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
PUSL1	126789	broad.mit.edu	37	1	1245971	1245971	+	Intron	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1245971C>T	uc001aed.2	+						ACAP3_uc001aeb.2_5'Flank|ACAP3_uc001aec.1_5'Flank|PUSL1_uc010nyi.1_Intron|PUSL1_uc009vjx.2_Missense_Mutation_p.A2V	NM_153339	NP_699170	Q8N0Z8	PUSL1_HUMAN	pseudouridylate synthase-like 1						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			skin(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;4.95e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CTGAGGATGGCAAACACTGCC	0.562													3	38	---	---	---	---	PASS
NPPA	4878	broad.mit.edu	37	1	11907351	11907351	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11907351G>T	uc001ati.2	-	2	368	c.269C>A	c.(268-270)GCC>GAC	p.A90D	CLCN6_uc010oav.1_Intron|CLCN6_uc010oaw.1_Intron|CLCN6_uc010oax.1_Intron|CLCN6_uc010oay.1_Intron|CLCN6_uc010oaz.1_Intron|CLCN6_uc010oba.1_Intron	NM_006172	NP_006163	P01160	ANF_HUMAN	natriuretic peptide precursor A preproprotein	90					cGMP biosynthetic process|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size	extracellular region	hormone activity			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.04e-06)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|Kidney(185;0.000733)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATCTCTCTGGGCTGGGCTGAC	0.667													3	4	---	---	---	---	PASS
ARID1A	8289	broad.mit.edu	37	1	27106271	27106271	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27106271G>A	uc001bmv.1	+	20	6255	c.5882G>A	c.(5881-5883)AGT>AAT	p.S1961N	ARID1A_uc001bmu.1_Missense_Mutation_p.S1744N|ARID1A_uc001bmx.1_Missense_Mutation_p.S807N|ARID1A_uc009vsm.1_Missense_Mutation_p.S289N|ARID1A_uc009vsn.1_Missense_Mutation_p.S203N	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1961					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GAACCCCACAGTAAGGATGAG	0.522			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								9	33	---	---	---	---	PASS
CLSPN	63967	broad.mit.edu	37	1	36230057	36230057	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36230057C>A	uc001bzi.2	-	3	472	c.392G>T	c.(391-393)TGC>TTC	p.C131F	CLSPN_uc009vux.2_Missense_Mutation_p.C131F	NM_022111	NP_071394	Q9HAW4	CLSPN_HUMAN	claspin	131					activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CAGCTCTAAGCAAGGTTTCAC	0.378													6	230	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39801310	39801310	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39801310C>A	uc010oiu.1	+	1	4501	c.4370C>A	c.(4369-4371)CCT>CAT	p.P1457H	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	3022					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)			AAGAGCCAACCTAGGGAAATG	0.383													13	80	---	---	---	---	PASS
CCDC30	728621	broad.mit.edu	37	1	43055004	43055004	+	Silent	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43055004T>C	uc009vwk.1	+	9	1343	c.1233T>C	c.(1231-1233)TAT>TAC	p.Y411Y	CCDC30_uc001chm.2_Silent_p.Y109Y|CCDC30_uc001chn.2_Silent_p.Y200Y|CCDC30_uc001chp.2_Silent_p.Y225Y	NM_001080850	NP_001074319	Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	411	Potential.										0						AACTTCTATATCAGAACGTAG	0.353													71	95	---	---	---	---	PASS
CCDC30	728621	broad.mit.edu	37	1	43111913	43111913	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43111913C>A	uc009vwk.1	+	14	2108	c.1998C>A	c.(1996-1998)AGC>AGA	p.S666R	CCDC30_uc001chm.2_Missense_Mutation_p.S364R|CCDC30_uc001chn.2_Missense_Mutation_p.S455R	NM_001080850	NP_001074319	Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	666											0						tcttcaccagcaacaatgcag	0.015													39	48	---	---	---	---	PASS
POMGNT1	55624	broad.mit.edu	37	1	46658149	46658149	+	Intron	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46658149C>A	uc001cpe.2	-						POMGNT1_uc010olx.1_Intron|POMGNT1_uc010oly.1_Intron|POMGNT1_uc010olz.1_Intron|POMGNT1_uc001cpg.2_Intron|POMGNT1_uc001cpf.2_Intron|POMGNT1_uc001cph.1_Translation_Start_Site|POMGNT1_uc001cpi.1_Intron	NM_017739	NP_060209	Q8WZA1	PMGT1_HUMAN	O-linked mannose						protein N-linked glycosylation|protein O-linked glycosylation	Golgi membrane|integral to membrane|microsome	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					TAGCTGAGGCCTCATAAACTC	0.567													14	71	---	---	---	---	PASS
L1TD1	54596	broad.mit.edu	37	1	62673128	62673128	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62673128T>G	uc001dae.3	+	3	1130	c.828T>G	c.(826-828)TTT>TTG	p.F276L		NM_019079	NP_061952	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	276										ovary(1)|skin(1)	2						aacctaaatttctgtgtgaag	0.000													15	62	---	---	---	---	PASS
CLCA2	9635	broad.mit.edu	37	1	86907161	86907161	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86907161A>G	uc001dlr.3	+	9	1585	c.1423A>G	c.(1423-1425)AGC>GGC	p.S475G		NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor	475	VWFA.|Extracellular (Potential).				cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)|skin(1)	3		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		AAACTCCAATAGCATGATTGA	0.328													13	352	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144620095	144620095	+	Splice_Site	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144620095G>T	uc009wig.1	+	8	854	c.778_splice	c.e8+1	p.V260_splice	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Splice_Site_p.V260_splice|NBPF9_uc010oxr.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_Splice_Site_p.V191_splice|NBPF9_uc001eli.3_Splice_Site|NBPF9_uc010oyf.1_Splice_Site_p.V191_splice|NBPF9_uc010oyg.1_Splice_Site_p.V225_splice|NBPF9_uc009wii.1_Splice_Site	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						ATTCTCCCAGGTAGCCTCTAT	0.393													4	59	---	---	---	---	PASS
ASH1L	55870	broad.mit.edu	37	1	155385552	155385552	+	Silent	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155385552G>A	uc009wqq.2	-	6	6471	c.5991C>T	c.(5989-5991)GAC>GAT	p.D1997D	ASH1L_uc001fkt.2_Silent_p.D1997D	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	1997					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTTTGTAAACGTCAGAATACA	0.393													85	125	---	---	---	---	PASS
OR6K2	81448	broad.mit.edu	37	1	158670428	158670428	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158670428A>C	uc001fsu.1	-	1	15	c.15T>G	c.(13-15)AAT>AAG	p.N5K		NM_001005279	NP_001005279	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K,	5	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_hematologic(112;0.0378)					TGGTGGTTCGATTGGGGCTCT	0.433													15	89	---	---	---	---	PASS
CFHR2	3080	broad.mit.edu	37	1	196918661	196918661	+	Silent	SNP	T	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196918661T>A	uc001gtq.1	+	2	212	c.135T>A	c.(133-135)GTT>GTA	p.V45V	CFHR2_uc001gtr.1_Intron	NM_005666	NP_005657	P36980	FHR2_HUMAN	H factor (complement)-like 3 precursor	45	Sushi 1.					extracellular region				skin(2)|ovary(1)	3						TTTCCCAAGTTCCTACAGGGG	0.358													6	305	---	---	---	---	PASS
MARK1	4139	broad.mit.edu	37	1	220835299	220835299	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220835299G>T	uc001hmn.3	+	18	2776	c.2179G>T	c.(2179-2181)GCA>TCA	p.A727S	MARK1_uc009xdw.2_Missense_Mutation_p.A728S|MARK1_uc010pun.1_Missense_Mutation_p.A712S|MARK1_uc001hmm.3_Missense_Mutation_p.A690S	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	727					intracellular protein kinase cascade	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(4)|central_nervous_system(2)|skin(2)|stomach(1)|lung(1)	10				GBM - Glioblastoma multiforme(131;0.0407)		AGTGTTAGATGCAAATAACTG	0.433													18	67	---	---	---	---	PASS
GREB1	9687	broad.mit.edu	37	2	11725906	11725906	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11725906G>T	uc002rbk.1	+	9	1334	c.1034G>T	c.(1033-1035)TGC>TTC	p.C345F	GREB1_uc002rbl.2_Missense_Mutation_p.C345F|GREB1_uc002rbn.1_Missense_Mutation_p.C345F|GREB1_uc002rbo.1_5'Flank	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	345						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GGCATGTCCTGCGTGCCGCAG	0.522													5	54	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15557689	15557689	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15557689T>C	uc002rcc.1	-	24	2751	c.2725A>G	c.(2725-2727)ATG>GTG	p.M909V	NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	909										ovary(2)|liver(1)|skin(1)	4						ATGTCTTTCATCTGCTGGAGT	0.338													5	288	---	---	---	---	PASS
GALM	130589	broad.mit.edu	37	2	38903134	38903134	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38903134G>T	uc002rqy.2	+	2	523	c.271G>T	c.(271-273)GAT>TAT	p.D91Y		NM_138801	NP_620156	Q96C23	GALM_HUMAN	galactose mutarotase	91					hexose metabolic process	cytoplasm	aldose 1-epimerase activity|carbohydrate binding				0		all_hematologic(82;0.248)				CTTCAAGGTGGATGGGAAGGA	0.498													33	77	---	---	---	---	PASS
CCDC88A	55704	broad.mit.edu	37	2	55573452	55573452	+	Silent	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55573452C>A	uc002ryv.2	-	10	1742	c.900G>T	c.(898-900)TCG>TCT	p.S300S	CCDC88A_uc010yoz.1_Silent_p.S300S|CCDC88A_uc010ypa.1_Silent_p.S300S|CCDC88A_uc010ypb.1_Silent_p.S202S	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1	300	Potential.				activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						AGCGAGCATCCGAAAGCAAAT	0.289													4	188	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61522139	61522139	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61522139G>A	uc002sbe.2	-	32	4428	c.4406C>T	c.(4405-4407)TCA>TTA	p.S1469L		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	1469					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			TGAATCATCTGAATCTGGATA	0.308													86	164	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	96646489	96646489	+	RNA	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96646489A>G	uc010yug.1	-	5		c.723T>C								Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		AAGAAGAATGACTATATCTTT	0.353													6	223	---	---	---	---	PASS
IL18RAP	8807	broad.mit.edu	37	2	103067330	103067330	+	Silent	SNP	C	T	T	rs140183707	byFrequency	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103067330C>T	uc002tbx.2	+	11	1717	c.1233C>T	c.(1231-1233)TTC>TTT	p.F411F	IL18RAP_uc010fiz.2_Silent_p.F269F	NM_003853	NP_003844	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	411	TIR.|Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|inflammatory response|innate immune response	integral to membrane	transmembrane receptor activity			skin(3)|ovary(2)	5						TTGATGCTTTCGTATCCTATG	0.343													70	140	---	---	---	---	PASS
POLR1B	84172	broad.mit.edu	37	2	113333412	113333412	+	3'UTR	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113333412G>T	uc002thw.2	+	15					POLR1B_uc010fkn.2_3'UTR|POLR1B_uc002thx.2_3'UTR|POLR1B_uc010fko.2_3'UTR|POLR1B_uc010fkp.2_3'UTR|POLR1B_uc010yxn.1_3'UTR|POLR1B_uc002thy.2_3'UTR|POLR1B_uc010yxo.1_3'UTR	NM_019014	NP_061887	Q9H9Y6	RPA2_HUMAN	RNA polymerase I polypeptide B isoform 1						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(1)	1						TTTTTCAACGGTGTTAGAACT	0.328													12	14	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152352866	152352866	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152352866T>C	uc010fnx.2	-	140	19033	c.18842A>G	c.(18841-18843)AAC>AGC	p.N6281S	NEB_uc002txr.2_Missense_Mutation_p.N2673S|RIF1_uc002txp.2_Intron|NEB_uc010zbz.1_Missense_Mutation_p.N81S|NEB_uc002txq.2_Missense_Mutation_p.N160S|NEB_uc010zca.1_Missense_Mutation_p.N112S|NEB_uc010zcb.1_Missense_Mutation_p.N81S	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	6281	Nebulin 172.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTTGCCCATGTTTTCTTTGTA	0.403													8	293	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166909391	166909391	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166909391C>A	uc010zcz.1	-	5	683	c.665G>T	c.(664-666)CGA>CTA	p.R222L	SCN1A_uc002udo.3_Missense_Mutation_p.R91L|SCN1A_uc010fpk.2_Missense_Mutation_p.R91L	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	222	Helical; Voltage-sensor; Name=S4 of repeat I; (By similarity).|I.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	CTTCAATGCTCGGAGAACTCT	0.453													50	125	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168102930	168102930	+	Silent	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168102930C>A	uc002udx.2	+	8	5046	c.5028C>A	c.(5026-5028)GGC>GGA	p.G1676G	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.G1501G|XIRP2_uc010fpq.2_Silent_p.G1454G|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1501					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						TAAAGAAAGGCATCTTAATTC	0.338													5	107	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191491	10191491	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191491T>C	uc003bvc.2	+	3	697	c.484T>C	c.(484-486)TGC>CGC	p.C162R	VHL_uc003bvd.2_Missense_Mutation_p.C121R	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	162	Interaction with Elongin BC complex.		C -> R (in VHLD; type I).|C -> F (in VHLD; type I; No effect on interaction with HIF1A nor on HIF1A degradation).|C -> Y (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.C162Y(3)|p.C162R(3)|p.C162F(2)|p.C162W(2)|p.C162*(1)|p.C162fs*12(1)|p.C162fs*9(1)|p.L158fs*6(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GAAAGAGCGATGCCTCCAGGT	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				25	22	---	---	---	---	PASS
RAF1	5894	broad.mit.edu	37	3	12641900	12641900	+	Silent	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12641900A>G	uc003bxf.3	-	8	1264	c.849T>C	c.(847-849)AGT>AGC	p.S283S	RAF1_uc011aut.1_Silent_p.S68S|RAF1_uc011auu.1_Silent_p.S201S	NM_002880	NP_002871	P04049	RAF1_HUMAN	v-raf-1 murine leukemia viral oncogene homolog	283					activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|SRGAP3/RAF1(4)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14					Sorafenib(DB00398)	ATTCGCTGTGACTTCGAATTG	0.423			T	SRGAP3	pilocytic astrocytoma				Noonan_syndrome				5	158	---	---	---	---	PASS
