGCCAGTAT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	38091517	38091517	+	IGR	DEL	T	-	-	rs35357005		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38091517delT								CSNK1A1L (411716 upstream) : POSTN (45203 downstream)																							tctttctttcttttttttttt	0.000													4	2	---	---	---	---	
ENOX1	55068	broad.mit.edu	37	13	44246347	44246347	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44246347delA	uc001uzc.3	-							NM_017993	NP_060463	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		CCTTTGAAGGAAAAAAATGTA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	51135291	51135292	+	Intron	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51135291_51135292delAC	uc001vet.1	+											Homo sapiens mRNA for B-cell neoplasia associated transcript, (BCMS gene), splice variant D, non coding transcript.																		GGATCcacatacacacacacac	0.292													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	51436018	51436018	+	IGR	DEL	C	-	-	rs35110983		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51436018delC								DLEU7 (18133 upstream) : RNASEH2B (47874 downstream)																							gggaacaacacacattagggc	0.000													4	2	---	---	---	---	
PCDH17	27253	broad.mit.edu	37	13	58208948	58208948	+	Frame_Shift_Del	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58208948delG	uc001vhq.1	+	1	3160	c.2268delG	c.(2266-2268)AAGfs	p.K756fs	PCDH17_uc010aec.1_Frame_Shift_Del_p.K756fs	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	756	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		GTGGGGGCAAGGGCAAGAAGA	0.557													27	22	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	65678821	65678821	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65678821delT								None (None upstream) : None (None downstream)																							ttttcatatgttttttggctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75217793	75217793	+	IGR	DEL	G	-	-	rs66585155		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75217793delG								KLF12 (509399 upstream) : LOC647288 (594097 downstream)																							AAAGGCAAAAGGGTGACATTA	0.403													3	3	---	---	---	---	
MYCBP2	23077	broad.mit.edu	37	13	77746340	77746341	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77746340_77746341insT	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		gctgacctgaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	87067065	87067068	+	IGR	DEL	TCTT	-	-	rs149911222		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87067065_87067068delTCTT								SLITRK6 (693582 upstream) : None (None downstream)																							ctctcctctctctttatcttttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	100719621	100719622	+	IGR	DEL	AA	-	-	rs145713923		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100719621_100719622delAA								ZIC2 (80603 upstream) : PCCA (21715 downstream)																							agacagtctcaaaaaaaaaaaa	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106744814	106744814	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106744814delC								DAOA (601432 upstream) : EFNB2 (397284 downstream)																							ggcaccgtctcggctcactgc	0.040													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108475402	108475402	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108475402delG	uc001vql.2	-						uc001vqm.2_Intron	NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						GGCTGACCATGGGAAATGCTG	0.378													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19012414	19012415	+	IGR	DEL	TA	-	-	rs113187065		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19012414_19012415delTA								None (None upstream) : OR11H12 (365179 downstream)																							tgttcaactctatatgagttga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19456335	19456335	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19456335delA								OR11H12 (77763 upstream) : POTEG (97030 downstream)																							ATTTACTGATAAAATAAGCTA	0.254													4	2	---	---	---	---	
MIPOL1	145282	broad.mit.edu	37	14	37979598	37979598	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37979598delT	uc001wuc.2	+						MIPOL1_uc001wub.3_Intron|MIPOL1_uc001wud.2_Intron|MIPOL1_uc010ams.2_Intron|MIPOL1_uc001wue.2_Intron|MIPOL1_uc010amt.2_Intron	NM_138731	NP_620059	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1											ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)		atttttggtgttttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	46509246	46509246	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46509246delT								C14orf106 (786641 upstream) : RPL10L (610976 downstream)																							ttttctgttcttatgtttgtt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57518539	57518539	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57518539delG								OTX2 (241355 upstream) : EXOC5 (150657 downstream)																							ctatgttcatggactacgtcg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	102411997	102411998	+	IGR	DEL	TT	-	-	rs67132128		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102411997_102411998delTT								PPP2R5C (17671 upstream) : DYNC1H1 (18867 downstream)																							CTAAGttttctttttttttttt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20109132	20109133	+	IGR	INS	-	ATG	ATG	rs141158961	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20109132_20109133insATG								None (None upstream) : GOLGA6L6 (627961 downstream)																							gaaatgatgaaatgaaaggatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20441424	20441424	+	IGR	DEL	T	-	-	rs71399652		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20441424delT								None (None upstream) : GOLGA6L6 (295670 downstream)																							tactacctaatttcagaacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20513708	20513712	+	IGR	DEL	CATTT	-	-	rs146275982		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20513708_20513712delCATTT								None (None upstream) : GOLGA6L6 (223382 downstream)																							GCATCCTATCCATTTCATTTCATGA	0.166													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20522572	20522573	+	IGR	INS	-	ATGAA	ATGAA	rs112120163		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20522572_20522573insATGAA								None (None upstream) : GOLGA6L6 (214521 downstream)																							aatgagattagatgaaatgaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20556467	20556467	+	IGR	DEL	A	-	-	rs113687016		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20556467delA								None (None upstream) : GOLGA6L6 (180627 downstream)																							ATGTGGGGGGAAACCCACACC	0.607													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20575385	20575386	+	IGR	INS	-	CT	CT	rs141924526	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20575385_20575386insCT								None (None upstream) : GOLGA6L6 (161708 downstream)																							ATAGCTTATGACTGtaatttat	0.257													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20595617	20595618	+	Intron	INS	-	A	A	rs138187612		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20595617_20595618insA	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																		GGGTTGACAATAAAAAATGTAC	0.203													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20857944	20857947	+	IGR	DEL	TTTA	-	-	rs143320551	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20857944_20857947delTTTA								GOLGA8C (76918 upstream) : BCL8 (12109 downstream)																							agaattcttctttatctaacggtt	0.093													5	3	---	---	---	---	
BCL8	606	broad.mit.edu	37	15	20891274	20891275	+	Intron	DEL	TG	-	-	rs150290313		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20891274_20891275delTG	uc010tze.1	-							NR_027992				RecName: Full=Putative protein BCL8;												0						CAAAATCATTTGTGACAGGCTC	0.312													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21898169	21898169	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21898169delA								NF1P1 (763544 upstream) : LOC646214 (34345 downstream)																							TCCATTAGTTAATTATATTCT	0.323													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21929570	21929571	+	IGR	INS	-	A	A	rs139686724		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21929570_21929571insA								NF1P1 (794945 upstream) : LOC646214 (2943 downstream)																							TTTGATAAAACAAGCCAGTCAC	0.183													13	6	---	---	---	---	
NF1P1	440225	broad.mit.edu	37	15	22148251	22148251	+	5'Flank	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22148251delA	uc010tzs.1	-											Human NF1-related locus DNA in A9 mouse DNA background.												0						ATTAAGATTTACAAGACCCTA	0.353													24	18	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22409693	22409693	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22409693delA								OR4N4 (25878 upstream) : OR4N3P (4009 downstream)																							GAGaagaaagaaaaaaaaata	0.174													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24691975	24691975	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24691975delA								PWRN2 (276880 upstream) : PWRN1 (86864 downstream)																							ATTCTTCAGGAAAAAAAAATC	0.403													4	2	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	33991773	33991773	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33991773delA	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AAGTCTTGAGAAAAAAAATGG	0.368													4	2	---	---	---	---	
TTBK2	146057	broad.mit.edu	37	15	43085437	43085437	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43085437delT	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		ggaataggcgttttttaaaaa	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	58661819	58661820	+	IGR	DEL	TC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58661819_58661820delTC								ALDH1A2 (90357 upstream) : LIPC (40955 downstream)																							Gctttctctttctctctctctc	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62670994	62670997	+	IGR	DEL	AAGG	-	-	rs35967809		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62670994_62670997delAAGG								C2CD4B (213512 upstream) : MGC15885 (258374 downstream)																							gaaggaaagaaaggaaggaaggac	0.044													4	4	---	---	---	---	