ZNF445	353274	broad.mit.edu	37	3	44541259	44541259	+	Intron	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44541259C>T	uc011azw.1	-						uc011azx.1_Missense_Mutation_p.S337N|uc011azy.1_Missense_Mutation_p.S303N	NM_181489	NP_852466	P59923	ZN445_HUMAN	zinc finger protein 445						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		TTTACTCCGACTGAAGGCTTT	0.433													19	20	---	---	---	---	PASS
ADPRH	141	broad.mit.edu	37	3	119301129	119301129	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119301129C>T	uc003ecs.2	+	3	411	c.113C>T	c.(112-114)GCC>GTC	p.A38V	ADPRH_uc010hqv.2_Missense_Mutation_p.A38V|ADPRH_uc011bjb.1_Intron|ADPRH_uc003ect.2_Missense_Mutation_p.A38V	NM_001125	NP_001116	P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	38					protein de-ADP-ribosylation		ADP-ribosylarginine hydrolase activity|magnesium ion binding			ovary(1)	1		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		CGGCAGTTGGCCCAGCTGGGC	0.587													3	40	---	---	---	---	PASS
SLC15A2	6565	broad.mit.edu	37	3	121659238	121659238	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121659238C>G	uc003eep.2	+	21	2069	c.1916C>G	c.(1915-1917)TCT>TGT	p.S639C	SLC15A2_uc011bjn.1_Missense_Mutation_p.S608C	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a	639					protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)	CAGGCTCCCTCTAGCATGAAA	0.498													16	82	---	---	---	---	PASS
PLSCR1	5359	broad.mit.edu	37	3	146239399	146239399	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146239399T>C	uc003evx.3	-	7	1058	c.670A>G	c.(670-672)AGA>GGA	p.R224G	PLSCR1_uc003evy.3_Missense_Mutation_p.R217G|PLSCR1_uc011bnn.1_Missense_Mutation_p.R143G|PLSCR1_uc003evz.3_Intron	NM_021105	NP_066928	O15162	PLS1_HUMAN	phospholipid scramblase 1	224	Cytoplasmic.				phospholipid scrambling|platelet activation|response to virus	integral to membrane|plasma membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding			ovary(2)	2						ACATCCTCTCTTTTCTCATTT	0.368													6	568	---	---	---	---	PASS
MED12L	116931	broad.mit.edu	37	3	151100523	151100523	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151100523G>T	uc003eyp.2	+	31	4603	c.4565G>T	c.(4564-4566)CGC>CTC	p.R1522L	MED12L_uc011bnz.1_Missense_Mutation_p.R1382L|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Missense_Mutation_p.R685L	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1522					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TTGCAACTCCGCCTAAATTTG	0.388													8	95	---	---	---	---	PASS
MECOM	2122	broad.mit.edu	37	3	168802651	168802651	+	3'UTR	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168802651C>T	uc003ffi.3	-	16					MECOM_uc010hwk.1_3'UTR|MECOM_uc003ffj.3_3'UTR|MECOM_uc011bpi.1_3'UTR|MECOM_uc003ffn.3_3'UTR|MECOM_uc003ffk.2_3'UTR|MECOM_uc003ffl.2_3'UTR|MECOM_uc011bpj.1_3'UTR|MECOM_uc011bpk.1_3'UTR	NM_005241	NP_005232	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform b						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						ATGAAAGAGCCATGCTACTGT	0.463													4	41	---	---	---	---	PASS
MAP3K13	9175	broad.mit.edu	37	3	185195185	185195185	+	Splice_Site	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185195185G>A	uc010hyf.2	+	13	2767	c.2501_splice	c.e13+1	p.R834_splice	MAP3K13_uc011brt.1_Splice_Site_p.R627_splice|MAP3K13_uc011bru.1_Splice_Site_p.R690_splice|MAP3K13_uc003fpi.2_Splice_Site_p.R834_splice|MAP3K13_uc010hyg.2_Splice_Site_p.R524_splice	NM_004721	NP_004712	O43283	M3K13_HUMAN	mitogen-activated protein kinase kinase kinase						activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			GAAGACAGAGGTAAAACCAAC	0.433													88	151	---	---	---	---	PASS
ATP13A4	84239	broad.mit.edu	37	3	193128778	193128778	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193128778C>T	uc003ftd.2	-	28	3398	c.3290G>A	c.(3289-3291)CGT>CAT	p.R1097H	ATP13A4_uc010hzi.2_RNA	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1097	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		TACATCCAAACGTCTATATAA	0.303													7	283	---	---	---	---	PASS
TFRC	7037	broad.mit.edu	37	3	195798910	195798910	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195798910C>T	uc003fvz.3	-	5	831	c.548G>A	c.(547-549)CGT>CAT	p.R183H	TFRC_uc003fwa.3_Missense_Mutation_p.R183H|TFRC_uc010hzy.2_Missense_Mutation_p.R102H|TFRC_uc011btr.1_Translation_Start_Site	NM_003234	NP_003225	P02786	TFR1_HUMAN	transferrin receptor	183	Extracellular (Potential).				cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)		ATGTTGATCACGCCAGACTTT	0.338			T	BCL6	NHL								4	159	---	---	---	---	PASS
RASGEF1B	153020	broad.mit.edu	37	4	82377852	82377852	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82377852T>C	uc003hmi.1	-	4	535	c.391A>G	c.(391-393)ATG>GTG	p.M131V	RASGEF1B_uc003hmj.1_Missense_Mutation_p.M131V|RASGEF1B_uc010ijq.1_Missense_Mutation_p.M90V|RASGEF1B_uc003hmk.2_Missense_Mutation_p.M131V	NM_152545	NP_689758	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	131	N-terminal Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0						AAGTTTCTCATCATTCTTTCA	0.468													5	242	---	---	---	---	PASS
C4orf21	55345	broad.mit.edu	37	4	113538927	113538927	+	Silent	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113538927A>G	uc003iau.2	-	6	2482	c.2271T>C	c.(2269-2271)AAT>AAC	p.N757N	C4orf21_uc003iaw.2_Silent_p.N757N	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	Error:Variant_position_missing_in_Q6ZU11_after_alignment						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		AAATGTGGGTATTTGATTTAT	0.343													4	203	---	---	---	---	PASS
TBC1D9	23158	broad.mit.edu	37	4	141600356	141600356	+	Silent	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141600356C>T	uc010ioj.2	-	5	863	c.591G>A	c.(589-591)GCG>GCA	p.A197A		NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	197	GRAM 1.					intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				TGACCAGTTTCGCTGAGCACA	0.512													19	23	---	---	---	---	PASS
RAPGEF2	9693	broad.mit.edu	37	4	160189294	160189294	+	5'UTR	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160189294T>C	uc003iqg.3	+	1						NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2						cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		CAGTTCAGCATATGTTTCTTC	0.398													31	138	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19838883	19838883	+	Silent	SNP	A	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19838883A>T	uc003jgc.2	-	2	590	c.213T>A	c.(211-213)CCT>CCA	p.P71P	CDH18_uc003jgd.2_Silent_p.P71P|CDH18_uc011cnm.1_Silent_p.P71P	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	71	Extracellular (Potential).|Cadherin 1.				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)					CAACATACTGAGGATCTGGTC	0.388													81	144	---	---	---	---	PASS
DHX29	54505	broad.mit.edu	37	5	54552206	54552206	+	3'UTR	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54552206G>A	uc003jpx.2	-	27					DHX29_uc010ivw.2_RNA	NM_019030	NP_061903	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29								ATP binding|ATP-dependent helicase activity|translation initiation factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				TTAATGGCTAGTACCAACATT	0.289													10	141	---	---	---	---	PASS
HOMER1	9456	broad.mit.edu	37	5	78752814	78752814	+	Silent	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78752814A>G	uc003kfy.2	-	2	1136	c.33T>C	c.(31-33)GCT>GCC	p.A11A	HOMER1_uc010jab.2_Silent_p.A11A|HOMER1_uc010jac.2_Silent_p.A11A|HOMER1_uc010jad.2_Intron	NM_004272	NP_004263	Q86YM7	HOME1_HUMAN	homer 1	11	WH1.				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic density|postsynaptic membrane					0		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)		GGAAGACATGAGCTCGAGTGC	0.423													6	366	---	---	---	---	PASS
ZFYVE16	9765	broad.mit.edu	37	5	79746381	79746381	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79746381A>G	uc003kgr.3	+	10	3660	c.3358A>G	c.(3358-3360)ACC>GCC	p.T1120A	ZFYVE16_uc003kgp.2_Missense_Mutation_p.T1120A|ZFYVE16_uc003kgq.3_Missense_Mutation_p.T1120A|ZFYVE16_uc003kgs.3_Missense_Mutation_p.T1120A|ZFYVE16_uc003kgt.3_Missense_Mutation_p.T208A	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1120					BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		ACTATTTATCACCATATATAA	0.348													7	254	---	---	---	---	PASS
KIF20A	10112	broad.mit.edu	37	5	137520633	137520633	+	Silent	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137520633C>T	uc003lcj.2	+	14	2317	c.1821C>T	c.(1819-1821)TGC>TGT	p.C607C	KIF20A_uc011cyo.1_Silent_p.C589C	NM_005733	NP_005724	O95235	KI20A_HUMAN	kinesin family member 20A	607					cytokinesis|M phase of mitotic cell cycle|microtubule-based movement|protein transport|vesicle-mediated transport	Golgi apparatus|microtubule|nucleoplasm	ATP binding|microtubule motor activity|protein binding|transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			AACAGTGGTGCAGGTACTAGC	0.493													29	48	---	---	---	---	PASS
CCNJL	79616	broad.mit.edu	37	5	159680605	159680605	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159680605G>T	uc003lyb.1	-	7	1340	c.1088C>A	c.(1087-1089)GCC>GAC	p.A363D	CCNJL_uc011dee.1_Missense_Mutation_p.A315D|CCNJL_uc003lyc.1_RNA	NM_024565	NP_078841	Q8IV13	CCNJL_HUMAN	cyclin J-like	363						nucleus					0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGAACGGTGGGCCTGCAAGGA	0.667													3	15	---	---	---	---	PASS
PGBD1	84547	broad.mit.edu	37	6	28251758	28251758	+	Silent	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28251758C>T	uc003nky.2	+	2	538	c.168C>T	c.(166-168)CAC>CAT	p.H56H	PGBD1_uc003nkz.2_Silent_p.H56H	NM_032507	NP_115896	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	56	SCAN box.				viral reproduction	membrane|nucleus	scavenger receptor activity|sequence-specific DNA binding transcription factor activity			ovary(4)	4						AGGAGGCTCACGGACCCCAGG	0.582													4	26	---	---	---	---	PASS
SCAND3	114821	broad.mit.edu	37	6	28543685	28543685	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28543685T>A	uc003nlo.2	-	3	1415	c.797A>T	c.(796-798)GAA>GTA	p.E266V		NM_052923	NP_443155	Q6R2W3	SCND3_HUMAN	SCAN domain containing 3	266	Potential.				DNA integration|viral reproduction	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1						GTCAACTGATTCCTTTTTCGC	0.353													118	221	---	---	---	---	PASS
UNC5CL	222643	broad.mit.edu	37	6	41001862	41001862	+	Silent	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41001862C>T	uc003opi.2	-	3	533	c.444G>A	c.(442-444)TCG>TCA	p.S148S	UNC5CL_uc010jxe.1_Silent_p.S148S	NM_173561	NP_775832	Q8IV45	UN5CL_HUMAN	unc-5 homolog C-like	148	ZU5.|Cytoplasmic (Potential).				signal transduction	cytoplasm|integral to membrane				ovary(2)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)					ATGGGGCGTCCGACAGGTCCC	0.657													2	1	---	---	---	---	PASS
TAAR9	134860	broad.mit.edu	37	6	132859640	132859640	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132859640T>A	uc011eci.1	+	2	214	c.212T>A	c.(211-213)ATT>AAT	p.I71N		NM_175057	NP_778227	Q96RI9	TAAR9_HUMAN	trace amine associated receptor 9	71	Helical; Name=2; (Potential).					plasma membrane	G-protein coupled receptor activity				0	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.0042)|GBM - Glioblastoma multiforme(226;0.00816)		AACTTTCTGATTGCGTCGCTG	0.507													69	175	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152647230	152647230	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152647230C>T	uc010kiw.2	-	80	15903	c.15301G>A	c.(15301-15303)GCT>ACT	p.A5101T	SYNE1_uc003qot.3_Missense_Mutation_p.A5030T|SYNE1_uc003qou.3_Missense_Mutation_p.A5101T|SYNE1_uc010kiz.2_Missense_Mutation_p.A856T	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5101	Spectrin 16.|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)		TGCCATTGAGCTGTGCATCTT	0.393										HNSCC(10;0.0054)			5	451	---	---	---	---	PASS
ZNF853	54753	broad.mit.edu	37	7	6661158	6661158	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6661158C>T	uc011jwz.1	+	3	815	c.536C>T	c.(535-537)ACG>ATG	p.T179M		NM_017560	NP_060030	P0CG23	ZN853_HUMAN	zinc finger protein 853	179	Gln-rich.					intracellular	nucleic acid binding|zinc ion binding				0						cagttacagacgcagcaagca	0.050													19	27	---	---	---	---	PASS
CYP51A1	1595	broad.mit.edu	37	7	91742934	91742934	+	3'UTR	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91742934T>C	uc003ulm.3	-	10					CYP51A1_uc011khn.1_3'UTR|CYP51A1_uc003uln.3_3'UTR	NM_000786	NP_000777	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A,						cholesterol biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|sterol 14-demethylase activity				0	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Fluconazole(DB00196)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Miconazole(DB01110)|Terconazole(DB00251)	AATGCCTTTGTGGCTTACAGT	0.338													5	227	---	---	---	---	PASS
TRRAP	8295	broad.mit.edu	37	7	98582635	98582635	+	Silent	SNP	A	G	G	rs147751423		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98582635A>G	uc003upp.2	+	61	9578	c.9369A>G	c.(9367-9369)GCA>GCG	p.A3123A	TRRAP_uc011kis.1_Silent_p.A3094A|TRRAP_uc003upr.2_Silent_p.A2811A	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3123	FAT.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AATTTTATGCACTGAAGGGAA	0.303													5	279	---	---	---	---	PASS
EPHB4	2050	broad.mit.edu	37	7	100411570	100411570	+	Silent	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100411570C>T	uc003uwn.1	-	9	2153	c.1662G>A	c.(1660-1662)GTG>GTA	p.V554V	EPHB4_uc003uwm.1_Silent_p.V461V|EPHB4_uc010lhj.1_Silent_p.V554V|EPHB4_uc011kkf.1_3'UTR	NM_004444	NP_004435	P54760	EPHB4_HUMAN	EPH receptor B4 precursor	554	Helical; (Potential).				cell proliferation|organ morphogenesis|regulation of angiogenesis	cell surface|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(4)|stomach(3)|skin(3)|central_nervous_system(2)|ovary(2)|breast(1)	15	Lung NSC(181;0.041)|all_lung(186;0.0581)					CCACAATGACCACCAGGACCA	0.642													5	16	---	---	---	---	PASS