CYP1A1	1543	broad.mit.edu	37	15	75013955	75013974	+	Frame_Shift_Del	DEL	ATGTTAATGATCTTCTCATC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75013955_75013974delATGTTAATGATCTTCTCATC	uc002ayp.3	-	3	1032_1051	c.910_929delGATGAGAAGATCATTAACAT	c.(910-930)GATGAGAAGATCATTAACATCfs	p.D304fs	CYP1A1_uc010bjv.2_RNA|CYP1A1_uc010bjw.2_RNA|CYP1A1_uc010bju.2_Frame_Shift_Del_p.D40fs|CYP1A1_uc010bjx.2_Frame_Shift_Del_p.D40fs|CYP1A1_uc002ayq.3_Frame_Shift_Del_p.D304fs|CYP1A1_uc010bjy.2_Frame_Shift_Del_p.D304fs|CYP1A1_uc010bjz.1_Frame_Shift_Del_p.D40fs	NM_000499	NP_000490	P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A,	304_310					cellular lipid metabolic process|drug metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding|vitamin D 24-hydroxylase activity			ovary(2)|breast(2)|pancreas(1)	5					Arsenic trioxide(DB01169)|Benzphetamine(DB00865)|Bleomycin(DB00290)|Chlorzoxazone(DB00356)|Dacarbazine(DB00851)|Dactinomycin(DB00970)|Esomeprazole(DB00736)|Estrone(DB00655)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Ginseng(DB01404)|Granisetron(DB00889)|Ketoconazole(DB01026)|Menadione(DB00170)|Picrotoxin(DB00466)|Primaquine(DB01087)|Quinidine(DB00908)|Quinine(DB00468)|Thiabendazole(DB00730)	GTCCAAGACGATGTTAATGATCTTCTCATCTGACAGCTGG	0.514									Endometrial_Cancer_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia				26	12	---	---	---	---	
SV2B	9899	broad.mit.edu	37	15	91674882	91674882	+	Intron	DEL	A	-	-	rs111276085		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91674882delA	uc010uqv.1	+						SV2B_uc002bqt.2_Intron|SV2B_uc002bqu.3_Intron	NM_014848	NP_055663	Q7L1I2	SV2B_HUMAN	synaptic vesicle protein 2B homolog						neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			aaaaaatttgaaaaAAAAAAA	0.015													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93586488	93586489	+	IGR	INS	-	CGCG	CGCG	rs148729417		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93586488_93586489insCGCG								CHD2 (15252 upstream) : RGMA (148 downstream)																							acaggcacgcacacacacaggc	0.129													4	2	---	---	---	---	
RGMA	56963	broad.mit.edu	37	15	93589938	93589938	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93589938delG	uc002bss.1	-						RGMA_uc002bsq.1_Intron|RGMA_uc010boi.1_Intron|RGMA_uc002bsr.1_Intron|RGMA_uc010urc.1_Intron	NM_020211	NP_064596	Q96B86	RGMA_HUMAN	RGM domain family, member A precursor						axon guidance	anchored to membrane|endoplasmic reticulum|plasma membrane					0	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)			GCTGCTGAAAGGGGTCCCCAA	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	868882	868887	+	IGR	DEL	GTGATG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:868882_868887delGTGATG								PRR25 (5022 upstream) : LMF1 (34748 downstream)																							gaagactgtagtgatggtgatgatga	0.073													4	2	---	---	---	---	
TSC2	7249	broad.mit.edu	37	16	2114697	2114698	+	Intron	INS	-	CTGGGG	CTGGGG	rs139950082	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2114697_2114698insCTGGGG	uc002con.2	+						TSC2_uc010bsd.2_Intron|TSC2_uc002coo.2_Intron|TSC2_uc010uvv.1_Intron|TSC2_uc010uvw.1_Intron|TSC2_uc002cop.2_Intron	NM_000548	NP_000539	P49815	TSC2_HUMAN	tuberous sclerosis 2 isoform 1						cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)				GGAGCCCAGACCTGGGGCTGGG	0.579			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				4	2	---	---	---	---	
DNAH3	55567	broad.mit.edu	37	16	21071096	21071097	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21071096_21071097insA	uc010vbe.1	-							NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		gactccatctcaaaaaaaaaaa	0.173													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	23744531	23744531	+	IGR	DEL	C	-	-	rs67174153		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23744531delC								ERN2 (19710 upstream) : CHP2 (21417 downstream)																							ggtgacagggccaagactcca	0.060													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29139600	29139600	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29139600delA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		TGAAAGAGGGAGGGAGAGACA	0.637													4	2	---	---	---	---	
STX1B	112755	broad.mit.edu	37	16	31000674	31000675	+	3'UTR	INS	-	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31000674_31000675insG	uc010cad.2	-	10						NM_052874	NP_443106	P61266	STX1B_HUMAN	syntaxin 1B						intracellular protein transport|neurotransmitter transport|synaptic transmission	integral to plasma membrane	extracellular-glutamate-gated ion channel activity|SNAP receptor activity				0						GCAGGGAGGAAGGGGGGGGCAG	0.564													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	31058256	31058257	+	IGR	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31058256_31058257insA								STX4 (6772 upstream) : ZNF668 (13915 downstream)																							aactccatctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32399060	32399060	+	IGR	DEL	C	-	-	rs113400643		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32399060delC								HERC2P4 (235186 upstream) : TP53TG3B (285781 downstream)																							caggcacgcaccaccacgcct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33584868	33584872	+	IGR	DEL	TTCAA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33584868_33584872delTTCAA								SLC6A10P (688405 upstream) : MIR1826 (380636 downstream)																							TCTTTAAACCTTCAATTCACTGTTA	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33895711	33895712	+	IGR	INS	-	TGG	TGG			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33895711_33895712insTGG								SLC6A10P (999248 upstream) : MIR1826 (69796 downstream)																							attccattcaatgattccattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33978210	33978211	+	IGR	INS	-	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33978210_33978211insC								MIR1826 (12618 upstream) : UBE2MP1 (425591 downstream)																							gttgaacctttttttggttgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33981946	33981946	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33981946delT								MIR1826 (16354 upstream) : UBE2MP1 (421856 downstream)																							aggcatgtggtgaaaaaggaa	0.000													13	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34181148	34181148	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34181148delT								MIR1826 (215556 upstream) : UBE2MP1 (222654 downstream)																							cattgatttctttttgatgat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34656477	34656477	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34656477delA								LOC283914 (30393 upstream) : LOC146481 (55308 downstream)																							TTCTTCTGTGAAGAATCTGTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46673955	46673956	+	IGR	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46673955_46673956delAC								SHCBP1 (18644 upstream) : VPS35 (19635 downstream)																							gtacacacagacacacacacac	0.079													4	2	---	---	---	---	
RBL2	5934	broad.mit.edu	37	16	53515565	53515565	+	Intron	DEL	T	-	-	rs72027669		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53515565delT	uc002ehi.3	+						RBL2_uc002ehj.2_Intron|RBL2_uc010vgw.1_Intron	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)						cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						gaattactgattttttttttt	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55468333	55468334	+	IGR	INS	-	C	C	rs145896020	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55468333_55468334insC								IRX6 (103662 upstream) : MMP2 (44747 downstream)																							aaacacctgggcaggcaggtga	0.168													1	6	---	---	---	---	
RSPRY1	89970	broad.mit.edu	37	16	57243271	57243272	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57243271_57243272insT	uc002elb.2	+						RSPRY1_uc002elc.2_Intron|RSPRY1_uc002eld.2_Intron	NM_133368	NP_588609	Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1							extracellular region	zinc ion binding			ovary(1)	1						ATTATGTCCTCtttttttttct	0.124													4	2	---	---	---	---	
WWP2	11060	broad.mit.edu	37	16	69856436	69856439	+	Intron	DEL	GTGT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69856436_69856439delGTGT	uc002exu.1	+						WWP2_uc002ext.2_Intron|WWP2_uc002exv.1_Intron	NM_007014	NP_008945	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase						entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6						cctgggtggggtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
SF3B3	23450	broad.mit.edu	37	16	70566260	70566261	+	Intron	INS	-	A	A	rs10524385		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70566260_70566261insA	uc002ezf.2	+							NM_012426	NP_036558	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3						protein complex assembly	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(1)	1		Ovarian(137;0.0694)				cctgtctctccaaaaaaaaaag	0.005													3	4	---	---	---	---	
VAC14	55697	broad.mit.edu	37	16	70773250	70773250	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70773250delG	uc002ezm.2	-						VAC14_uc010cfw.2_Intron|VAC14_uc002ezn.2_Intron|VAC14_uc010cfx.1_Intron	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog						interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)				TCCTGGGGCTGGTGTGGCTGG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74274845	74274845	+	IGR	DEL	A	-	-	rs112916091		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74274845delA								None (None upstream) : PSMD7 (55836 downstream)																							actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
WDR59	79726	broad.mit.edu	37	16	74943867	74943868	+	Intron	INS	-	TT	TT	rs113238843		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74943867_74943868insTT	uc002fdh.1	-						WDR59_uc002fdi.2_Intron|WDR59_uc002fdg.1_Intron	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59											ovary(1)|breast(1)	2						TCTCTGATAGGttttttttttt	0.252													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	85877901	85877913	+	IGR	DEL	TCCCCTTCCTTCC	-	-	rs58567112		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85877901_85877913delTCCCCTTCCTTCC								COX4I1 (37296 upstream) : IRF8 (54861 downstream)																							cttccttccttccccttccttccttcctacctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86560535	86560535	+	IGR	DEL	T	-	-	rs66612482		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86560535delT								FOXF1 (12466 upstream) : MTHFSD (3248 downstream)																							TTTCCACCCCTATCCCATTTT	0.473													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87027612	87027613	+	IGR	INS	-	G	G	rs140153246	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87027612_87027613insG								FOXL1 (412309 upstream) : FBXO31 (335331 downstream)																							cggctgcctttggggagcccaa	0.223													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88864637	88864638	+	IGR	INS	-	TGA	TGA			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88864637_88864638insTGA								FAM38A (13262 upstream) : CDT1 (5548 downstream)																							ggtgaggatggtgatgatgatg	0.000													4	2	---	---	---	---	
C16orf81	283860	broad.mit.edu	37	16	89223966	89223967	+	5'Flank	INS	-	CA	CA	rs143260245	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89223966_89223967insCA	uc002fms.3	+							NR_024347				Homo sapiens cDNA FLJ36701 fis, clone UTERU2009147.												0						tgtatgtgtctcacgcctgcat	0.045													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	89670555	89670555	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89670555delG								CPNE7 (6902 upstream) : DPEP1 (9161 downstream)																							GGGGGCTGGAGGGAAGCACTG	0.726													4	3	---	---	---	---	
DPEP1	1800	broad.mit.edu	37	16	89701030	89701030	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89701030delT	uc010cin.2	+						DPEP1_uc002fnr.3_Intron|DPEP1_uc002fns.3_Intron	NM_001128141	NP_001121613	P16444	DPEP1_HUMAN	dipeptidase 1 precursor						proteolysis	anchored to membrane|apical plasma membrane|microvillus membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity|protein binding			large_intestine(1)	1		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)	cCCttccttctcctttccctt	0.025													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	9654898	9654898	+	IGR	DEL	T	-	-	rs111418397		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9654898delT								USP43 (21897 upstream) : DHRS7C (19858 downstream)																							AGAGCTGttcttttttttttt	0.214													1	5	---	---	---	---	
C17orf48	56985	broad.mit.edu	37	17	10605036	10605036	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10605036delT	uc002gmt.2	+						C17orf48_uc002gmu.2_Intron|C17orf48_uc002gmv.2_Intron	NM_020233	NP_064618	Q3LIE5	ADPRM_HUMAN	ADP-ribose/CDP-alcohol pyrophosphatase								ADP-ribose diphosphatase activity|CDP-glycerol diphosphatase activity|metal ion binding				0						TACTCACTGATTTTTTTGTGT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	19896886	19896887	+	IGR	INS	-	TTTCT	TTTCT	rs143329929	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19896886_19896887insTTTCT								AKAP10 (15757 upstream) : CYTSB (15727 downstream)																							ctctttctttctttcttttctt	0.020													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20951658	20951658	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20951658delC								USP22 (4585 upstream) : DHRS7B (78600 downstream)																							aaattccaagcagccaaacta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21225356	21225356	+	IGR	DEL	G	-	-	rs66917376		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21225356delG								MAP2K3 (6807 upstream) : KCNJ12 (54343 downstream)																							CTGCTGGGGTGGGGGTATTGC	0.597													9	5	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21305833	21305838	+	Intron	DEL	GGGGCA	-	-	rs34207186		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21305833_21305838delGGGGCA	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	AATGGGGCCTGGGGCAGAGCGATAGG	0.587										Prostate(3;0.18)			5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21563644	21563646	+	IGR	DEL	AAT	-	-	rs113960374	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21563644_21563646delAAT								C17orf51 (85913 upstream) : FAM27L (261724 downstream)																							TTTCCAAAAAAATAAAAGGATAG	0.360													8	4	---	---	---	---	
FAM27L	284123	broad.mit.edu	37	17	21825841	21825842	+	Intron	DEL	TG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21825841_21825842delTG	uc002gyz.2	+							NR_028336				Homo sapiens family with sequence similarity 27-like, mRNA (cDNA clone MGC:35151 IMAGE:5169482), complete cds.												0				UCEC - Uterine corpus endometrioid carcinoma (53;0.11)|BRCA - Breast invasive adenocarcinoma(1;0.00463)		tcggtttgtatgtgtgtgtgtg	0.233													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25297755	25297756	+	IGR	INS	-	GA	GA	rs74789093		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25297755_25297756insGA								None (None upstream) : WSB1 (323350 downstream)																							tgtgtgtgtgtgagagtgtgtg	0.025													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25299254	25299256	+	IGR	DEL	CTT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25299254_25299256delCTT								None (None upstream) : WSB1 (321850 downstream)																							tcccagttgccttcttctatgag	0.000													5	4	---	---	---	---	
NF1	4763	broad.mit.edu	37	17	29637959	29637959	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29637959delT	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron|NF1_uc010cso.2_Intron|EVI2B_uc002hgk.2_Intron|EVI2B_uc010csq.2_Intron	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AGACATGttcttttttttttt	0.114			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			3	3	---	---	---	---	
LRRC37B	114659	broad.mit.edu	37	17	30343496	30343496	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30343496delA	uc010wbx.1	+							NM_052888	NP_443120	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B precursor							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				ATCCTGTTGTAATCGTGCCTC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39629879	39629879	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39629879delA								KRT32 (6241 upstream) : KRT35 (3063 downstream)																							actccgtctcaaaaaaaaaaa	0.209													4	2	---	---	---	---	
ATP6V0A1	535	broad.mit.edu	37	17	40626025	40626025	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40626025delT	uc002hzr.2	+						ATP6V0A1_uc002hzq.2_Intron|ATP6V0A1_uc002hzs.2_Intron|ATP6V0A1_uc010wgj.1_Intron|ATP6V0A1_uc010wgk.1_Intron|ATP6V0A1_uc010cyg.2_Intron|ATP6V0A1_uc010wgl.1_Intron	NM_001130021	NP_001123493	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytoplasmic vesicle membrane|endosome membrane|Golgi apparatus|integral to membrane|melanosome|nucleus|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		CCCTCTCCTAttttttttttt	0.199													4	2	---	---	---	---	
G6PC	2538	broad.mit.edu	37	17	41055723	41055723	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41055723delA	uc002icb.1	+						G6PC_uc010whf.1_Intron	NM_000151	NP_000142	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit						gluconeogenesis|glucose homeostasis|transmembrane transport	integral to endoplasmic reticulum membrane	glucose-6-phosphatase activity|phosphate binding			ovary(1)|breast(1)|kidney(1)|skin(1)	4		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		atcctgtctcaaaaaaaaaaa	0.159									Glycogen_Storage_Disease_type_Ia				6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	41433935	41433936	+	IGR	INS	-	C	C	rs143980654	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41433935_41433936insC								TMEM106A (62346 upstream) : LOC100130581 (13277 downstream)																							tcaaggaatagccgaggcagat	0.000													4	2	---	---	---	---	
ARL17B	641522	broad.mit.edu	37	17	44367295	44367295	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44367295delG	uc002ikf.2	-											Homo sapiens full length insert cDNA clone ZD50C03.												0						agagcagcctggccacatggt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	47994366	47994366	+	IGR	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47994366delC								TAC4 (68987 upstream) : DLX4 (52196 downstream)																							ttccatggctccctgttgcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51648481	51648482	+	IGR	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51648481_51648482insA								None (None upstream) : KIF2B (251757 downstream)																							GGGCAACACAGAAAAAAAAATC	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	55259330	55259331	+	IGR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55259330_55259331insT								AKAP1 (60621 upstream) : MSI2 (73881 downstream)																							gtagttttctctttttttttga	0.000													4	2	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	59283627	59283627	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59283627delT	uc002iyv.3	+						BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyy.3_Intron|BCAS3_uc002iyz.3_Intron|BCAS3_uc002iza.3_Intron|BCAS3_uc002izb.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			AACCATTGCCTTATGCACAGG	0.453													4	2	---	---	---	---	
TLK2	11011	broad.mit.edu	37	17	60550365	60550365	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60550365delA	uc002izx.3	+									Q86UE8	TLK2_HUMAN	SubName: Full=Putative uncharacterized protein TLK1; Flags: Fragment;						cell cycle|chromatin modification|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|kidney(1)	2						ACTTACAAGCAAAAAAATAAC	0.468													4	2	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	64183294	64183295	+	Intron	DEL	TC	-	-	rs112685794		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64183294_64183295delTC	uc002jfl.2	-						CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			agcctcatcatctgtctcccta	0.005													2	4	---	---	---	---	