KIAA1147	57189	broad.mit.edu	37	7	141365016	141365016	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141365016C>A	uc003vwk.2	-	6	923	c.923G>T	c.(922-924)AGC>ATC	p.S308I		NM_001080392	NP_001073861	A4D1U4	LCHN_HUMAN	hypothetical protein LOC57189	308										ovary(1)	1	Melanoma(164;0.0171)					TACCTCCAGGCTCTCGATGTC	0.602													18	25	---	---	---	---	PASS
RB1CC1	9821	broad.mit.edu	37	8	53536112	53536112	+	3'UTR	SNP	T	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53536112T>A	uc003xre.3	-	24					RB1CC1_uc003xrf.3_3'UTR	NM_014781	NP_055596	Q8TDY2	RBCC1_HUMAN	Rb1-inducible coiled coil protein 1 isoform 1						autophagy|cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding			ovary(8)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	11		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				GTTGTCTGGGTAAAAAAAAAA	0.328													2	0	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77761277	77761277	+	Silent	SNP	T	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77761277T>G	uc003yav.2	+	7	3810	c.3423T>G	c.(3421-3423)GGT>GGG	p.G1141G	ZFHX4_uc003yau.1_Silent_p.G1186G|ZFHX4_uc003yaw.1_Silent_p.G1141G	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1141						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)			TGGCAGGGGGTACCCAGCCAC	0.383										HNSCC(33;0.089)			6	29	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77776702	77776702	+	Silent	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77776702G>A	uc003yav.2	+	11	11004	c.10617G>A	c.(10615-10617)AAG>AAA	p.K3539K		NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3535						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)			TGAGCCAGAAGCTAGAAGACT	0.453										HNSCC(33;0.089)			13	49	---	---	---	---	PASS
ATP6V1C1	528	broad.mit.edu	37	8	104078550	104078550	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104078550T>C	uc003ykz.3	+	12	1173	c.928T>C	c.(928-930)TAT>CAT	p.Y310H	ATP6V1C1_uc010mbz.2_Missense_Mutation_p.Y235H|ATP6V1C1_uc003yla.2_Missense_Mutation_p.Y310H|ATP6V1C1_uc011lhl.1_Missense_Mutation_p.Y235H	NM_001695	NP_001686	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal V1 subunit	310					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|plasma membrane|proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism				0	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)			TTTTGTAAGGTATGGCTTGCC	0.328													4	170	---	---	---	---	PASS
SLA	6503	broad.mit.edu	37	8	134060024	134060024	+	Intron	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134060024A>G	uc003ytz.2	-						TG_uc003ytw.2_Intron|TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron|SLA_uc011lje.1_Intron|SLA_uc011ljf.1_Intron|SLA_uc011ljg.1_Intron|SLA_uc010mdy.1_Silent_p.L135L|SLA_uc011ljd.1_Intron	NM_001045556	NP_001039021	Q13239	SLAP1_HUMAN	Src-like-adaptor isoform a							endosome	SH3/SH2 adaptor activity			lung(1)|liver(1)	2	all_epithelial(106;3.51e-21)|Lung NSC(106;4.24e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0279)|Breast(495;0.037)	BRCA - Breast invasive adenocarcinoma(115;0.000701)			GCCAGGAGCAAAACATGCTTG	0.517													6	24	---	---	---	---	PASS
FAM135B	51059	broad.mit.edu	37	8	139164359	139164359	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139164359C>A	uc003yuy.2	-	13	2530	c.2359G>T	c.(2359-2361)GAC>TAC	p.D787Y	FAM135B_uc003yux.2_Missense_Mutation_p.D688Y|FAM135B_uc003yuz.2_RNA|FAM135B_uc003yva.2_Missense_Mutation_p.D349Y|FAM135B_uc003yvb.2_Missense_Mutation_p.D349Y	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	787										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TGCTTGGTGTCCGCATCTTCA	0.522										HNSCC(54;0.14)			9	8	---	---	---	---	PASS
AQP7	364	broad.mit.edu	37	9	33384977	33384977	+	3'UTR	SNP	T	G	G	rs13434	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33384977T>G	uc003zst.2	-	8					SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_3'UTR	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		TATTGGGGAATGGATGGGATC	0.557													4	31	---	---	---	---	PASS
C9orf144	389715	broad.mit.edu	37	9	34835451	34835451	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34835451T>G	uc003zvp.3	-	4	943	c.29A>C	c.(28-30)CAC>CCC	p.H10P		NR_024481				RecName: Full=Uncharacterized protein C9orf144A;												0						AAATGGCAGGTGGGCAGGGAG	0.537													3	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68414561	68414561	+	RNA	SNP	T	G	G	rs111423473		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68414561T>G	uc004aex.2	+	1		c.1116T>G								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		catctgttaatagcatggttt	0.005													3	4	---	---	---	---	PASS
GDA	9615	broad.mit.edu	37	9	74863260	74863260	+	3'UTR	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74863260A>G	uc004aiq.2	+	14					GDA_uc011lse.1_3'UTR|GDA_uc011lsf.1_3'UTR|GDA_uc004air.2_Intron|GDA_uc010mow.1_RNA|GDA_uc004ais.2_Intron	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)		TCAGTGTAAGACCCTCGGGCG	0.448													6	87	---	---	---	---	PASS
ZCCHC6	79670	broad.mit.edu	37	9	88938408	88938408	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88938408C>G	uc004aoq.2	-	13	2472	c.2257G>C	c.(2257-2259)GAG>CAG	p.E753Q	ZCCHC6_uc011ltf.1_RNA|ZCCHC6_uc004aor.2_RNA|ZCCHC6_uc004aos.2_RNA|ZCCHC6_uc004aot.2_Missense_Mutation_p.E630Q|ZCCHC6_uc004aou.2_Missense_Mutation_p.E753Q	NM_024617	NP_078893	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	753					RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2						CCAACTTTCTCTTTCTCGTTT	0.438													60	135	---	---	---	---	PASS
ZNF189	7743	broad.mit.edu	37	9	104162271	104162271	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104162271T>C	uc004bbh.1	+	2	415	c.139T>C	c.(139-141)TAT>CAT	p.Y47H	MRPL50_uc011lvj.1_5'Flank|MRPL50_uc004bbe.2_5'Flank|ZNF189_uc004bbg.1_Missense_Mutation_p.Y5H|ZNF189_uc004bbi.1_Missense_Mutation_p.Y33H|ZNF189_uc011lvk.1_Missense_Mutation_p.Y32H	NM_003452	NP_003443	O75820	ZN189_HUMAN	zinc finger protein 189 isoform 1	47	KRAB.				negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|kidney(1)|central_nervous_system(1)	6		Acute lymphoblastic leukemia(62;0.0559)				GATGGAGAATTATGGAAACCT	0.413													36	97	---	---	---	---	PASS
TMEM38B	55151	broad.mit.edu	37	9	108483903	108483903	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108483903G>C	uc004bcu.1	+	3	472	c.355G>C	c.(355-357)GAA>CAA	p.E119Q	TMEM38B_uc010mtn.1_Intron	NM_018112	NP_060582	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B	119	Cytoplasmic (Potential).					integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			ovary(1)|skin(1)	2						GGGAATGAAGGAAGTGACCAG	0.418													34	118	---	---	---	---	PASS
OR1L3	26735	broad.mit.edu	37	9	125437494	125437494	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125437494C>T	uc011lzb.1	+	1	86	c.86C>T	c.(85-87)GCC>GTC	p.A29V		NM_001005234	NP_001005234	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L,	29	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						CCACTCTTTGCCCTCTTTCTT	0.448													26	80	---	---	---	---	PASS
GOLGA1	2800	broad.mit.edu	37	9	127650593	127650593	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127650593T>G	uc004bpc.2	-	19	2186	c.1844A>C	c.(1843-1845)GAT>GCT	p.D615A	GOLGA1_uc010mws.2_RNA	NM_002077	NP_002068	Q92805	GOGA1_HUMAN	golgin 97	615	Potential.					Golgi cisterna membrane				ovary(1)	1						CTGTGTGAGATCCATGGCCCC	0.527													14	54	---	---	---	---	PASS
CCDC3	83643	broad.mit.edu	37	10	13040481	13040481	+	Nonsense_Mutation	SNP	C	A	A	rs139188420	byFrequency	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13040481C>A	uc001ilq.1	-	2	540	c.406G>T	c.(406-408)GGA>TGA	p.G136*	CCDC3_uc009xjb.1_Intron|CCDC3_uc001ilr.2_RNA|CCDC3_uc009xjc.1_Intron	NM_031455	NP_113643	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3 precursor	136						endoplasmic reticulum|extracellular region				ovary(1)	1		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			AAATTGACTCCGTGAGGCAAG	0.453													5	86	---	---	---	---	PASS
ANK3	288	broad.mit.edu	37	10	61833421	61833421	+	Silent	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61833421A>G	uc001jky.2	-	37	7410	c.7218T>C	c.(7216-7218)TAT>TAC	p.Y2406Y	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	2406					establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						AAGACTCCAGATAAGAAGGCA	0.423													21	83	---	---	---	---	PASS
DCHS1	8642	broad.mit.edu	37	11	6643734	6643734	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6643734G>A	uc001mem.1	-	21	9583	c.9173C>T	c.(9172-9174)TCC>TTC	p.S3058F		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	3058	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGCCAGAGAGGAGGCCACACT	0.582													6	1	---	---	---	---	PASS
STT3A	3703	broad.mit.edu	37	11	125476271	125476271	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125476271C>T	uc001qcd.2	+	8	801	c.691C>T	c.(691-693)CGT>TGT	p.R231C	STT3A_uc009zbm.2_Missense_Mutation_p.R231C|STT3A_uc001qce.2_Missense_Mutation_p.R231C|STT3A_uc010sbg.1_Missense_Mutation_p.R139C|STT3A_uc009zbn.2_Missense_Mutation_p.R5C	NM_152713	NP_689926	P46977	STT3A_HUMAN	integral membrane protein 1	231	Cytoplasmic (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity				0	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		GCTCACAGGCCGTTTCTCTCA	0.478													5	428	---	---	---	---	PASS
KLRC2	3822	broad.mit.edu	37	12	10583714	10583714	+	3'UTR	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10583714T>C	uc001qyk.2	-	6					KLRC3_uc001qyh.2_Intron|KLRC2_uc010she.1_Intron	NM_002260	NP_002251	P26717	NKG2C_HUMAN	killer cell lectin-like receptor subfamily C,						cellular defense response	integral to plasma membrane	sugar binding|transmembrane receptor activity				0						AATGCTTTACTTCTAAAGCTT	0.303													6	248	---	---	---	---	PASS
CNTN1	1272	broad.mit.edu	37	12	41302164	41302164	+	5'UTR	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41302164T>C	uc001rmm.1	+	2					CNTN1_uc009zjy.1_5'UTR|CNTN1_uc001rmn.1_5'UTR|CNTN1_uc001rmo.2_5'UTR	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor						axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TGCAGGTGTTTAAAATTATCC	0.269													73	117	---	---	---	---	PASS
ARF3	377	broad.mit.edu	37	12	49332697	49332697	+	3'UTR	SNP	T	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49332697T>G	uc001rsr.2	-	5					ARF3_uc010smc.1_3'UTR	NM_001659	NP_001650	P61204	ARF3_HUMAN	ADP-ribosylation factor 3						protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	Golgi apparatus|perinuclear region of cytoplasm	GTP binding|GTPase activity				0						ATGTCAGGGGTGGGTGGGGTG	0.592													7	28	---	---	---	---	PASS
SMARCC2	6601	broad.mit.edu	37	12	56558430	56558430	+	Silent	SNP	A	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56558430A>C	uc001skb.2	-	27	3331	c.3225T>G	c.(3223-3225)GGT>GGG	p.G1075G	SMARCC2_uc001skd.2_Splice_Site_p.A1106_splice|SMARCC2_uc001ska.2_Splice_Site_p.D1106_splice|SMARCC2_uc001skc.2_Splice_Site_p.A1105_splice|SMARCC2_uc010sqf.1_Splice_Site_p.D995_splice	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	1075	Pro-rich.				chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)			AAGGAGCATTACCCGCCACGC	0.567													5	15	---	---	---	---	PASS
AMDHD1	144193	broad.mit.edu	37	12	96360253	96360253	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96360253A>G	uc001tel.1	+	8	1266	c.1160A>G	c.(1159-1161)AAA>AGA	p.K387R	AMDHD1_uc009zth.1_Missense_Mutation_p.K278R	NM_152435	NP_689648	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	387					histidine catabolic process to glutamate and formamide	cytosol	imidazolonepropionase activity|metal ion binding			central_nervous_system(1)	1						GAAGTTGGCAAACAGGGAGAT	0.473													31	55	---	---	---	---	PASS
RILPL1	353116	broad.mit.edu	37	12	123957223	123957223	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123957223G>T	uc001ufe.2	-	7	1310	c.1074C>A	c.(1072-1074)AGC>AGA	p.S358R	RILPL1_uc001ufd.2_Missense_Mutation_p.S207R|RILPL1_uc010tas.1_3'UTR	NM_178314	NP_847884	Q5EBL4	RIPL1_HUMAN	Rab interacting lysosomal protein-like 1	358					neuroprotection	cytosol					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)		GGGAGAAGAAGCTAAACCTTT	0.498													10	77	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23915483	23915483	+	Silent	SNP	T	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23915483T>G	uc001uon.2	-	10	3121	c.2532A>C	c.(2530-2532)GTA>GTC	p.V844V	SACS_uc001uoo.2_Silent_p.V697V|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	844					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)		CAAGTTTTTGTACAATGTCTG	0.358													28	150	---	---	---	---	PASS
GPR12	2835	broad.mit.edu	37	13	27333242	27333242	+	Silent	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27333242C>T	uc010aal.2	-	2	945	c.723G>A	c.(721-723)TCG>TCA	p.S241S	GPR12_uc010tdl.1_Silent_p.S82S	NM_005288	NP_005279	P47775	GPR12_HUMAN	G protein-coupled receptor 12	241	Cytoplasmic (Potential).					integral to plasma membrane					0	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		TCACATAGTGCGACGTGGCCA	0.547													7	31	---	---	---	---	PASS
TPT1	7178	broad.mit.edu	37	13	45914820	45914820	+	Intron	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45914820C>A	uc001uzy.1	-						TPT1_uc001uzz.1_Intron|TPT1_uc010tfp.1_Silent_p.G43G|LOC100190939_uc010tfr.1_5'Flank|LOC100190939_uc001vac.2_5'Flank	NM_003295	NP_003286	P13693	TCTP_HUMAN	tumor protein, translationally-controlled 1						anti-apoptosis|response to virus	extracellular space|multivesicular body	calcium ion binding|protein binding				0		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000232)		GCCCGGACTCCCCCACGCGCA	0.677											OREG0022394	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	1	---	---	---	---	PASS