PRKAR1A	5573	broad.mit.edu	37	17	66518742	66518742	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66518742delT	uc002jhg.2	+						PRKAR1A_uc002jhh.2_Intron|PRKAR1A_uc002jhi.2_Intron|PRKAR1A_uc002jhj.2_Intron|PRKAR1A_uc002jhk.2_Intron|PRKAR1A_uc002jhl.2_Intron|PRKAR1A_uc002jhm.2_Intron	NM_212471	NP_997636	P10644	KAP0_HUMAN	cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding			adrenal_gland(4)|lung(3)|thyroid(2)|soft_tissue(2)|breast(1)	12	Breast(10;1.64e-13)					TGTTACTCTCTTTTTTTCCCC	0.358			T|Mis|N|F|S	RET	papillary thyroid	myxoma|endocrine|papillary thyroid			Carney_Complex|Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial|Cardiac_Myxomas_Familial_Clustering_of				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	67865760	67865761	+	IGR	INS	-	AA	AA			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67865760_67865761insAA								MAP2K6 (327298 upstream) : KCNJ16 (205665 downstream)																							aaaggaaaaggaaaaaaaaaaT	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	74648132	74648133	+	IGR	INS	-	AATG	AATG	rs141491864	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74648132_74648133insAATG								ST6GALNAC1 (8238 upstream) : MXRA7 (23676 downstream)																							AGACGAGGAACAATGCAAAGAT	0.351													7	4	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75480920	75480921	+	Intron	INS	-	TGA	TGA	rs146453342	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75480920_75480921insTGA	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron|SEPT9_uc010wtl.1_Intron|SEPT9_uc002jty.3_Intron|SEPT9_uc010wtm.1_Intron|SEPT9_uc010wtn.1_Intron|SEPT9_uc010dhd.2_Intron	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			ggcgatggtggttgtgatggtg	0.000													4	2	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77384084	77384085	+	Intron	DEL	GT	-	-	rs148425512		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77384084_77384085delGT	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			gaatgtgtacgtgtgtgtgtgt	0.099													3	3	---	---	---	---	
TBC1D16	125058	broad.mit.edu	37	17	77988599	77988600	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77988599_77988600insA	uc002jxj.2	-							NM_019020	NP_061893	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16							intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			aagaaaaaaagaaaaaaaaaat	0.277													4	2	---	---	---	---	
BAIAP2	10458	broad.mit.edu	37	17	79048067	79048068	+	Intron	INS	-	GTGCCTGT	GTGCCTGT	rs138162499	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79048067_79048068insGTGCCTGT	uc002jzg.2	+						BAIAP2_uc002jyz.3_Intron|BAIAP2_uc002jza.2_Intron|BAIAP2_uc002jzc.2_Intron|BAIAP2_uc002jzb.2_Intron|BAIAP2_uc002jzd.2_Intron|BAIAP2_uc002jzf.2_Intron|BAIAP2_uc002jze.2_Intron|BAIAP2_uc010wuh.1_Intron	NM_017451	NP_059345	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2 isoform 2						axonogenesis|filopodium assembly|insulin receptor signaling pathway|regulation of actin cytoskeleton organization|response to bacterium	cell junction|cytoskeleton|cytosol|filopodium|nucleus|ruffle	cytoskeletal adaptor activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding				0	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			ggctgaaaaaagtgcctgtgtg	0.000													5	4	---	---	---	---	
TBCD	6904	broad.mit.edu	37	17	80819319	80819319	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80819319delG	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			ATGGATCAGTGGATGGAGAAA	0.483													4	2	---	---	---	---	
METRNL	284207	broad.mit.edu	37	17	81046955	81046956	+	Intron	INS	-	TA	TA	rs148826215		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:81046955_81046956insTA	uc002kgh.2	+						METRNL_uc002kgi.2_Intron	NM_001004431	NP_001004431	Q641Q3	METRL_HUMAN	meteorin, glial cell differentiation							extracellular region					0	Breast(20;0.000443)|all_neural(118;0.0779)		BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			AGGGCAGGGGCTATGGGGCCAA	0.663													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	78556	78556	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:78556delG								None (None upstream) : USP14 (79927 downstream)																							tcaacctttaggggcataaga	0.000													3	3	---	---	---	---	
TYMS	7298	broad.mit.edu	37	18	660442	660442	+	Intron	DEL	A	-	-	rs66567989		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:660442delA	uc010dka.1	+						C18orf56_uc002kkr.2_5'Flank|TYMS_uc010dkb.1_Intron|TYMS_uc010dkc.1_Intron	NM_001071	NP_001062	P04818	TYSY_HUMAN	thymidylate synthase						DNA repair|DNA replication|phosphatidylinositol-mediated signaling|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process|regulation of transcription involved in G1/S phase of mitotic cell cycle|response to organophosphorus	cytosol	thymidylate synthase activity				0					Capecitabine(DB01101)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Leucovorin(DB00650)|Pemetrexed(DB00642)|Raltitrexed(DB00293)|Trifluridine(DB00432)	tagaagggggacagcaggtag	0.000													2	5	---	---	---	---	
YES1	7525	broad.mit.edu	37	18	779910	779910	+	Intron	DEL	T	-	-	rs541436		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:779910delT	uc002kky.2	-						YES1_uc002kkz.2_Intron	NM_005433	NP_005424	P07947	YES_HUMAN	viral oncogene yes-1 homolog 1						blood coagulation|leukocyte migration|regulation of vascular permeability|T cell costimulation	cytosol|plasma membrane	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|ovary(1)	3					Dasatinib(DB01254)	TATGTAGTCCTTTTTTTTTTT	0.214													4	3	---	---	---	---	
PTPRM	5797	broad.mit.edu	37	18	8276091	8276092	+	Intron	DEL	GT	-	-	rs34169991		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8276091_8276092delGT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)				ACCTTTCCAAGTCCTTTAGGTT	0.505													2	5	---	---	---	---	
ZNF521	25925	broad.mit.edu	37	18	22932017	22932017	+	5'UTR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22932017delG	uc002kvk.2	-	1					ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_5'UTR|ZNF521_uc002kvl.2_5'UTR	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					ACATAATAATGGAAAATGGAA	0.488			T	PAX5	ALL								12	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	24770697	24770698	+	IGR	INS	-	GT	GT	rs150860723	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24770697_24770698insGT								C18orf16 (47 upstream) : CDH2 (760232 downstream)																							tgtgcatgtgcgtgtgtgtgtg	0.272													4	2	---	---	---	---	
MEP1B	4225	broad.mit.edu	37	18	29779631	29779632	+	Intron	INS	-	TTCCTTCC	TTCCTTCC	rs71177848		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29779631_29779632insTTCCTTCC	uc002kxj.3	+							NM_005925	NP_005916	Q16820	MEP1B_HUMAN	meprin A beta precursor						digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2						cctttcgttcgttccttccttc	0.074													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	44856592	44856592	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44856592delC	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																		TTCCAAACTTCCTTCTTGGAG	0.493													3	3	---	---	---	---	
CCDC102B	79839	broad.mit.edu	37	18	66480419	66480420	+	Intron	DEL	TC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66480419_66480420delTC	uc002lkk.2	+						CCDC102B_uc002lki.2_Intron	NM_001093729	NP_001087198	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				atttcccacttctctctctctc	0.000													3	3	---	---	---	---	
DOK6	220164	broad.mit.edu	37	18	67072023	67072024	+	Intron	DEL	GT	-	-	rs72398603		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67072023_67072024delGT	uc002lkl.2	+							NM_152721	NP_689934	Q6PKX4	DOK6_HUMAN	docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				GGATAGGGTGgtgtgtgtgtgt	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71838948	71838948	+	IGR	DEL	T	-	-	rs111517640		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71838948delT								C18orf55 (12744 upstream) : CYB5A (81580 downstream)																							ttctcttttctttttttttat	0.234													1	5	---	---	---	---	
CNDP1	84735	broad.mit.edu	37	18	72222729	72222729	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72222729delC	uc002llq.2	+							NM_032649	NP_116038	Q96KN2	CNDP1_HUMAN	carnosinase 1 precursor						proteolysis	extracellular region	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity|tripeptidase activity				0		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		GCTGGCAGCTCCCACTCCAGA	0.637													4	2	---	---	---	---	
ATP9B	374868	broad.mit.edu	37	18	76940741	76940741	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76940741delG	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933	O43861	ATP9B_HUMAN	ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		aaatctgctagagattgtcag	0.000													4	2	---	---	---	---	
GNG7	2788	broad.mit.edu	37	19	2515432	2515432	+	Intron	DEL	T	-	-	rs66486341		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2515432delT	uc002lwd.2	-						GNG7_uc010dte.1_Intron	NM_052847	NP_443079	O60262	GBG7_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		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)		catttctttcttttttttttt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	2897226	2897227	+	IGR	DEL	TT	-	-	rs112679428		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2897226_2897227delTT								ZNF556 (18725 upstream) : ZNF57 (3669 downstream)																							ACTGTGAACAtttttttttttt	0.228													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	4815473	4815476	+	IGR	DEL	TCAT	-	-	rs112626718		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4815473_4815476delTCAT								FEM1A (19904 upstream) : TICAM1 (463 downstream)																							actcgctcactcattcattcattc	0.000													5	3	---	---	---	---	
MLLT1	4298	broad.mit.edu	37	19	6213426	6213427	+	Intron	INS	-	G	G			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6213426_6213427insG	uc002mek.2	-							NM_005934	NP_005925	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|protein binding			skin(1)	1						AGGCCTGGGGAGGGGGGGCAGG	0.678			T	MLL	AL								24	17	---	---	---	---	