ZC3H13	23091	broad.mit.edu	37	13	46537894	46537894	+	Intron	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46537894A>G	uc010tfw.1	-						ZC3H13_uc001vaq.2_Intron|ZC3H13_uc001vas.1_3'UTR	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13								nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		GTTAAGTGCTACATAAGAACA	0.279													3	45	---	---	---	---	PASS
OR11H6	122748	broad.mit.edu	37	14	20692576	20692576	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20692576C>A	uc010tlc.1	+	1	708	c.708C>A	c.(706-708)TAC>TAA	p.Y236*		NM_001004480	NP_001004480	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H,	236	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		TGGGATCTTACACTCTGGTCA	0.488													4	172	---	---	---	---	PASS
DHRS4L1	728635	broad.mit.edu	37	14	24518003	24518003	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24518003A>G	uc010alc.2	+	8	658	c.658A>G	c.(658-660)ACT>GCT	p.T220A	DHRS4L1_uc010tnu.1_RNA	NM_001082488	NP_001075957	P0CG22	DR4L1_HUMAN	dehydrogenase/reductase (SDR family) member 4	220							binding|oxidoreductase activity				0						ACTTATCAAGACTAGCTTCAG	0.532													22	64	---	---	---	---	PASS
PRKD1	5587	broad.mit.edu	37	14	30046365	30046365	+	3'UTR	SNP	T	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30046365T>G	uc001wqh.2	-	18						NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1						cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		ATAATGGCAGTTCTGCAAGGC	0.383													8	31	---	---	---	---	PASS
UPF0639	400224	broad.mit.edu	37	14	69989009	69989009	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69989009C>T	uc010ttf.1	+	7	777	c.565C>T	c.(565-567)CGC>TGC	p.R189C		NM_001161498	NP_001154970	B9EJC2	B9EJC2_HUMAN	similar to pleckstrin homology domain protein	189											0						GGAGCTTGAGCGCCTTAACCA	0.582													14	84	---	---	---	---	PASS
YLPM1	56252	broad.mit.edu	37	14	75245373	75245373	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75245373C>T	uc001xqj.3	+	2	1221	c.1097C>T	c.(1096-1098)CCT>CTT	p.P366L	YLPM1_uc001xql.3_5'Flank	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	186	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CCTCTCCCACCTGAGGAACCC	0.393													3	72	---	---	---	---	PASS
EML5	161436	broad.mit.edu	37	14	89093186	89093186	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89093186C>T	uc001xxg.2	-	35	4922	c.4736G>A	c.(4735-4737)GGT>GAT	p.G1579D	EML5_uc001xxf.2_Missense_Mutation_p.G366D|EML5_uc001xxh.1_Missense_Mutation_p.G710D	NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like	1571	WD 23.					cytoplasm|microtubule				ovary(3)	3						ACATACTGCACCAAATGCAAT	0.443													22	50	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106780513	106780513	+	RNA	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106780513T>C	uc010tyt.1	-	413		c.15349A>G								Parts of antibodies, mostly variable regions.												0						TCACTGTGTTTCTCGCACAGT	0.617													3	13	---	---	---	---	PASS
SLC12A6	9990	broad.mit.edu	37	15	34546785	34546785	+	Silent	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34546785A>G	uc001zhw.2	-	8	1046	c.882T>C	c.(880-882)TAT>TAC	p.Y294Y	SLC12A6_uc001zhv.2_Silent_p.Y243Y|SLC12A6_uc001zhx.2_Silent_p.Y279Y|SLC12A6_uc001zhy.2_RNA|SLC12A6_uc001zhz.2_RNA|SLC12A6_uc001zia.2_Silent_p.Y235Y|SLC12A6_uc001zib.2_Silent_p.Y285Y|SLC12A6_uc001zic.2_Silent_p.Y294Y|SLC12A6_uc010bau.2_Silent_p.Y294Y|SLC12A6_uc001zid.2_Silent_p.Y235Y|SLC12A6_uc001zhu.2_Silent_p.Y106Y	NM_133647	NP_598408	Q9UHW9	S12A6_HUMAN	solute carrier family 12, member 6 isoform a	294	Helical; (Potential).				angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity			central_nervous_system(5)|ovary(1)|skin(1)	7		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	GGGGGACGATATAGACCTGTT	0.393													14	54	---	---	---	---	PASS
AQR	9716	broad.mit.edu	37	15	35240518	35240518	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35240518A>G	uc001ziv.2	-	5	458	c.277T>C	c.(277-279)TCA>CCA	p.S93P		NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius	93						catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		CAGCAGATTGACATTAAATAG	0.363													6	255	---	---	---	---	PASS
ANXA2	302	broad.mit.edu	37	15	60641324	60641324	+	Silent	SNP	T	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60641324T>G	uc002agn.2	-	13	1070	c.910A>C	c.(910-912)AGG>CGG	p.R304R	ANXA2_uc002agk.2_Silent_p.R304R|ANXA2_uc002agl.2_Silent_p.R304R|ANXA2_uc002agm.2_Silent_p.R322R|ANXA2_uc010uhd.1_RNA	NM_001136015	NP_001129487	P07355	ANXA2_HUMAN	annexin A2 isoform 2	304	Annexin 4.				angiogenesis|positive regulation of vesicle fusion|skeletal system development	basement membrane|melanosome|midbody|soluble fraction	calcium ion binding|calcium-dependent phospholipid binding|cytoskeletal protein binding|phospholipase inhibitor activity			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Tenecteplase(DB00031)	AATTCAGACCTAATTTTCAAC	0.493													26	33	---	---	---	---	PASS
MGRN1	23295	broad.mit.edu	37	16	4727555	4727555	+	Silent	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4727555G>A	uc002cwz.2	+	11	1183	c.1047G>A	c.(1045-1047)CTG>CTA	p.L349L	MGRN1_uc002cxa.2_Silent_p.L349L|MGRN1_uc010btx.2_Silent_p.L350L|MGRN1_uc010btw.2_Silent_p.L350L|MGRN1_uc002cxb.2_Silent_p.L388L|MGRN1_uc010uxo.1_Silent_p.L349L|MGRN1_uc010uxp.1_Silent_p.L349L|MGRN1_uc010uxq.1_Intron	NM_001142290	NP_001135762	O60291	MGRN1_HUMAN	mahogunin, ring finger 1 isoform 3	349					endosome to lysosome transport|negative regulation of cAMP-mediated signaling|negative regulation of G-protein coupled receptor protein signaling pathway|protein monoubiquitination	cytosol|early endosome|nucleus|plasma membrane|plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2						CCCAGAGCCTGGAGCATGATG	0.697													2	1	---	---	---	---	PASS
LCMT1	51451	broad.mit.edu	37	16	25162930	25162930	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25162930C>G	uc002dnx.1	+	5	618	c.460C>G	c.(460-462)CAG>GAG	p.Q154E	LCMT1_uc002dny.1_Intron|LCMT1_uc002dnz.1_Missense_Mutation_p.Q54E|LCMT1_uc002doa.1_Intron|uc002dob.1_5'Flank	NM_016309	NP_057393	Q9UIC8	LCMT1_HUMAN	leucine carboxyl methyltransferase 1 isoform a	154							protein binding|protein C-terminal carboxyl O-methyltransferase activity|S-adenosylmethionine-dependent methyltransferase activity				0				GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)	GGACACACTTCAGATGGGCAA	0.423													62	136	---	---	---	---	PASS
SLC5A2	6524	broad.mit.edu	37	16	31501699	31501699	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31501699G>C	uc002ecf.3	+	14	1881	c.1862G>C	c.(1861-1863)GGG>GCG	p.G621A	SLC5A2_uc010car.2_RNA|C16orf58_uc002ecg.2_5'Flank|C16orf58_uc002ech.1_3'UTR|C16orf58_uc002eci.1_3'UTR	NM_003041	NP_003032	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose	621	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to membrane	low-affinity glucose:sodium symporter activity			ovary(1)	1						AGCAGAGGTGGGGTGGGCAGT	0.652													4	6	---	---	---	---	PASS
TAF1C	9013	broad.mit.edu	37	16	84212370	84212370	+	3'UTR	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84212370A>G	uc002fhn.2	-	14					TAF1C_uc002fhm.2_3'UTR|TAF1C_uc010vnx.1_3'UTR|TAF1C_uc010vny.1_3'UTR|TAF1C_uc010vnz.1_3'UTR|TAF1C_uc002fho.2_3'UTR|TAF1C_uc010voa.1_3'UTR|TAF1C_uc002fhp.1_RNA	NM_005679	NP_005670	Q15572	TAF1C_HUMAN	TBP-associated factor 1C isoform 1						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						AGAAACTACTACTGTATTTTG	0.493													4	2	---	---	---	---	PASS
GP1BA	2811	broad.mit.edu	37	17	4837666	4837666	+	Silent	SNP	A	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4837666A>C	uc010vsq.1	+	3	1803	c.1728A>C	c.(1726-1728)ACA>ACC	p.T576T	uc002fzn.1_RNA	NM_000173	NP_000164	P07359	GP1BA_HUMAN	platelet glycoprotein Ib alpha polypeptide	589											0						GGCAAGTGACAGTGCCCCGGG	0.627											OREG0024109	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	17	---	---	---	---	PASS
TNFSF12-TNFSF13	407977	broad.mit.edu	37	17	7464289	7464289	+	3'UTR	SNP	T	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7464289T>G	uc002ghi.1	+	11					SENP3_uc002ghm.2_5'Flank|TNFSF13_uc002ghj.2_Intron|TNFSF13_uc002ghk.2_3'UTR|TNFSF13_uc002ghl.2_3'UTR|TNFSF13_uc010cmk.2_3'UTR|TNFSF13_uc010vua.1_3'UTR	NM_172089	NP_742086	Q8IZK7	Q8IZK7_HUMAN	TNFSF12-TNFSF13 protein						immune response	extracellular space|membrane	cytokine activity|tumor necrosis factor receptor binding				0		Prostate(122;0.157)				CGTTCCTCACTTTTCCCTTTT	0.507											OREG0024138	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	60	132	---	---	---	---	PASS
MYH8	4626	broad.mit.edu	37	17	10304870	10304870	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10304870G>A	uc002gmm.2	-	23	3016	c.2921C>T	c.(2920-2922)ACG>ATG	p.T974M	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	974	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						CTTGTTCTCCGTGGCATGTTT	0.393									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				7	385	---	---	---	---	PASS
SLFN14	342618	broad.mit.edu	37	17	33875959	33875959	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33875959T>C	uc010ctu.1	-	4	2067	c.2038A>G	c.(2038-2040)AAC>GAC	p.N680D		NM_001129820	NP_001123292	P0C7P3	SLN14_HUMAN	schlafen family member 14	680							ATP binding			central_nervous_system(1)	1						TGGGTGATGTTCTTAGCCTTC	0.423													5	228	---	---	---	---	PASS
KRTAP1-3	81850	broad.mit.edu	37	17	39190639	39190639	+	Silent	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39190639G>A	uc002hvv.2	-	1	469	c.435C>T	c.(433-435)CGC>CGT	p.R145R		NM_030966	NP_112228	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	155						extracellular region|keratin filament	structural constituent of epidermis				0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGTAGGATGGGCGGCAGCAGG	0.612													3	11	---	---	---	---	PASS
ATP6V0A1	535	broad.mit.edu	37	17	40630546	40630546	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40630546G>T	uc002hzr.2	+	7	739	c.572G>T	c.(571-573)TGC>TTC	p.C191F	ATP6V0A1_uc002hzq.2_Missense_Mutation_p.C191F|ATP6V0A1_uc002hzs.2_Missense_Mutation_p.C198F|ATP6V0A1_uc010wgj.1_Missense_Mutation_p.C148F|ATP6V0A1_uc010wgk.1_Missense_Mutation_p.C148F|ATP6V0A1_uc010cyg.2_Intron|ATP6V0A1_uc010wgl.1_Missense_Mutation_p.C50F	NM_001130021	NP_001123493	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	191	Cytoplasmic (Potential).				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)		TGGCGGGTATGCCGGGGAAAT	0.532													6	88	---	---	---	---	PASS
AARSD1	80755	broad.mit.edu	37	17	41122331	41122331	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41122331G>T	uc002icf.2	-	7	754	c.536C>A	c.(535-537)CCT>CAT	p.P179H	AARSD1_uc002icd.2_Missense_Mutation_p.P118H|AARSD1_uc002ice.2_Missense_Mutation_p.P88H|AARSD1_uc010whg.1_Missense_Mutation_p.P179H|AARSD1_uc002icg.2_RNA|AARSD1_uc002ich.2_Missense_Mutation_p.P141H|AARSD1_uc010whh.1_Missense_Mutation_p.P146H	NM_025267	NP_079543	Q9BTE6	AASD1_HUMAN	alanyl-tRNA synthetase domain containing 1	Error:Variant_position_missing_in_Q9BTE6_after_alignment					alanyl-tRNA aminoacylation	cytoplasm	alanine-tRNA ligase activity|ATP binding|metal ion binding|nucleic acid binding				0		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		GGCAGGTGGAGGTCTCTTGGT	0.448													45	131	---	---	---	---	PASS
MED13	9969	broad.mit.edu	37	17	60106973	60106973	+	Silent	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60106973T>C	uc002izo.2	-	8	1289	c.1212A>G	c.(1210-1212)GAA>GAG	p.E404E	MED13_uc002izp.2_Silent_p.E20E	NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	404					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						CAGCTGTCGCTTCTTCGCATA	0.368													5	207	---	---	---	---	PASS
KCNH6	81033	broad.mit.edu	37	17	61607502	61607502	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61607502G>T	uc002jay.2	+	3	438	c.358G>T	c.(358-360)GGG>TGG	p.G120W	KCNH6_uc002jax.1_Missense_Mutation_p.G120W|KCNH6_uc010wpl.1_5'UTR|KCNH6_uc010wpm.1_Missense_Mutation_p.G120W|KCNH6_uc002jaz.1_Missense_Mutation_p.G120W	NM_030779	NP_110406	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H,	120	PAC.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent|signal transduction					skin(1)	1					Ibutilide(DB00308)	GAACGAGGACGGGGCTGTCAT	0.627													6	10	---	---	---	---	PASS
ANKRD30B	374860	broad.mit.edu	37	18	14769345	14769345	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14769345A>G	uc010dlo.2	+	8	1409	c.1229A>G	c.(1228-1230)GAT>GGT	p.D410G	ANKRD30B_uc010xak.1_RNA	NM_001145029	NP_001138501	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	410										ovary(1)|skin(1)	2						TTAATAGTGGATGTGAGTTCT	0.224													5	199	---	---	---	---	PASS
SF4	57794	broad.mit.edu	37	19	19388598	19388598	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19388598T>C	uc002nmh.2	-	12	1728	c.1726A>G	c.(1726-1728)AAG>GAG	p.K576E	SF4_uc002nmf.2_Missense_Mutation_p.K126E|SF4_uc002nmg.2_Missense_Mutation_p.K126E|SF4_uc002nmi.2_Missense_Mutation_p.K366E|SF4_uc002nmj.2_Missense_Mutation_p.K366E|SF4_uc002nme.2_Missense_Mutation_p.K126E	NM_172231	NP_757386	Q8IWZ8	SUGP1_HUMAN	splicing factor 4	576	G-patch.				nuclear mRNA splicing, via spliceosome	nucleoplasm|spliceosomal complex	RNA binding				0						TCGCCCTCCTTCCAGCCCATC	0.582													3	19	---	---	---	---	PASS
ZNF761	388561	broad.mit.edu	37	19	53959771	53959771	+	Silent	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53959771C>T	uc010eqp.2	+	7	2468	c.2010C>T	c.(2008-2010)ACC>ACT	p.T670T	ZNF761_uc010ydy.1_Silent_p.T616T|ZNF761_uc002qbt.1_Silent_p.T616T	NM_001008401	NP_001008401	Q86XN6	ZN761_HUMAN	zinc finger protein 761	670	C2H2-type 17.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00786)		GTGGCAAGACCTTTAGTCGGA	0.378													10	70	---	---	---	---	PASS