SH2D3A	10045	broad.mit.edu	37	19	6762882	6762882	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6762882delC	uc002mft.2	-						SH2D3A_uc010xjg.1_Intron	NM_005490	NP_005481	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A						JNK cascade|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			breast(2)	2						ggtcaaatgtcctgcccaagg	0.010													4	2	---	---	---	---	
DNMT1	1786	broad.mit.edu	37	19	10289998	10289998	+	Intron	DEL	T	-	-	rs112064261		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10289998delT	uc002mng.2	-						DNMT1_uc010xlc.1_Intron|DNMT1_uc002mnh.2_Intron|DNMT1_uc010xld.1_Intron|DNMT1_uc010dxb.1_Intron	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b						chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)	GAAAACAACATTTTTTTTTTT	0.274													2	4	---	---	---	---	
SMARCA4	6597	broad.mit.edu	37	19	11168782	11168783	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11168782_11168783insA	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc010dxq.2_Intron|SMARCA4_uc010dxr.2_Intron|SMARCA4_uc002mqj.3_Intron|SMARCA4_uc010dxs.2_Intron|SMARCA4_uc002mqh.3_Intron	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity			lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				aactccgtctcaaaaaaaaaaa	0.228			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				4	2	---	---	---	---	
ZNF763	284390	broad.mit.edu	37	19	12066212	12066212	+	Intron	DEL	T	-	-	rs113495720		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12066212delT	uc010xmf.1	+							NM_001012753	NP_001012771	Q0D2J5	ZN763_HUMAN	zinc finger protein 763						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1						tctttctttcttttttttttt	0.134													6	3	---	---	---	---	
PKN1	5585	broad.mit.edu	37	19	14571914	14571917	+	Intron	DEL	TATC	-	-	rs144969098		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14571914_14571917delTATC	uc002myp.2	+						PKN1_uc002myq.2_Intron	NM_002741	NP_002732	Q16512	PKN1_HUMAN	protein kinase N1 isoform 2						activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8						ccatctatattatctatctatcat	0.059													4	3	---	---	---	---	
ZNF254	9534	broad.mit.edu	37	19	24241216	24241216	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24241216delT	uc010xrk.1	+						uc002nrr.1_Intron|uc002nrs.1_Intron	NM_203282	NP_975011	O75437	ZN254_HUMAN	zinc finger protein 254						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				tctttctttcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24575195	24575196	+	IGR	INS	-	TTGA	TTGA	rs111495385		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24575195_24575196insTTGA								LOC100101266 (228946 upstream) : None (None downstream)																							tgaaactttctttgagcagttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30653654	30653657	+	IGR	DEL	CATC	-	-	rs72002020		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30653654_30653657delCATC								C19orf2 (147043 upstream) : ZNF536 (209671 downstream)																							ttcatccattcatccatccatcca	0.034													4	2	---	---	---	---	
GRAMD1A	57655	broad.mit.edu	37	19	35509863	35509863	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35509863delA	uc010xse.1	+						GRAMD1A_uc002nxk.2_Intron|GRAMD1A_uc002nxl.2_Intron|GRAMD1A_uc010xsf.1_Intron|GRAMD1A_uc002nxm.1_Intron|GRAMD1A_uc002nxn.1_Intron	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1							integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TCCAATGCTCAGGGCAGAAGC	0.582													4	2	---	---	---	---	
THAP8	199745	broad.mit.edu	37	19	36540151	36540152	+	Intron	INS	-	A	A			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36540151_36540152insA	uc002oda.1	-						THAP8_uc010xtb.1_Intron|THAP8_uc010xtc.1_Intron	NM_152658	NP_689871	Q8NA92	THAP8_HUMAN	THAP domain containing 8								DNA binding|metal ion binding				0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			atgaaaaaaacaaaaaaaaagg	0.000													4	2	---	---	---	---	
ZNF529	57711	broad.mit.edu	37	19	37092081	37092082	+	Intron	INS	-	T	T	rs139807493		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37092081_37092082insT	uc010xth.1	-						ZNF529_uc010xti.1_Intron|ZNF529_uc002oej.2_Intron	NM_001145649	NP_001139121	Q6P280	ZN529_HUMAN	zinc finger protein 529 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	Esophageal squamous(110;0.198)					TACAAGTGTAAttttttttttt	0.198													4	2	---	---	---	---	
DPF1	8193	broad.mit.edu	37	19	38717606	38717607	+	5'Flank	INS	-	TTTCTTTTCTTT	TTTCTTTTCTTT	rs142546029	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38717606_38717607insTTTCTTTTCTTT	uc002ohl.2	-						DPF1_uc002ohm.2_5'Flank|DPF1_uc002ohn.2_Intron|DPF1_uc010xtu.1_Intron|DPF1_uc010xtv.1_Intron|DPF1_uc010xtw.1_Intron	NM_004647	NP_004638	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1 isoform						induction of apoptosis|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nBAF complex	zinc ion binding				0	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			ttctatttttctttcttttctt	0.213													3	3	---	---	---	---	
FCGBP	8857	broad.mit.edu	37	19	40402603	40402603	+	Intron	DEL	C	-	-	rs67912454		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40402603delC	uc002omp.3	-							NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor							extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCAGAGTCCTCATGTCTAGGA	0.363													3	6	---	---	---	---	
AKT2	208	broad.mit.edu	37	19	40763493	40763494	+	Intron	INS	-	AC	AC	rs141698656	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40763493_40763494insAC	uc002onf.2	-						AKT2_uc010egs.2_Intron|AKT2_uc010egt.2_Intron|AKT2_uc010xvj.1_Intron|AKT2_uc010egu.1_Intron|AKT2_uc010xvk.1_Intron	NM_001626	NP_001617	P31751	AKT2_HUMAN	AKT2 kinase						insulin receptor signaling pathway|negative regulation of plasma membrane long-chain fatty acid transport|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2			Lung(22;0.000499)			tatgcacacaaacacacacaca	0.223			A		ovarian|pancreatic 								2	5	---	---	---	---	
ADCK4	79934	broad.mit.edu	37	19	41211838	41211838	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41211838delA	uc002oor.2	-						ADCK4_uc002ooq.1_Intron|ADCK4_uc002oos.2_Intron	NM_024876	NP_079152	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4 isoform a							integral to membrane	protein serine/threonine kinase activity				0			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			ctgtctcgggaaaaaaaaaaa	0.015													4	2	---	---	---	---	
ADCK4	79934	broad.mit.edu	37	19	41221746	41221747	+	Intron	INS	-	TC	TC			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41221746_41221747insTC	uc002oor.2	-						ADCK4_uc002ooq.1_5'Flank|ADCK4_uc002oos.2_Intron|ITPKC_uc002oot.2_5'Flank	NM_024876	NP_079152	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4 isoform a							integral to membrane	protein serine/threonine kinase activity				0			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			CTATCTTTCTTTCTCtgtgtgt	0.470													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	41617198	41617198	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41617198delA								CYP2A13 (15100 upstream) : CYP2F1 (3155 downstream)																							catcacaggtaaattttacct	0.154													4	2	---	---	---	---	
PSG6	5675	broad.mit.edu	37	19	43594726	43594727	+	Intron	DEL	AT	-	-	rs71780530		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43594726_43594727delAT	uc010xwk.1	-									Q00889	PSG6_HUMAN	SubName: Full=Pregnancy-specific beta-1 glycoprotein; Flags: Fragment;						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)				taaatataacatagagaaggtt	0.035													4	2	---	---	---	---	
IRGQ	126298	broad.mit.edu	37	19	44096824	44096826	+	In_Frame_Del	DEL	TCT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44096824_44096826delTCT	uc002oww.2	-	2	1342_1344	c.1224_1226delAGA	c.(1222-1227)TCAGAG>TCG	p.E409del	IRGQ_uc010eiv.2_In_Frame_Del_p.E409del	NM_001007561	NP_001007562	Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	409							protein binding			ovary(1)|pancreas(1)	2		Prostate(69;0.0199)				AGCGGCCCGCTCTGAGTCGCCAC	0.660													65	32	---	---	---	---	
SAE1	10055	broad.mit.edu	37	19	47676025	47676025	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47676025delA	uc002pgc.2	+						SAE1_uc002pgd.2_Intron|SAE1_uc010ekx.2_Intron|SAE1_uc010ekw.2_Intron|SAE1_uc010xyk.1_Intron|SAE1_uc002pge.2_Intron	NM_016402	NP_057486	Q9UBE0	SAE1_HUMAN	SubName: Full=SUMO-1 activating enzyme subunit 1, isoform CRA_b; SubName: Full=cDNA, FLJ96708, Homo sapiens SUMO-1 activating enzyme subunit 1 (SAE1), mRNA;						protein sumoylation|protein ubiquitination	nucleus	ATP-dependent protein binding|enzyme activator activity|ligase activity|protein C-terminus binding|protein heterodimerization activity|ubiquitin activating enzyme activity			ovary(1)	1		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		TGTACACGCCaaaaaaaaaaa	0.224													4	2	---	---	---	---	
LMTK3	114783	broad.mit.edu	37	19	48991996	48991996	+	Intron	DEL	T	-	-	rs35544294		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48991996delT	uc002pjk.2	-							NM_001080434	NP_001073903			lemur tyrosine kinase 3											lung(5)|central_nervous_system(1)	6		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		taaattacacttttttttttt	0.000													3	3	---	---	---	---	
PTH2	113091	broad.mit.edu	37	19	49927508	49927511	+	5'Flank	DEL	TGTC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49927508_49927511delTGTC	uc002pnn.1	-							NM_178449	NP_848544	Q96A98	TIP39_HUMAN	parathyroid hormone 2 preproprotein						neuropeptide signaling pathway	extracellular region					0				OV - Ovarian serous cystadenocarcinoma(262;0.0015)|GBM - Glioblastoma multiforme(486;0.044)|Lung(386;0.0785)|LUSC - Lung squamous cell carcinoma(496;0.0836)		tgtgtgtgtttgtctgtttgagat	0.201													3	3	---	---	---	---	