RRBP1	6238	broad.mit.edu	37	20	17605265	17605265	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17605265C>G	uc002wpv.1	-	14	2158	c.1804G>C	c.(1804-1806)GAG>CAG	p.E602Q	RRBP1_uc002wpt.1_5'Flank|RRBP1_uc002wpu.2_Missense_Mutation_p.E376Q|RRBP1_uc002wpw.1_Missense_Mutation_p.E602Q|RRBP1_uc010gcl.1_Missense_Mutation_p.E376Q|RRBP1_uc010gcm.1_Intron	NM_001042576	NP_001036041	Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1035	Cytoplasmic (Potential).				protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1						CAGGCCTGCTCGGCCGTGGCC	0.632													3	8	---	---	---	---	PASS
JAM2	58494	broad.mit.edu	37	21	27066208	27066208	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27066208C>A	uc002ylp.1	+	4	927	c.382C>A	c.(382-384)CTG>ATG	p.L128M	JAM2_uc011ace.1_Missense_Mutation_p.L128M|JAM2_uc002ylq.1_RNA|JAM2_uc011acf.1_Missense_Mutation_p.L92M|JAM2_uc010glh.1_RNA|JAM2_uc002ylr.1_Missense_Mutation_p.L128M|JAM2_uc010gli.1_Missense_Mutation_p.L128M	NM_021219	NP_067042	P57087	JAM2_HUMAN	junctional adhesion molecule 2 precursor	128	Extracellular (Potential).				blood coagulation|cell-cell adhesion|leukocyte migration	integral to plasma membrane|tight junction					0						TACAGTCACTCTGGAAGTATT	0.498													4	166	---	---	---	---	PASS
ENTHD1	150350	broad.mit.edu	37	22	40231918	40231918	+	Missense_Mutation	SNP	A	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40231918A>T	uc003ayg.2	-	4	889	c.638T>A	c.(637-639)GTT>GAT	p.V213D		NM_152512	NP_689725	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	213										ovary(2)|skin(1)	3	Melanoma(58;0.0749)					AGGCAAATGAACATCTTGGCA	0.338													123	243	---	---	---	---	PASS
DACH2	117154	broad.mit.edu	37	X	86069820	86069820	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86069820G>T	uc004eew.2	+	10	1837	c.1667G>T	c.(1666-1668)GGC>GTC	p.G556V	DACH2_uc004eex.2_Missense_Mutation_p.G543V|DACH2_uc010nmq.2_Missense_Mutation_p.G422V|DACH2_uc011mra.1_Missense_Mutation_p.G389V|DACH2_uc010nmr.2_Missense_Mutation_p.G337V|DACH2_uc004eey.2_Missense_Mutation_p.G249V|DACH2_uc004eez.2_Missense_Mutation_p.G239V	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a	556					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5						AGTGACAGTGGCCTGAGGATG	0.363													7	60	---	---	---	---	PASS
TCEAL8	90843	broad.mit.edu	37	X	102508844	102508844	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102508844G>A	uc004ejx.2	-	3	291	c.64C>T	c.(64-66)CGC>TGC	p.R22C	TCEAL8_uc004ejy.2_Missense_Mutation_p.R22C	NM_153333	NP_699164	Q8IYN2	TCAL8_HUMAN	transcription elongation factor A (SII)-like 8	22					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1						TCCAAAGGGCGATCTTCCTCG	0.443													70	36	---	---	---	---	PASS
HS6ST2	90161	broad.mit.edu	37	X	131842489	131842489	+	Intron	SNP	C	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131842489C>T	uc011mve.1	-						HS6ST2_uc011mvb.1_Splice_Site_p.S181_splice|HS6ST2_uc011mvc.1_Intron|HS6ST2_uc011mvd.1_Splice_Site_p.S327_splice|HS6ST2_uc011mva.1_Intron	NM_147175	NP_671704	Q96MM7	H6ST2_HUMAN	heparan sulfate 6-O-sulfotransferase 2 isoform							integral to membrane	sulfotransferase activity				0	Acute lymphoblastic leukemia(192;0.000127)					TTGTTACTTACCTTGCTGCAT	0.363													5	182	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2965	2965	+	5'Flank	SNP	A	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2965A>C	uc004coq.3	-						uc004cos.3_RNA|uc011mfh.1_5'Flank					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		TCTAGAGTCCATATCAACAAT	0.433													42	8	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	12009	12009	+	RNA	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:12009G>A	uc004cov.3	+	1		c.1432G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank|uc004coy.2_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		AACACAATGGGGCTCACTCAC	0.443													44	19	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15591	15591	+	3'UTR	SNP	G	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15591G>A	uc004coy.2	+	1					uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		CACAATTCTCCGATCCGTCCC	0.478											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	12	52	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	38706776	38706776	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38706776delG								POU3F1 (194326 upstream) : RRAGC (598239 downstream)																							gcaggaggcagggagagatgg	0.000													4	2	---	---	---	---	
RNF220	55182	broad.mit.edu	37	1	45000632	45000632	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45000632delA	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						TTAGAGCGGGAAAGGGGGAGC	0.423													4	2	---	---	---	---	
PLK3	1263	broad.mit.edu	37	1	45269620	45269620	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45269620delC	uc001cmn.2	+	10	1282	c.1182delC	c.(1180-1182)GGCfs	p.G394fs	PLK3_uc001cmo.2_RNA	NM_004073	NP_004064	Q9H4B4	PLK3_HUMAN	polo-like kinase 3	394						membrane	ATP binding|protein binding|protein serine/threonine kinase activity				0	Acute lymphoblastic leukemia(166;0.155)					CAGCTTCTGGCCCAGCCCCTG	0.627													4	2	---	---	---	---	
CELSR2	1952	broad.mit.edu	37	1	109816863	109816864	+	3'UTR	INS	-	C	C	rs145508961	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109816863_109816864insC	uc001dxa.3	+	34						NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2						dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|lung(3)|skin(1)	8		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TAGTGCCAACTCCCCCCCCACC	0.550													4	2	---	---	---	---	
OTUD7B	56957	broad.mit.edu	37	1	149935950	149935950	+	Intron	DEL	C	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149935950delC	uc001etn.2	-						OTUD7B_uc001eto.2_3'UTR	NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne						negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			AGGTCTCATGCCCACCACCAG	0.428													4	2	---	---	---	---	
ATF6	22926	broad.mit.edu	37	1	161885415	161885416	+	Intron	DEL	TT	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161885415_161885416delTT	uc001gbr.2	+							NM_007348	NP_031374	P18850	ATF6A_HUMAN	activating transcription factor 6						positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)			tacaaatgtctttttttttttt	0.000													4	2	---	---	---	---	
DENND1B	163486	broad.mit.edu	37	1	197611602	197611602	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197611602delA	uc001guf.3	-						DENND1B_uc010ppe.1_Intron|DENND1B_uc010ppf.1_Intron|DENND1B_uc001gue.3_Intron|DENND1B_uc001gug.3_Intron	NM_144977	NP_659414	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B isoform 2							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0						AGTTAAAAAGAAAAAAAAACT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	219681702	219681702	+	IGR	DEL	T	-	-	rs68078464		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219681702delT								LYPLAL1 (295496 upstream) : SLC30A10 (177067 downstream)																							aaaagatacatttttttttcc	0.144													0	6	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	231856842	231856842	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231856842delT	uc001huz.2	+						TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwo.1_Intron|DISC1_uc010pwp.1_Intron|DISC1_uc010pwq.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron|DISC1_uc001hux.1_Intron|DISC1_uc001hvc.3_Intron|DISC1_uc010pwn.1_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				TGAGAAATGATGtcctcatct	0.219													40	28	---	---	---	---	
ROCK2	9475	broad.mit.edu	37	2	11407634	11407634	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11407634delA	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)		TTTCACATACAAaaaaaaaaa	0.323													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12435354	12435355	+	Intron	DEL	TC	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12435354_12435355delTC	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		TACCATGCCTTCTCTCTCTCTC	0.302													4	2	---	---	---	---	
XDH	7498	broad.mit.edu	37	2	31599403	31599405	+	Intron	DEL	TAG	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31599403_31599405delTAG	uc002rnv.1	-							NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase						purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)	acagcagtaatagtagtagtagt	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38078671	38078671	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38078671delA								CDC42EP3 (179345 upstream) : FAM82A1 (73791 downstream)																							gtcacagcttaaatgtcactt	0.114													4	2	---	---	---	---	
EML4	27436	broad.mit.edu	37	2	42515211	42515213	+	Intron	DEL	GTA	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42515211_42515213delGTA	uc002rsi.2	+						EML4_uc010fap.2_Intron|EML4_uc002rsj.2_Intron	NM_019063	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4						microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250						AAATACAATTGTAGTAAATAGTG	0.305			T	ALK	NSCLC								39	24	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46228548	46228548	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46228548delA	uc002rut.2	+	7	1026	c.829delA	c.(829-831)AAAfs	p.K277fs		NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon	277	Phorbol-ester/DAG-type 2.				activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			TACAGTCTGCAAAATGAATGT	0.448													103	51	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	46894082	46894083	+	IGR	INS	-	T	T	rs142005664	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46894082_46894083insT								CRIPT (41202 upstream) : SOCS5 (32016 downstream)																							ATATATTTTACTTTTTGGTTTT	0.411													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66562252	66562253	+	IGR	INS	-	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66562252_66562253insA								SPRED2 (902596 upstream) : MEIS1 (100279 downstream)																							CAATTTAGAGGAAAAAAAAGAG	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91694509	91694509	+	IGR	DEL	C	-	-	rs12105565	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91694509delC								None (None upstream) : LOC654342 (110683 downstream)																							TGCAATTTTTCTTTCCTTCAT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91771590	91771591	+	IGR	DEL	TT	-	-	rs71250102		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91771590_91771591delTT								None (None upstream) : LOC654342 (33601 downstream)																							caggatttccttttttttttct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91778669	91778669	+	IGR	DEL	G	-	-	rs111253530		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91778669delG								None (None upstream) : LOC654342 (26523 downstream)																							CTCAGGGCCTGGGCACAAGTG	0.567													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131407580	131407581	+	IGR	INS	-	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131407580_131407581insA								LOC150527 (100109 upstream) : C2orf14 (30042 downstream)																							TGAAGAAAATGAAAAAAAAGAG	0.396													4	2	---	---	---	---	
ZAK	51776	broad.mit.edu	37	2	173956354	173956354	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173956354delT	uc002uhz.2	+						ZAK_uc002uhx.2_Intron|ZAK_uc002uhy.2_Intron|ZAK_uc010zei.1_Intron|ZAK_uc002uia.1_Intron	NM_016653	NP_057737	Q9NYL2	MLTK_HUMAN	MLK-related kinase isoform 1						activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			lung(3)|stomach(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.176)			TAAGACACTGTTTTTTTTAAC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174454287	174454288	+	IGR	DEL	TG	-	-	rs112705953		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174454287_174454288delTG								CDCA7 (220569 upstream) : SP3 (318971 downstream)																							TTCAAAGCACTGTGTGTGTGTG	0.366													4	2	---	---	---	---	
COL4A4	1286	broad.mit.edu	37	2	227906981	227906981	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227906981delA	uc010zlt.1	-							NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CCTGAGGATGACAGGGAAGTT	0.493													32	20	---	---	---	---	
COL4A4	1286	broad.mit.edu	37	2	227906983	227906984	+	Intron	DEL	AG	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227906983_227906984delAG	uc010zlt.1	-							NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TGAGGATGACAGGGAAGTTTTG	0.485													32	20	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	30317725	30317725	+	IGR	DEL	A	-	-	rs61005881	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30317725delA								RBMS3 (271106 upstream) : TGFBR2 (330269 downstream)																							gaatgagaggaaaaaaaaaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75605142	75605143	+	IGR	INS	-	A	A	rs145455361	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75605142_75605143insA								FAM86D (120876 upstream) : MIR1324 (74771 downstream)																							aacaaactgtgaaaaaagaaag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	80003942	80003942	+	IGR	DEL	G	-	-	rs77429452		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80003942delG								ROBO1 (186883 upstream) : None (None downstream)																							CGTCCTGAAAGATAAGCCCAA	0.403													4	2	---	---	---	---	
KIAA1524	57650	broad.mit.edu	37	3	108278419	108278419	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108278419delA	uc003dxb.3	-							NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen							cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3						acaaggtagcaaaaaaaaatc	0.025													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	125405184	125405184	+	IGR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125405184delT								OSBPL11 (90803 upstream) : MIR548I1 (104063 downstream)																							TGGCGATGAGTAGAGGCACAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145327274	145327275	+	IGR	INS	-	T	T	rs3057336		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145327274_145327275insT								None (None upstream) : PLOD2 (459953 downstream)																							atatctgggtcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	154410957	154410957	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154410957delA								GPR149 (263453 upstream) : MME (330956 downstream)																							gttgcaagttaaaaaaaaagg	0.075													4	2	---	---	---	---	
PHC3	80012	broad.mit.edu	37	3	169888973	169888974	+	Intron	DEL	CT	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169888973_169888974delCT	uc010hws.1	-						PHC3_uc003fgl.2_Intron|PHC3_uc011bpq.1_Intron|PHC3_uc011bpr.1_Intron|PHC3_uc003fgm.2_Intron|PHC3_uc003fgo.1_Intron|PHC3_uc003fgp.3_3'UTR|PHC3_uc003fgq.3_3'UTR	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)			TTTTTTAAGACTCAGATTTTCA	0.277													4	2	---	---	---	---	
UBXN7	26043	broad.mit.edu	37	3	196099171	196099172	+	Intron	INS	-	TC	TC	rs144595952	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196099171_196099172insTC	uc003fwm.3	-						UBXN7_uc003fwn.3_Intron|UBXN7_uc010iae.2_Intron	NM_015562	NP_056377	O94888	UBXN7_HUMAN	UBX domain containing 7								protein binding			ovary(2)|pancreas(1)	3						TAATAGCTGATtctctctctct	0.163													3	3	---	---	---	---	
TMEM175	84286	broad.mit.edu	37	4	946486	946487	+	Intron	DEL	TG	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:946486_946487delTG	uc003gbq.2	+						TMEM175_uc010ibl.1_Intron|TMEM175_uc003gbp.1_Intron|TMEM175_uc003gbr.2_Intron|TMEM175_uc003gbu.2_Intron|TMEM175_uc003gbs.2_Intron|TMEM175_uc003gbt.2_Intron|TMEM175_uc003gbv.2_Intron|TMEM175_uc010ibm.2_Intron	NM_032326	NP_115702	Q9BSA9	TM175_HUMAN	transmembrane protein 175							integral to membrane					0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TCCTGTGCTCtgtgtgtgtgtg	0.342													4	2	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20410162	20410163	+	Intron	INS	-	CT	CT	rs138651650	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20410162_20410163insCT	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						cagtttgctgactctgctgtgc	0.074													3	4	---	---	---	---	
KIAA1211	57482	broad.mit.edu	37	4	57064906	57064906	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57064906delA	uc003hbk.2	+							NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482											ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)					GAAAGTAAACAAAAAAAAGAC	0.318													8	4	---	---	---	---	
MAPK10	5602	broad.mit.edu	37	4	87248667	87248667	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87248667delT	uc003hpq.2	-						MAPK10_uc010ikg.2_Intron|MAPK10_uc003hpr.2_Intron|MAPK10_uc003hps.2_Intron|MAPK10_uc003hpt.2_Intron|MAPK10_uc003hpu.2_Intron|MAPK10_uc003hpv.2_Intron|MAPK10_uc010ikh.1_Intron	NM_138982	NP_620448	P53779	MK10_HUMAN	mitogen-activated protein kinase 10 isoform 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		AATTACTATCTTTTTTTTTTG	0.308													4	2	---	---	---	---	
ELOVL6	79071	broad.mit.edu	37	4	111055820	111055820	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111055820delA	uc003hzz.2	-						ELOVL6_uc003iaa.2_Intron	NM_001130721	NP_001124193	Q9H5J4	ELOV6_HUMAN	elongation of very long chain fatty acids-like						fatty acid elongation, saturated fatty acid|long-chain fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process		fatty acid elongase activity|protein binding			haematopoietic_and_lymphoid_tissue(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.00462)		TACAGTGTTTAAAAGGGATGA	0.194													4	2	---	---	---	---	
LARP7	51574	broad.mit.edu	37	4	113571071	113571072	+	Intron	DEL	AC	-	-	rs36087422		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113571071_113571072delAC	uc003iay.2	+						LARP7_uc003iaz.2_Intron|LARP7_uc003iba.2_Intron|LARP7_uc003ibb.2_Intron|uc011cfy.1_5'Flank|MIR367_hsa-mir-367|MI0000775_5'Flank|MIR302D_hsa-mir-302d|MI0000774_5'Flank|uc011cfz.1_5'Flank|MIR302A_hsa-mir-302a|MI0000738_5'Flank|MIR302C_hsa-mir-302c|MI0000773_5'Flank|MIR302B_hsa-mir-302b|MI0000772_5'Flank|uc011cga.1_5'Flank	NM_016648	NP_057732	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7						RNA processing	nucleoplasm|ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(3)	3		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		AGTTTTCTCTACAGTTTTCATC	0.317													1	5	---	---	---	---	
HHIP	64399	broad.mit.edu	37	4	145658352	145658352	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145658352delA	uc003ijs.1	+							NM_022475	NP_071920	Q96QV1	HHIP_HUMAN	hedgehog-interacting protein precursor							cytoplasm|extracellular region	catalytic activity|protein binding|zinc ion binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		AGAGACTTCTAAGTGTAATCA	0.438													4	2	---	---	---	---	
FAM160A1	729830	broad.mit.edu	37	4	152431873	152431873	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152431873delA	uc003imj.2	+							NM_001109977	NP_001103447	Q05DH4	F16A1_HUMAN	hypothetical protein LOC729830												0						TTTTACATTTAAAAATGTTTT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190545398	190545399	+	IGR	INS	-	ATT	ATT	rs35790619		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190545398_190545399insATT								None (None upstream) : FRG1 (316575 downstream)																							ttgtggaagacgttgtgatcac	0.119													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	19247127	19247127	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19247127delA								None (None upstream) : CDH18 (226030 downstream)																							ACTACTGGATAAAAAAAAAGT	0.239													4	3	---	---	---	---	
NIPBL	25836	broad.mit.edu	37	5	36985915	36985915	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36985915delG	uc003jkl.3	+	10	3132	c.2633delG	c.(2632-2634)AGGfs	p.R878fs	NIPBL_uc003jkk.3_Frame_Shift_Del_p.R878fs|NIPBL_uc003jkm.1_Frame_Shift_Del_p.R757fs	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	878					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			GGGGACTCAAGGGAAAGACCA	0.363													42	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	52429190	52429190	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52429190delG								MOCS2 (23592 upstream) : FST (347405 downstream)																							GCCCAAGCTAGGGGGAACTGT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	52550744	52550744	+	IGR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52550744delT								MOCS2 (145146 upstream) : FST (225851 downstream)																							AATCTCAACCTTTTTTTTTTA	0.358													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	55882910	55882910	+	IGR	DEL	C	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55882910delC								ANKRD55 (353724 upstream) : MAP3K1 (227990 downstream)																							CCTTATTCCTCCCCCCAACAA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87404829	87404829	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87404829delA								CCNH (695993 upstream) : TMEM161B (86195 downstream)																							AAATAATTGGAAAAAGGGCTG	0.393													4	2	---	---	---	---	
ZMAT2	153527	broad.mit.edu	37	5	140084376	140084376	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140084376delT	uc003lgy.1	+							NM_144723	NP_653324	Q96NC0	ZMAT2_HUMAN	zinc finger, matrin type 2							nucleus	DNA binding|zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGGCCttattttttttttt	0.209													4	2	---	---	---	---	
PCDHB14	56122	broad.mit.edu	37	5	140602823	140602823	+	5'Flank	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140602823delA	uc003ljb.2	+						PCDHB14_uc011dal.1_5'Flank	NM_018934	NP_061757	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14 precursor						calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTTTTTAATGAAAAAAAAAAC	0.294													2	4	---	---	---	---	
LARS	51520	broad.mit.edu	37	5	145539765	145539765	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145539765delT	uc003lnx.1	-						LARS_uc011dbq.1_Intron|LARS_uc011dbr.1_Intron|LARS_uc011dbs.1_Intron	NM_020117	NP_064502	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase						leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	gcctggctaattttttttttt	0.050													4	2	---	---	---	---	
SPINK13	153218	broad.mit.edu	37	5	147649399	147649399	+	Intron	DEL	A	-	-	rs71764680		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147649399delA	uc003lpc.2	+						uc003lpb.1_Intron|SPINK13_uc010jgt.2_Intron	NM_001040129	NP_001035218	Q1W4C9	ISK13_HUMAN	serine PI Kazal type 5-like 3 precursor							extracellular region	serine-type endopeptidase inhibitor activity				0						TTTTTGGCAGAAAAAAAAAAG	0.393													5	4	---	---	---	---	
ZNF300	91975	broad.mit.edu	37	5	150276178	150276179	+	Frame_Shift_Ins	INS	-	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150276178_150276179insA	uc003lsy.1	-	6	889_890	c.622_623insT	c.(622-624)TCAfs	p.S208fs	IRGM_uc011dcl.1_Intron	NM_052860	NP_443092	Q96RE9	ZN300_HUMAN	zinc finger protein 300	208					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTTTTTTCTTGAATTGCTCTTA	0.327													133	76	---	---	---	---	
KCNIP1	30820	broad.mit.edu	37	5	170000647	170000647	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170000647delA	uc003mas.2	+						KCNIP1_uc003map.2_Intron|KCNIP1_uc003mat.2_Intron|KCNIP1_uc010jjp.2_Intron|KCNIP1_uc010jjq.2_Intron	NM_001034837	NP_001030009	Q9NZI2	KCIP1_HUMAN	Kv channel interacting protein 1 isoform 1						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			acccattgagaaaaaaaaaat	0.005													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	175348042	175348044	+	IGR	DEL	ATG	-	-	rs139572932		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175348042_175348044delATG								CPLX2 (37019 upstream) : THOC3 (38492 downstream)																							agtgaggataatgagattgacct	0.236													3	4	---	---	---	---	
DCDC2	51473	broad.mit.edu	37	6	24302523	24302523	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24302523delA	uc003ndx.2	-						DCDC2_uc003ndy.2_Intron	NM_016356	NP_057440	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2						cellular defense response|intracellular signal transduction|neuron migration					ovary(1)	1		Ovarian(999;0.101)				TGATCTGTGGAAAAAAAAAAA	0.303													3	3	---	---	---	---	
HLA-B	3106	broad.mit.edu	37	6	31256478	31256479	+	Intron	INS	-	AT	AT			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31256478_31256479insAT	uc003ntf.2	-						HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron			P01889	1B07_HUMAN	SubName: Full=MHC class I antigen;						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0						TCCTGTGGTGACACCTCTTCCA	0.450									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				4	5	---	---	---	---	
HLA-B	3106	broad.mit.edu	37	6	31256479	31256480	+	Intron	INS	-	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31256479_31256480insA	uc003ntf.2	-						HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron			P01889	1B07_HUMAN	SubName: Full=MHC class I antigen;						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0						CCTGTGGTGACACCTCTTCCAC	0.455									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				4	5	---	---	---	---	
TRERF1	55809	broad.mit.edu	37	6	42195939	42195939	+	3'UTR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42195939delT	uc003osd.2	-	18					TRERF1_uc011duq.1_3'UTR|TRERF1_uc003osb.2_3'UTR|TRERF1_uc003osc.2_3'UTR|TRERF1_uc003ose.2_3'UTR	NM_033502	NP_277037	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1						cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			AGAAATAGGATTTTTTTTTCT	0.328													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	47388057	47388057	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47388057delA								TNFRSF21 (110377 upstream) : CD2AP (57468 downstream)																							ACTTATTAAGAAAAAAAAAGA	0.388													10	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57235037	57235037	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57235037delT	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	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)		AGAATGAGTATTTTTTTTAGG	0.303													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57432144	57432145	+	Intron	INS	-	T	T	rs11435895		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57432144_57432145insT	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)		gtatgcacctctaaaaaaaata	0.030													6	3	---	---	---	---	
MRAP2	112609	broad.mit.edu	37	6	84760025	84760025	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84760025delT	uc003pkg.3	+						MRAP2_uc010kbo.2_Intron	NM_138409	NP_612418	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2						positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding			skin(2)	2						CATGTTACTGTTTTTTTAAAG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	87241857	87241858	+	IGR	INS	-	A	A	rs151334269		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87241857_87241858insA								SNHG5 (853406 upstream) : HTR1E (405166 downstream)																							aataacagagtaaaaaaaaaca	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	98168924	98168924	+	IGR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98168924delT								C6orf167 (437863 upstream) : MIR2113 (303483 downstream)																							tctttacccatttttttttgg	0.000													4	2	---	---	---	---	
CDC40	51362	broad.mit.edu	37	6	110534599	110534599	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110534599delT	uc003pua.2	+							NM_015891	NP_056975	O60508	PRP17_HUMAN	cell division cycle 40 homolog						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm					0		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		tgtttttttgttttttttttt	0.154													4	2	---	---	---	---	