FAM71E2	284418	broad.mit.edu	37	19	55873276	55873276	+	Intron	DEL	C	-	-	rs55852607		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55873276delC	uc002qkr.2	-						FAM71E2_uc002qkq.2_Intron	NM_001145402	NP_001138874	Q8N5Q1	F71E2_HUMAN	hypothetical protein LOC284418												0						gctcctccgtcagacccagga	0.000													3	3	---	---	---	---	
TMEM190	147744	broad.mit.edu	37	19	55888543	55888544	+	Intron	DEL	GG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55888543_55888544delGG	uc002qkt.1	+							NM_139172	NP_631911	Q8WZ59	TM190_HUMAN	transmembrane protein 190 precursor							integral to membrane					0	Breast(117;0.191)		BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		aggaggggctgggggcctggat	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57465875	57465876	+	IGR	INS	-	TCCT	TCCT	rs150799707	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57465875_57465876insTCCT								MIMT1 (105953 upstream) : USP29 (165633 downstream)																							ttatccattcatccatccatct	0.109													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57519808	57519809	+	IGR	INS	-	TG	TG	rs142805423		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57519808_57519809insTG								MIMT1 (159886 upstream) : USP29 (111700 downstream)																							acacacacacacgcacacacac	0.114													4	2	---	---	---	---	
RPS5	6193	broad.mit.edu	37	19	58905673	58905674	+	Intron	DEL	TG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58905673_58905674delTG	uc002qsn.2	+						RPS5_uc002qso.2_Intron	NM_001009	NP_001000	P46782	RS5_HUMAN	ribosomal protein S5						endocrine pancreas development|regulation of translational fidelity|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	mRNA binding|structural constituent of ribosome				0		all_cancers(17;1.71e-22)|all_epithelial(17;1.69e-16)|Lung NSC(17;2.25e-06)|all_lung(17;9.97e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Breast(46;0.0194)|Ovarian(87;0.0443)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.171)|GBM - Glioblastoma multiforme(193;0.0323)|Lung(386;0.0543)|LUSC - Lung squamous cell carcinoma(496;0.176)		AACTTCAGCCTGTGTGTGTGTG	0.426													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	2046619	2046619	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2046619delA								PDYN (71916 upstream) : STK35 (35909 downstream)																							acttcttctcaaaaaaaaaaa	0.164													3	3	---	---	---	---	
PAK7	57144	broad.mit.edu	37	20	9613907	9613907	+	Intron	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9613907delC	uc002wnl.2	-						PAK7_uc002wnk.2_Intron|PAK7_uc002wnj.2_Intron|PAK7_uc010gby.1_Intron	NM_020341	NP_065074	Q9P286	PAK7_HUMAN	p21-activated kinase 7								ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)			CCATGTGAGTCCCATGCAAAT	0.413													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	9908901	9908902	+	IGR	DEL	GA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9908901_9908902delGA								PAK7 (89214 upstream) : ANKRD5 (106795 downstream)																							ATAGTCTAGTgagagagagaga	0.252													4	2	---	---	---	---	
TASP1	55617	broad.mit.edu	37	20	13327786	13327786	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13327786delA	uc010zri.1	-									Q9H6P5	TASP1_HUMAN	Homo sapiens cDNA FLJ20212 fis, clone COLF1860.						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0						GTTTTTGTTTAAAATGCCTAT	0.393													4	2	---	---	---	---	
BANF2	140836	broad.mit.edu	37	20	17688575	17688575	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17688575delG	uc002wpz.2	+						BANF2_uc010zrs.1_Intron|BANF2_uc002wqa.2_Intron	NM_178477	NP_848572	Q9H503	BAFL_HUMAN	barrier to autointegration factor 2 isoform 1							cytoplasm|nucleus	DNA binding			skin(1)	1						ggctggacacggtgtctcatg	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	21244369	21244371	+	IGR	DEL	AGG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21244369_21244371delAGG								PLK1S1 (17113 upstream) : XRN2 (39571 downstream)																							aaggaggagaaggaggagaagag	0.079													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23181094	23181094	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23181094delA								CD93 (114117 upstream) : NXT1 (150279 downstream)																							TAGACCCAGTAAAAAAAACTA	0.264													2	4	---	---	---	---	
NAPB	63908	broad.mit.edu	37	20	23384241	23384241	+	Intron	DEL	A	-	-	rs71920266		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23384241delA	uc002wta.2	-						NAPB_uc002wtc.2_Intron|NAPB_uc002wtb.2_Intron|NAPB_uc002wtd.3_Intron|NAPB_uc010zst.1_Intron	NM_022080	NP_071363	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment						intracellular protein transport|vesicle-mediated transport	membrane				ovary(1)	1	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					actatgtctcaaaaaaaaaaa	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	24132206	24132207	+	IGR	INS	-	T	T	rs143819599	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24132206_24132207insT								GGTLC1 (162790 upstream) : TMEM90B (317628 downstream)																							TCTCTTTTTACTTTACTTTGAT	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26210810	26210812	+	IGR	DEL	ACA	-	-	rs149589991		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26210810_26210812delACA								MIR663 (21896 upstream) : None (None downstream)																							CTTCAAAATCACAACAACTTTAT	0.177													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26244581	26244582	+	IGR	INS	-	T	T	rs145145780	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26244581_26244582insT								MIR663 (55667 upstream) : None (None downstream)																							tgttgagcatctttcatgtgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29458820	29458820	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29458820delA								None (None upstream) : FRG1B (153059 downstream)																							tgccacttttaaaaccatcag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29589385	29589385	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29589385delT								None (None upstream) : FRG1B (22494 downstream)																							tgatttcttcttttacccaat	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29593345	29593346	+	IGR	DEL	AG	-	-	rs113305967		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29593345_29593346delAG								None (None upstream) : FRG1B (18533 downstream)																							aaattgactaagacaATTGGTG	0.158													6	4	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29636111	29636112	+	Intron	INS	-	TGTTA	TGTTA	rs140827717		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29636111_29636112insTGTTA	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						acacaactgattattttaattt	0.040													5	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29647652	29647653	+	Intron	INS	-	AGGG	AGGG	rs144300611	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29647652_29647653insAGGG	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						aggaaggaagtagggagggagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	32311930	32311930	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32311930delA								PXMP4 (3794 upstream) : ZNF341 (7878 downstream)																							aaaaaagaagaaaaaaaaaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	32907829	32907829	+	IGR	DEL	A	-	-	rs77680831		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32907829delA								AHCY (8221 upstream) : ITCH (43233 downstream)																							actccgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
PIGU	128869	broad.mit.edu	37	20	33154706	33154707	+	Intron	DEL	GA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33154706_33154707delGA	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron	NM_080476	NP_536724	Q9H490	PIGU_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0						TCACTCAGTGGAGAGAGAGAGA	0.505													4	2	---	---	---	---	
RBL1	5933	broad.mit.edu	37	20	35680244	35680244	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35680244delA	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron	NM_002895	NP_002886	P28749	RBL1_HUMAN	retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)				cacagattagaaaaaaaaaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	35958078	35958079	+	IGR	INS	-	TT	TT	rs140178258	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35958078_35958079insTT								MANBAL (12417 upstream) : SRC (15009 downstream)																							GACCTGGACACTATTGGCCCTG	0.530													4	4	---	---	---	---	
PLCG1	5335	broad.mit.edu	37	20	39769517	39769517	+	Intron	DEL	G	-	-	rs6102290		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39769517delG	uc002xjp.1	+						uc002xjn.1_5'Flank|PLCG1_uc002xjo.1_Intron	NM_182811	NP_877963	P19174	PLCG1_HUMAN	phospholipase C, gamma 1 isoform b						activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			lung(3)|breast(3)|skin(2)	8		Myeloproliferative disorder(115;0.00878)				ttgtgcccaaggtgttgtgtc	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	40264758	40264759	+	IGR	DEL	GA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40264758_40264759delGA								CHD6 (17625 upstream) : PTPRT (436634 downstream)																							aaagaacagggagagagagaga	0.193													4	2	---	---	---	---	
SULF2	55959	broad.mit.edu	37	20	46306144	46306145	+	Intron	INS	-	TG	TG			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46306144_46306145insTG	uc002xto.2	-						SULF2_uc002xtr.2_Intron|SULF2_uc002xtq.2_Intron	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor						bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6						ACCCAAGTAACtgtgtgtgtgt	0.480													4	4	---	---	---	---	
ATP9A	10079	broad.mit.edu	37	20	50323134	50323134	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50323134delA	uc002xwg.1	-						ATP9A_uc010gih.1_Intron	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4						ataaagaattaaaaagttagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50907920	50907921	+	IGR	DEL	TG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50907920_50907921delTG								ZFP64 (99396 upstream) : TSHZ2 (680956 downstream)																							ACAAACTTCCtgtgtgtgtgtg	0.460													4	2	---	---	---	---	
C20orf43	51507	broad.mit.edu	37	20	55093825	55093826	+	3'UTR	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55093825_55093826insT	uc002xxt.2	+	9					C20orf43_uc010zzf.1_3'UTR|C20orf43_uc002xxu.2_3'UTR|C20orf43_uc002xxv.2_3'UTR|GCNT7_uc010zzg.1_Intron	NM_016407	NP_057491	Q9BY42	CT043_HUMAN	hypothetical protein LOC51507											ovary(1)	1			Colorectal(105;0.202)			GATCCTTGTTGGTCTAGCTAAA	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	57858638	57858638	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57858638delT								ZNF831 (24473 upstream) : EDN3 (16861 downstream)																							ctttctgttattttgataata	0.000													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	59857962	59857964	+	Intron	DEL	GGC	-	-	rs6101291		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59857962_59857964delGGC	uc002ybn.1	+							NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			cgtgtgctgtggcgtgtgtgatg	0.039													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	60810459	60810459	+	Intron	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60810459delG	uc002ycj.1	+											Homo sapiens cDNA FLJ44790 fis, clone BRACE3039288.																		GGTCGTAGGCGGGACTGGTgc	0.328													4	2	---	---	---	---	
ZGPAT	84619	broad.mit.edu	37	20	62339826	62339831	+	Intron	DEL	CGTGCC	-	-	rs71903646		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62339826_62339831delCGTGCC	uc002ygk.2	+						ARFRP1_uc002yga.2_5'Flank|ARFRP1_uc002ygc.2_5'Flank|ARFRP1_uc002ygh.3_5'Flank|ARFRP1_uc011abf.1_5'Flank|ARFRP1_uc011abg.1_5'Flank|ARFRP1_uc002yge.2_5'Flank|ARFRP1_uc002ygd.2_5'Flank|ARFRP1_uc002ygf.2_5'Flank|ARFRP1_uc002ygg.2_5'Flank|ARFRP1_uc011abh.1_5'Flank|ZGPAT_uc002ygi.2_Intron|ZGPAT_uc002ygj.2_Intron|ZGPAT_uc010gkk.1_Intron|ZGPAT_uc010gkl.1_Intron|ZGPAT_uc002ygm.2_Intron|ZGPAT_uc002ygn.3_5'Flank	NM_032527	NP_115916	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain						negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					GGAAAGGGGACGTGCCCGTGCCCGTG	0.714													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9582500	9582501	+	IGR	INS	-	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9582500_9582501insC								None (None upstream) : None (None downstream)																							GAGTAGTGTCTCAAGGCCACAG	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10437036	10437036	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10437036delT								None (None upstream) : TPTE (469707 downstream)																							ctggtagcagtgggatttgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10637450	10637450	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10637450delT								None (None upstream) : TPTE (269293 downstream)																							ACATCTCGAATTTTTTTCACT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10711592	10711592	+	IGR	DEL	T	-	-	rs59817963		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10711592delT								None (None upstream) : TPTE (195151 downstream)																							aaaaaaaaaatgttaaactct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10758392	10758392	+	IGR	DEL	C	-	-	rs71225086		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10758392delC								None (None upstream) : TPTE (148351 downstream)																							gcacacatcacaaagatgttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10764703	10764703	+	IGR	DEL	T	-	-	rs112066621		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10764703delT								None (None upstream) : TPTE (142040 downstream)																							aatgcactcatcacaaaggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10780119	10780123	+	IGR	DEL	TGGAA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10780119_10780123delTGGAA								None (None upstream) : TPTE (126620 downstream)																							tgaagtggagtggaatggagtggaa	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11129890	11129891	+	IGR	INS	-	T	T	rs138525903		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11129890_11129891insT								BAGE (30953 upstream) : None (None downstream)																							cttcttttttgttttttttttt	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11178962	11178965	+	IGR	DEL	AAAG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11178962_11178965delAAAG								BAGE (80025 upstream) : None (None downstream)																							ctgtattcttaaagaaagagaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14362623	14362623	+	IGR	DEL	T	-	-	rs151299636		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14362623delT								None (None upstream) : C21orf99 (47864 downstream)																							tgtgaggatatttccttttct	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	25630291	25630292	+	IGR	INS	-	GT	GT	rs143834645	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25630291_25630292insGT								None (None upstream) : None (None downstream)																							atgtggtataCgtgtgtgtgtg	0.084													3	3	---	---	---	---	
RCAN1	1827	broad.mit.edu	37	21	35909352	35909352	+	Intron	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35909352delA	uc002yue.2	-						RCAN1_uc002yuc.2_Intron|RCAN1_uc002yud.2_Intron	NM_004414	NP_004405	P53805	RCAN1_HUMAN	calcipressin 1 isoform a						blood circulation|calcium-mediated signaling|central nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0						CTGATGACTTAAAAGCCTGAT	0.423													4	2	---	---	---	---	
DOPEY2	9980	broad.mit.edu	37	21	37547414	37547415	+	Intron	INS	-	T	T	rs112181862		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37547414_37547415insT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						tcttcttcttcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	39321957	39321958	+	IGR	INS	-	T	T	rs145446039	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39321957_39321958insT								KCNJ6 (33261 upstream) : DSCR4 (104356 downstream)																							TGCATGCTGACTTTTGCTATTT	0.475													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	39698918	39698918	+	IGR	DEL	C	-	-	rs79105163		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39698918delC								KCNJ15 (25174 upstream) : ERG (53034 downstream)																							CTGAGTCCCACCGCTACCTTC	0.512													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	42503366	42503367	+	IGR	INS	-	GT	GT	rs150478749	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42503366_42503367insGT								DSCAM (284327 upstream) : C21orf130 (10060 downstream)																							tgtgtgtgcacgtgtgtgtgtg	0.351													3	3	---	---	---	---	
BACE2	25825	broad.mit.edu	37	21	42588863	42588864	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42588863_42588864insT	uc002yyw.2	+						BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_012105	NP_036237	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2 isoform A						membrane protein ectodomain proteolysis|negative regulation of amyloid precursor protein biosynthetic process|peptide hormone processing	cell surface|endoplasmic reticulum|endosome|Golgi apparatus|integral to membrane	aspartic-type endopeptidase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				ttctttttttgtttttttttct	0.233													4	2	---	---	---	---	
ADARB1	104	broad.mit.edu	37	21	46575986	46575986	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46575986delT	uc002zgy.2	+						ADARB1_uc002zgr.2_Intron|ADARB1_uc002zgs.2_Intron|ADARB1_uc002zgw.2_Intron|ADARB1_uc002zgv.2_Intron|ADARB1_uc002zgt.2_Intron|ADARB1_uc010gpx.2_Intron|ADARB1_uc002zgq.2_Intron|ADARB1_uc002zgu.2_Intron|ADARB1_uc011afo.1_Intron	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2						adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)		ccatcatccattcatccatcc	0.000													4	3	---	---	---	---	
PCBP3	54039	broad.mit.edu	37	21	47159500	47159501	+	Intron	INS	-	C	C	rs140242801	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47159500_47159501insC	uc010gqb.2	+							NM_020528	NP_065389	P57721	PCBP3_HUMAN	poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		TCCTCTGGGTGCCCCCCCCCAT	0.619													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17352555	17352556	+	IGR	DEL	GT	-	-	rs140967896		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17352555_17352556delGT								HSFYL1 (42330 upstream) : GAB4 (90273 downstream)																							TTGAATGCTGGTAAGTAATGTT	0.386													4	2	---	---	---	---	
CECR5	27440	broad.mit.edu	37	22	17648946	17648947	+	5'Flank	INS	-	TT	TT	rs5844290		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17648946_17648947insTT	uc002zmh.2	-							NM_017829	NP_060299	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5								hydrolase activity				0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				ttctttctttcttttttttttt	0.163													3	3	---	---	---	---	
C22orf25	128989	broad.mit.edu	37	22	20031316	20031317	+	Intron	INS	-	TGAG	TGAG			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20031316_20031317insTGAG	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_Intron|C22orf25_uc002zrg.2_Intron|C22orf25_uc011ahh.1_Intron|C22orf25_uc002zrf.2_Intron|C22orf25_uc011ahi.1_Intron|C22orf25_uc010gry.1_Intron|C22orf25_uc002zrh.1_Intron	NM_152906	NP_690870	Q6ICL3	CV025_HUMAN	hypothetical protein LOC128989												0	Colorectal(54;0.0533)					ACCCAGTCATATGAgtgtgtgc	0.347													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22469229	22469230	+	Intron	INS	-	C	C			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22469229_22469230insC	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						GCCGGTTGGGGCCGCCGCTAGG	0.743													14	7	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22657416	22657419	+	Intron	DEL	ACTA	-	-	rs138873705		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22657416_22657419delACTA	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_Intron|LOC96610_uc010gto.2_Intron					Parts of antibodies, mostly variable regions.												0						ATGATGAAATACTAACTGTTTTAC	0.402													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	24328950	24328951	+	IGR	DEL	GT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24328950_24328951delGT								DDT (6931 upstream) : GSTTP1 (11645 downstream)																							tgtgtgtgaggtgtgtgtgtgt	0.139													4	2	---	---	---	---	