SLC16A10	117247	broad.mit.edu	37	6	111493825	111493825	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111493825delT	uc003pus.2	+						SLC16A10_uc003pur.3_Intron	NM_018593	NP_061063	Q8TF71	MOT10_HUMAN	solute carrier family 16, member 10						aromatic amino acid transport|cellular nitrogen compound metabolic process|ion transport	basolateral plasma membrane|integral to membrane	amino acid transmembrane transporter activity				0		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)		TAAATGTGTATTATATCAATG	0.323													60	37	---	---	---	---	
IL22RA2	116379	broad.mit.edu	37	6	137469116	137469116	+	Intron	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137469116delG	uc003qhl.2	-						IL22RA2_uc003qhm.2_Intron|IL22RA2_uc003qhn.2_Intron	NM_052962	NP_443194	Q969J5	I22R2_HUMAN	interleukin 22-binding protein isoform 1						regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	interleukin-22 receptor activity				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000313)|OV - Ovarian serous cystadenocarcinoma(155;0.00407)		TCAGCATggtgggaggatcac	0.129													12	6	---	---	---	---	
SHPRH	257218	broad.mit.edu	37	6	146242677	146242678	+	Intron	DEL	TT	-	-	rs146207931		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146242677_146242678delTT	uc003qlf.2	-						SHPRH_uc003qld.2_Intron|SHPRH_uc003qle.2_Intron|SHPRH_uc003qlg.1_Intron|SHPRH_uc003qlh.2_Intron|SHPRH_uc003qli.1_Intron	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a						DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		ATTTGGCCAGTTTTTTTTTTTT	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	151169498	151169498	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151169498delG								PLEKHG1 (4699 upstream) : MTHFD1L (17193 downstream)																							actatccaaagggaaacccgc	0.010													4	2	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162174219	162174220	+	Intron	DEL	GT	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162174219_162174220delGT	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		tgatattaaagtaatgctgatg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164993399	164993400	+	IGR	INS	-	G	G	rs75116119	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164993399_164993400insG								QKI (998507 upstream) : C6orf118 (699755 downstream)																							agtgatactgagtttttttttt	0.000													3	4	---	---	---	---	
EIF3B	8662	broad.mit.edu	37	7	2403011	2403024	+	Intron	DEL	TTGAGCCTGGGAGG	-	-	rs66483346		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2403011_2403024delTTGAGCCTGGGAGG	uc003slx.2	+						EIF3B_uc003sly.2_Intron|EIF3B_uc003slz.1_Intron|EIF3B_uc003sma.2_Intron	NM_003751	NP_003742	P55884	EIF3B_HUMAN	eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	nucleotide binding|protein complex scaffold|translation initiation factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		ggaggatcacttgagcctgggaggttgagcctgg	0.009													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	11297721	11297721	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11297721delT	uc003ssb.2	+											Homo sapiens cDNA clone IMAGE:4830466.																		CATGTTTTCCTTTTTTTCTGT	0.299													4	2	---	---	---	---	
TMEM196	256130	broad.mit.edu	37	7	19794457	19794457	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19794457delT	uc011jyg.1	-						TMEM196_uc003sur.2_Intron	NM_152774	NP_689987	Q5HYL7	TM196_HUMAN	transmembrane protein 196							integral to membrane					0						agctctgacattttctgatCA	0.179													8	4	---	---	---	---	
SNX10	29887	broad.mit.edu	37	7	26411530	26411530	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26411530delT	uc003sxx.2	+	6	616	c.401delT	c.(400-402)GTTfs	p.V134fs	SNX10_uc011jzg.1_Frame_Shift_Del_p.V157fs|SNX10_uc010kuu.2_Frame_Shift_Del_p.V134fs|SNX10_uc010kuv.2_Frame_Shift_Del_p.V130fs|SNX10_uc010kuw.2_Frame_Shift_Del_p.V50fs	NM_013322	NP_037454	Q9Y5X0	SNX10_HUMAN	sorting nexin 10	134					cell communication|endosome organization|protein transport	extrinsic to endosome membrane	1-phosphatidylinositol binding				0						GAGGCGTGTGTTTCTGGGCAG	0.388													227	101	---	---	---	---	
C7orf10	79783	broad.mit.edu	37	7	40192303	40192303	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40192303delT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13								transferase activity			ovary(2)	2						AATTAAGGTGttttttttttt	0.154													8	4	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146458922	146458923	+	Intron	INS	-	TACTC	TACTC	rs145974941	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146458922_146458923insTACTC	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)			TACAACTTCTTTATTCAATGGT	0.317										HNSCC(39;0.1)			4	2	---	---	---	---	
VIPR2	7434	broad.mit.edu	37	7	158846838	158846839	+	Intron	INS	-	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158846838_158846839insA	uc003woh.2	-						VIPR2_uc010lqx.2_Intron|VIPR2_uc010lqy.2_Intron	NM_003382	NP_003373	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2						cell-cell signaling	integral to plasma membrane				lung(1)|central_nervous_system(1)	2	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		tcccggacaacgggatacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2207206	2207207	+	IGR	INS	-	G	G	rs111932510		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2207206_2207207insG								MYOM2 (113827 upstream) : CSMD1 (585669 downstream)																							GTGGGGTTTTAGAATTCTACTC	0.490													2	4	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	31900272	31900272	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31900272delA	uc003xip.2	+						uc003xiq.2_Intron	NM_013962	NP_039256	Q02297	NRG1_HUMAN	neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		taactcaattaaaaaaaaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	51796925	51796926	+	IGR	INS	-	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51796925_51796926insC								SNTG1 (91498 upstream) : PXDNL (435218 downstream)																							TTTTACATTTACCCCCCCATAT	0.297													2	5	---	---	---	---	
RGS20	8601	broad.mit.edu	37	8	54782823	54782824	+	Intron	DEL	AC	-	-	rs112678663		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54782823_54782824delAC	uc003xrp.2	+						RGS20_uc003xrq.2_Intron|RGS20_uc010lye.2_Intron|RGS20_uc010lyf.2_Intron	NM_170587	NP_733466	O76081	RGS20_HUMAN	regulator of G-protein signaling 20 isoform a						negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|nucleus|plasma membrane	GTPase activator activity|protein binding|signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			ATATGTGTGTacacacacacac	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	74115597	74115597	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74115597delG								C8orf84 (110090 upstream) : RPL7 (87278 downstream)																							GAGTCGAAGTGGGGAGTTGCT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	88617628	88617628	+	IGR	DEL	C	-	-	rs35698263		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88617628delC								CNBD1 (222673 upstream) : DCAF4L2 (265345 downstream)																							GCCTAGAGTTCAGCAGTGATT	0.348													2	4	---	---	---	---	
SLC26A7	115111	broad.mit.edu	37	8	92261724	92261727	+	Intron	DEL	TCTC	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92261724_92261727delTCTC	uc003yex.2	+						SLC26A7_uc003yey.2_Intron|SLC26A7_uc003yez.2_Intron|SLC26A7_uc003yfa.2_Intron	NM_052832	NP_439897	Q8TE54	S26A7_HUMAN	solute carrier family 26, member 7 isoform a							basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)			CTTCTGTTAATCTCTCTCTCTCTC	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120436855	120436855	+	IGR	DEL	T	-	-	rs143072343	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120436855delT								NOV (177 upstream) : ENPP2 (132464 downstream)																							AGCCCTGATCTTTTTTTTTCT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	47212494	47212494	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:47212494delG								KGFLP1 (464109 upstream) : None (None downstream)																							atcttattgtggggactggcg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66545695	66545695	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66545695delA	uc010mnh.1	-						uc004aef.2_Intron					Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																		CTGTAAGAGGAAAAAAAAACA	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68356752	68356752	+	IGR	DEL	C	-	-	rs75577840		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68356752delC								FAM27B (562563 upstream) : MIR1299 (645487 downstream)																							GAAGTCTCATCCCCATATTTT	0.368													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68404895	68404896	+	IGR	INS	-	C	C			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68404895_68404896insC								FAM27B (610706 upstream) : MIR1299 (597343 downstream)																							tagcctaccaaccccccaaaaa	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111575665	111575665	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111575665delG								None (None upstream) : ACTL7B (41206 downstream)																							CAGTCTACTTGAAGGATGGGG	0.443													4	2	---	---	---	---	
CREM	1390	broad.mit.edu	37	10	35480866	35480867	+	Intron	INS	-	CCACCTGGTG	CCACCTGGTG	rs148904125	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35480866_35480867insCCACCTGGTG	uc001iyb.2	+						CREM_uc001ixy.2_Intron|CREM_uc001ixz.2_Intron|CREM_uc001iya.2_Intron|CREM_uc001iyc.2_Intron|CREM_uc001iyd.2_Intron|CREM_uc001iye.2_Intron|CREM_uc001iyf.2_Intron|CREM_uc001iyg.2_Intron|CREM_uc001iyh.2_Intron|CREM_uc001iyi.2_Intron|CREM_uc001iyj.2_Intron|CREM_uc001iyk.2_Intron	NM_181571	NP_853549	Q03060	CREM_HUMAN	cAMP responsive element modulator isoform a						cell differentiation|multicellular organismal development|signal transduction|spermatogenesis	nucleus	cAMP response element binding protein binding|protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CCACTACTATCCTTGATGCCAG	0.465													4	4	---	---	---	---	
ANK3	288	broad.mit.edu	37	10	61845226	61845227	+	Intron	INS	-	A	A			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61845226_61845227insA	uc001jky.2	-						ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jla.1_Intron|ANK3_uc001jlb.1_Intron|ANK3_uc001jkv.2_5'Flank	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						Gatattaaattaaaaaaaaatt	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80115564	80115565	+	Intron	INS	-	G	G			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80115564_80115565insG	uc010qlp.1	+						uc001jzw.1_Intron					SubName: Full=cDNA FLJ57363;																		gctctgagtatgggggggttat	0.000													4	2	---	---	---	---	
ANKRD1	27063	broad.mit.edu	37	10	92676188	92676189	+	Intron	DEL	TG	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92676188_92676189delTG	uc001khe.1	-							NM_014391	NP_055206	Q15327	ANKR1_HUMAN	cardiac ankyrin repeat protein						cellular lipid metabolic process|defense response|signal transduction		DNA binding				0		Colorectal(252;0.0475)				CTAAATTACAtgtgtgtgtgtg	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102953663	102953663	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102953663delA								TLX1 (56118 upstream) : LBX1 (33071 downstream)																							taatcatgagaaaactgccag	0.000													4	2	---	---	---	---	
DPCD	25911	broad.mit.edu	37	10	103367859	103367859	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103367859delT	uc001ktn.2	+							NM_015448	NP_056263	Q9BVM2	DPCD_HUMAN	DPCD protein								protein binding			skin(1)	1						ATCTGTTCtattttttttttt	0.284													4	2	---	---	---	---	
VTI1A	143187	broad.mit.edu	37	10	114220019	114220020	+	Intron	INS	-	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114220019_114220020insT	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron	NM_145206	NP_660207	Q96AJ9	VTI1A_HUMAN	SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		GGGCAACATAATTTTTAGTCTC	0.327													4	2	---	---	---	---	
C10orf119	79892	broad.mit.edu	37	10	121595352	121595352	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121595352delT	uc001ler.2	-						C10orf119_uc001leq.1_Intron|C10orf119_uc001les.1_Intron	NM_024834	NP_079110	Q9BTE3	MCMBP_HUMAN	chromosome 10 open reading frame 119						cell division|DNA-dependent DNA replication|mitosis|S phase of mitotic cell cycle|sister chromatid cohesion	nucleus	chromatin binding				0		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.0044)		GGGAATAATGtttttttttct	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	127454785	127454786	+	IGR	DEL	TT	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127454785_127454786delTT								C10orf137 (2073 upstream) : MMP21 (242 downstream)																							gtacactgtgtttagagaaatg	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	1641767	1641768	+	IGR	INS	-	T	T	rs144195697		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1641767_1641768insT								KRTAP5-3 (12074 upstream) : KRTAP5-4 (420 downstream)																							TGACTCTTACCTTTTTTTTTTT	0.426													2	4	---	---	---	---	
SYT9	143425	broad.mit.edu	37	11	7440686	7440686	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7440686delA	uc001mfe.2	+						SYT9_uc001mfd.2_Intron|SYT9_uc009yfi.2_Intron	NM_175733	NP_783860	Q86SS6	SYT9_HUMAN	synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		TGCAGGAGGGAAAAAAAAAAG	0.398													4	2	---	---	---	---	