SFI1	9814	broad.mit.edu	37	22	31930860	31930861	+	Intron	INS	-	T	T			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31930860_31930861insT	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						ACTTCAAATGCttttttttttt	0.149													4	3	---	---	---	---	
SFI1	9814	broad.mit.edu	37	22	31969425	31969425	+	Intron	DEL	T	-	-	rs72194101		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31969425delT	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron|SFI1_uc010gwi.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						TGTAGATAGAttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	32736129	32736131	+	IGR	DEL	CCT	-	-	rs35241553		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32736129_32736131delCCT								SLC5A4 (84811 upstream) : RFPL3 (14741 downstream)																							tctctccgagcctcctcggtgtc	0.025													4	4	---	---	---	---	
SYN3	8224	broad.mit.edu	37	22	33010957	33010958	+	Intron	INS	-	AA	AA	rs113640571		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33010957_33010958insAA	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						ACAAATGTTCCAAAAAAAAAAA	0.381													6	3	---	---	---	---	
CARD10	29775	broad.mit.edu	37	22	37890147	37890147	+	Frame_Shift_Del	DEL	C	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37890147delC	uc003asx.1	-	16	2425	c.2422delG	c.(2422-2424)GTGfs	p.V808fs	CARD10_uc003ast.1_RNA|CARD10_uc003asu.1_5'Flank|CARD10_uc003asv.1_5'UTR|CARD10_uc011ank.1_Frame_Shift_Del_p.V126fs|CARD10_uc003asw.1_Frame_Shift_Del_p.V522fs|CARD10_uc003asy.1_Frame_Shift_Del_p.V808fs	NM_014550	NP_055365	Q9BWT7	CAR10_HUMAN	caspase recruitment domain protein 10	808					activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1)	6	Melanoma(58;0.0574)					GGCGCCCCCACGGGCTTGGGC	0.677													4	3	---	---	---	---	
SUN2	25777	broad.mit.edu	37	22	39161640	39161641	+	Intron	DEL	AC	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39161640_39161641delAC	uc010gxr.1	-							NM_015374	NP_056189	Q9UH99	SUN2_HUMAN	unc-84 homolog B						centrosome localization|cytoskeletal anchoring at nuclear membrane|mitotic spindle organization|nuclear envelope organization|nuclear matrix anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	endosome membrane|integral to membrane|nuclear inner membrane|SUN-KASH complex	lamin binding|microtubule binding			large_intestine(1)|skin(1)	2						atacatcgaaacacacacacac	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	39558761	39558762	+	IGR	INS	-	TTC	TTC	rs150984438	by1000genomes	TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39558761_39558762insTTC								CBX7 (10223 upstream) : PDGFB (60925 downstream)																							atgtggaacaattcttcttctt	0.000													3	3	---	---	---	---	
TEF	7008	broad.mit.edu	37	22	41766125	41766125	+	Intron	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41766125delT	uc003azx.2	+							NM_001145398	NP_001138870	Q10587	TEF_HUMAN	thyrotrophic embryonic factor isoform 2						rhythmic process	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						tctttcccccttttttttttt	0.229													4	2	---	---	---	---	
MEI1	150365	broad.mit.edu	37	22	42194230	42194231	+	Intron	DEL	CA	-	-	rs67867435		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42194230_42194231delCA	uc003baz.1	+						WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|CCDC134_uc003bbh.1_5'Flank|CCDC134_uc011apg.1_5'Flank|MEI1_uc011apd.1_Intron|MEI1_uc003bbb.1_Intron|MEI1_uc003bbc.1_Intron|MEI1_uc010gym.1_Intron|MEI1_uc003bbd.1_Intron|MEI1_uc010gyn.1_Intron|MEI1_uc003bbe.1_Intron|MEI1_uc003bbf.2_Intron|MEI1_uc003bbg.2_Intron	NM_152513	NP_689726	Q5TIA1	MEI1_HUMAN	meiosis defective 1								binding			central_nervous_system(1)|skin(1)	2						TGGCCAGGTGcacacacacaca	0.223													7	4	---	---	---	---	
MPPED1	758	broad.mit.edu	37	22	43900015	43900017	+	Intron	DEL	TAA	-	-	rs71848776		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43900015_43900017delTAA	uc011apv.1	+						MPPED1_uc011apw.1_Intron|MPPED1_uc011apx.1_Intron|MPPED1_uc011apy.1_Intron|MPPED1_uc011apz.1_Intron	NM_001044370	NP_001037835	O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1								hydrolase activity				0		all_neural(38;0.0244)|Ovarian(80;0.0694)				atggtgatagtaataatgtcaat	0.049													5	3	---	---	---	---	
PHF21B	112885	broad.mit.edu	37	22	45279900	45279902	+	Intron	DEL	CCA	-	-	rs111413747		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45279900_45279902delCCA	uc003bfn.2	-						PHF21B_uc003bfm.2_Intron|PHF21B_uc011aqk.1_Intron|PHF21B_uc011aql.1_Intron	NM_138415	NP_612424	Q96EK2	PF21B_HUMAN	PHD finger protein 21B isoform 1								zinc ion binding			ovary(2)|skin(1)	3		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		atcaccaccgccaccaccatcac	0.049													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49150310	49150311	+	IGR	DEL	GT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49150310_49150311delGT								FAM19A5 (2568 upstream) : C22orf34 (657865 downstream)																							gtgtgcgcacgtgtgtgtgtgC	0.238													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	465661	465677	+	IGR	DEL	TCCTTCCTTCCTTCCTG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:465661_465677delTCCTTCCTTCCTTCCTG								PPP2R3B (118034 upstream) : SHOX (119402 downstream)																							cttcccttcttccttccttccttcctgtccttccttc	0.147													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	861631	861631	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:861631delA								SHOX (241486 upstream) : CRLF2 (453256 downstream)																							TAACACCAGGAAAAAAAAAAT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	19283112	19283112	+	IGR	DEL	G	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19283112delG								GPR64 (142435 upstream) : PDHA1 (78899 downstream)																							ggccaagataggcagatcact	0.060													4	2	---	---	---	---	
CYBB	1536	broad.mit.edu	37	X	37663222	37663222	+	Frame_Shift_Del	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37663222delA	uc004ddr.2	+	9	1051	c.990delA	c.(988-990)CCAfs	p.P330fs	CYBB_uc011mke.1_RNA|CYBB_uc011mkf.1_Frame_Shift_Del_p.P298fs|CYBB_uc011mkg.1_Frame_Shift_Del_p.P63fs	NM_000397	NP_000388	P04839	CY24B_HUMAN	cytochrome b-245 beta polypeptide	330	Cytoplasmic (Potential).|FAD-binding FR-type.				electron transport chain|inflammatory response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|heme binding|protein heterodimerization activity|superoxide-generating NADPH oxidase activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2						TCAAGTGCCCAAAGGTGTCCA	0.478													13	30	---	---	---	---	
GAGE10	643832	broad.mit.edu	37	X	49158062	49158062	+	5'Flank	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49158062delT	uc010nir.1	+							NM_001098413	NP_001091883	A6NGK3	GAG10_HUMAN	G antigen 10												0	Ovarian(276;0.236)					acatcattccttttttttttt	0.000													4	2	---	---	---	---	
XAGE5	170627	broad.mit.edu	37	X	52842128	52842129	+	Intron	DEL	CA	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52842128_52842129delCA	uc004drd.1	+							NM_130775	NP_570131	Q8WWM1	GAGD5_HUMAN	X antigen family, member 5											ovary(1)	1						TTTTTATCTCCACACACACACA	0.426													5	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61815445	61815445	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61815445delA								None (None upstream) : SPIN4 (751663 downstream)																							atcttcacataaaaagtagac	0.000													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	92643879	92643880	+	IGR	DEL	TT	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:92643879_92643880delTT								PCDH11X (765653 upstream) : NAP1L3 (282049 downstream)																							CAtttttttctttttttttttt	0.312													7	5	---	---	---	---	
NXF3	56000	broad.mit.edu	37	X	102334777	102334778	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102334777_102334778delAG	uc004eju.2	-	13	1144_1145	c.1073_1074delCT	c.(1072-1074)TCTfs	p.S358fs	NXF3_uc010noi.1_Frame_Shift_Del_p.S208fs	NM_022052	NP_071335	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	358	NTF2.					cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3						GTCGATCTCCAGAGTCATAGAT	0.520													19	46	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9937814	9937814	+	IGR	DEL	T	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9937814delT								TTTY22 (286960 upstream) : None (None downstream)																							ttgatggacatttaggttgat	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9965980	9965980	+	IGR	DEL	A	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9965980delA								TTTY22 (315126 upstream) : None (None downstream)																							ttagacaggcatggtggtagg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13271213	13271214	+	IGR	INS	-	G	G	rs77070715		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13271213_13271214insG								None (None upstream) : None (None downstream)																							ttaaaaaaaaaaaagaaaaaag	0.069													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13285655	13285656	+	IGR	INS	-	GA	GA	rs113499634		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13285655_13285656insGA								None (None upstream) : None (None downstream)																							caataccacgggggggtgtata	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13410352	13410352	+	IGR	DEL	C	-	-	rs140676082		TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13410352delC								None (None upstream) : None (None downstream)																							TCATCTTTAACCTTTCCATAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13452114	13452118	+	IGR	DEL	ACTTG	-	-			TCGA-46-3768-01A-01D-0983-08	TCGA-46-3768-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13452114_13452118delACTTG								None (None upstream) : None (None downstream)																							attccattccacttgattccattcc	0.000													4	2	---	---	---	---	