WT1	7490	broad.mit.edu	37	11	32449907	32449907	+	Intron	DEL	C	-	-	rs5030165		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32449907delC	uc001mtn.1	-						WT1_uc001mtl.1_Intron|WT1_uc001mtm.1_Intron|WT1_uc001mto.1_Intron|WT1_uc001mtp.1_Intron|WT1_uc001mtq.1_Intron|WT1_uc009yjs.1_Intron	NM_024426	NP_077744	P19544	WT1_HUMAN	Wilms tumor 1 isoform D						adrenal cortex formation|branching involved in ureteric bud morphogenesis|camera-type eye development|cardiac muscle cell fate commitment|cellular response to cAMP|cellular response to gonadotropin stimulus|germ cell development|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male genitalia development|male gonad development|mesenchymal to epithelial transition|metanephric epithelium development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of female gonad development|negative regulation of metanephric glomerular mesangial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of translation|positive regulation of male gonad development|positive regulation of transcription, DNA-dependent|posterior mesonephric tubule development|regulation of organ formation|RNA splicing|sex determination|vasculogenesis|visceral serous pericardium development	cytoplasm|nuclear speck|nucleoplasm	C2H2 zinc finger domain binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding		EWSR1/WT1(231)	haematopoietic_and_lymphoid_tissue(318)|soft_tissue(231)|kidney(132)|pleura(2)|lung(2)|upper_aerodigestive_tract(1)|peritoneum(1)	687	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			AAATACAGTGCCATTGGGGTA	0.478			D|Mis|N|F|S	EWSR1	Wilms|desmoplastic small round cell tumor	Wilms			Denys-Drash_syndrome|Frasier_syndrome|Familial_Wilms_tumor|Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				4	2	---	---	---	---	
LDLRAD3	143458	broad.mit.edu	37	11	36018660	36018660	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36018660delT	uc001mwk.1	+						LDLRAD3_uc010rey.1_Intron|LDLRAD3_uc010rez.1_Intron	NM_174902	NP_777562	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain							integral to membrane	receptor activity			central_nervous_system(1)	1	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				atgatggctatttttatGATT	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37413169	37413169	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37413169delA								C11orf74 (716779 upstream) : None (None downstream)																							aaaagtaaacaaaaggggcaa	0.000													4	2	---	---	---	---	
SLC39A13	91252	broad.mit.edu	37	11	47378902	47378903	+	Intron	DEL	CA	-	-	rs145538426		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47378902_47378903delCA	uc001nfd.2	+						SPI1_uc001nfb.1_Intron|SPI1_uc001nfc.1_Intron			Q96H72	S39AD_HUMAN	RecName: Full=Zinc transporter ZIP13; AltName: Full=Zrt- and Irt-like protein 13;          Short=ZIP-13; AltName: Full=Solute carrier family 39 member 13; AltName: Full=LIV-1 subfamily of ZIP zinc transporter 9; AltName: Full=LZT-Hs9;						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				Lung(87;0.0936)		ACTCATATTTCACACCACTTAC	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	55277926	55277926	+	IGR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55277926delT								OR4A15 (141533 upstream) : OR4C15 (43857 downstream)																							CCTCTCCACCTGTGGCTCCCA	0.488													4	2	---	---	---	---	
FAM111A	63901	broad.mit.edu	37	11	58921177	58921177	+	3'UTR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58921177delT	uc010rkp.1	+	5					FAM111A_uc010rkq.1_3'UTR|FAM111A_uc010rkr.1_3'UTR|FAM111A_uc001nno.2_3'UTR|FAM111A_uc001nnp.2_3'UTR|FAM111A_uc001nnq.2_3'UTR	NM_001142521	NP_001135993	Q96PZ2	F111A_HUMAN	hypothetical protein LOC63901						proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_epithelial(135;0.139)				cttgcccaAAttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	60814181	60814185	+	IGR	DEL	TAACA	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60814181_60814185delTAACA								CD6 (26335 upstream) : CD5 (55745 downstream)																							acttaatcattaacataccaataaa	0.137													4	2	---	---	---	---	
CASP4	837	broad.mit.edu	37	11	104818145	104818145	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104818145delA	uc001pid.1	-						CASP4_uc001pib.1_Intron|CASP4_uc009yxg.1_Intron	NM_001225	NP_001216	P49662	CASP4_HUMAN	caspase 4 isoform alpha precursor						apoptosis|induction of apoptosis|proteolysis	intracellular	cysteine-type endopeptidase activity|protein binding			lung(2)|ovary(1)|skin(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		ATTGCAAGAGATTGTGTATTG	0.338													4	2	---	---	---	---	
GRIA4	2893	broad.mit.edu	37	11	105836404	105836405	+	Intron	INS	-	A	A	rs139321638	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105836404_105836405insA	uc001pix.2	+						GRIA4_uc001piw.2_Intron|GRIA4_uc010rvm.1_Intron|GRIA4_uc009yxl.1_Intron	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform						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)	ACTGTTTTGCCAAAAAAAATCC	0.312													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	106298655	106298656	+	IGR	DEL	AC	-	-	rs71844710		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106298655_106298656delAC								AASDHPPT (329236 upstream) : GUCY1A2 (259254 downstream)																							ACACTAGCAAacacacacacac	0.292													4	3	---	---	---	---	
NNMT	4837	broad.mit.edu	37	11	114179878	114179879	+	Intron	INS	-	TTA	TTA			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114179878_114179879insTTA	uc001por.1	+						NNMT_uc001pos.1_Intron	NM_006169	NP_006160	P40261	NNMT_HUMAN	nicotinamide N-methyltransferase						xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)	TGATATACACTTTATTATTATT	0.347													4	2	---	---	---	---	
CADM1	23705	broad.mit.edu	37	11	115281367	115281367	+	Intron	DEL	A	-	-	rs34869817		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115281367delA	uc001ppi.3	-						CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001ppl.2_Intron	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1						adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		TTCGATGTTTAAAAAAAGGGA	0.343													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	130922134	130922134	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130922134delG								SNX19 (135752 upstream) : NTM (318237 downstream)																							CAGAATTACTGGGGGAAACAA	0.498													4	2	---	---	---	---	
ERC1	23085	broad.mit.edu	37	12	1421549	1421549	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1421549delT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			AGTAAAGCAATTTTTTTTTTC	0.224													3	3	---	---	---	---	
NCAPD2	9918	broad.mit.edu	37	12	6618240	6618241	+	Intron	INS	-	T	T	rs72012060		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6618240_6618241insT	uc001qoo.2	+						NCAPD2_uc009zen.1_Intron|NCAPD2_uc010sfd.1_Intron|SCARNA10_uc009zeo.1_5'Flank	NM_014865	NP_055680	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2						cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5						ataggataaactTTTTTTTTTT	0.168													4	2	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11273970	11273970	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11273970delT	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						TTACATTGAGTTTTTTTTAAG	0.313										HNSCC(22;0.051)			4	2	---	---	---	---	
LRP6	4040	broad.mit.edu	37	12	12291106	12291106	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12291106delA	uc001rah.3	-						BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Intron	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)				ctccgtctccaaaaaaaaaaa	0.139													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	14320015	14320015	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14320015delA								GRIN2B (186993 upstream) : ATF7IP (198596 downstream)																							TCCAGAAAAGAAAAAAAGCCA	0.423											OREG0021694	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ATF7IP	55729	broad.mit.edu	37	12	14613931	14613931	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14613931delT	uc001rbw.2	+	9	2819	c.2661delT	c.(2659-2661)ACTfs	p.T887fs	ATF7IP_uc010shs.1_3'UTR|ATF7IP_uc001rbu.2_Frame_Shift_Del_p.T887fs|ATF7IP_uc001rbv.1_Frame_Shift_Del_p.T886fs|ATF7IP_uc001rbx.2_Frame_Shift_Del_p.T886fs|ATF7IP_uc010sht.1_3'UTR|ATF7IP_uc001rby.3_Frame_Shift_Del_p.T887fs|ATF7IP_uc001rca.2_Frame_Shift_Del_p.T887fs	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	887					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						CCACAAGGACTTCTTTACCCA	0.458													57	30	---	---	---	---	
BAZ2A	11176	broad.mit.edu	37	12	56999208	56999208	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56999208delT	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc009zov.1_5'Flank|BAZ2A_uc009zow.1_Intron	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A						chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0						TTTTATGTAAttttttttttt	0.174													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	70015632	70015633	+	IGR	INS	-	CT	CT			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70015632_70015633insCT								LRRC10 (10690 upstream) : BEST3 (21507 downstream)																							CTACCAAGAAGCCTGAGGAGTA	0.510													3	4	---	---	---	---	
NAV3	89795	broad.mit.edu	37	12	78334655	78334655	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78334655delT	uc001syp.2	+						NAV3_uc001syo.2_Intron	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						TTCTCACTCATTTTTTTTTTT	0.398										HNSCC(70;0.22)			7	4	---	---	---	---	
CABP1	9478	broad.mit.edu	37	12	121097610	121097610	+	Intron	DEL	C	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121097610delC	uc001tyu.2	+						CABP1_uc001tyv.2_Intron|CABP1_uc001tyw.2_Intron|CABP1_uc001tyx.2_Intron	NM_001033677	NP_001028849	Q9NZU7	CABP1_HUMAN	calcium binding protein 1 isoform 3							cell cortex|cell junction|Golgi apparatus|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|calcium-dependent protein binding|enzyme inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ACGTGGATGGCCCCCAGGTTA	0.537													109	68	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127962038	127962040	+	IGR	DEL	ACG	-	-	rs148386789		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127962038_127962040delACG								None (None upstream) : TMEM132C (937251 downstream)																							ctgaaaacccacgacttttatta	0.039													2	4	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	130379292	130379292	+	Intron	DEL	T	-	-	rs71749162		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130379292delT	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							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)		GTAGTTTCTCTTTTTTTTTTC	0.269													5	3	---	---	---	---	
RIMBP2	23504	broad.mit.edu	37	12	130881469	130881469	+	3'UTR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130881469delA	uc001uil.2	-	19						NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2							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)		GCAGAACATCAAGGCGAATTA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132373315	132373315	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132373315delA								MMP17 (36999 upstream) : ULK1 (5964 downstream)																							catggtgtggaccttgtggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	29111285	29111285	+	IGR	DEL	G	-	-	rs79392711		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29111285delG								FLT1 (42020 upstream) : POMP (121956 downstream)																							TTGATGTTTTGGAGAGTATGC	0.418													4	2	---	---	---	---	
HMGB1	3146	broad.mit.edu	37	13	31086078	31086078	+	Intron	DEL	T	-	-	rs35026251		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31086078delT	uc001usz.2	-							NM_002128	NP_002119	P09429	HMGB1_HUMAN	high-mobility group box 1						base-excision repair, DNA ligation|dendritic cell chemotaxis|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|inflammatory response to antigenic stimulus|innate immune response|myeloid dendritic cell activation|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|neuron projection development|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	cell surface|condensed chromosome|extracellular space|nucleolus|nucleoplasm	chemoattractant activity|cytokine activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|repressing transcription factor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		CTGATTCTTCTTTGTGGGGGC	0.423													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	60202476	60202477	+	IGR	DEL	AA	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60202476_60202477delAA								None (None upstream) : DIAPH3 (37248 downstream)																							gatagaaagtaaaaagaggtag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	83085417	83085417	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83085417delG								None (None upstream) : None (None downstream)																							GAGGGTTTCTGGGGGATTGTT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20470853	20470853	+	IGR	DEL	T	-	-	rs67430133		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20470853delT								OR4K15 (26131 upstream) : OR4K14 (11568 downstream)																							GGTGGAAAACTTTTTTTTGTG	0.463													4	2	---	---	---	---	
METT11D1	64745	broad.mit.edu	37	14	21461941	21461941	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21461941delT	uc001vyn.2	+						METT11D1_uc001vym.2_Intron|METT11D1_uc001vyo.2_Intron|METT11D1_uc001vyp.2_Intron|METT11D1_uc001vyq.2_Intron	NM_022734	NP_073571	Q9H7H0	MET17_HUMAN	methyltransferase 11 domain containing 1 isoform						translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)		TGAGTCTACCTTTTTTTTTTT	0.139													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49688539	49688539	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49688539delA								None (None upstream) : SDCCAG1 (344488 downstream)																							ACATCTGTCTAAAAAATGTAT	0.413													4	2	---	---	---	---	
SAMD4A	23034	broad.mit.edu	37	14	55071987	55071988	+	Intron	INS	-	A	A	rs112722076		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55071987_55071988insA	uc001xbb.2	+						SAMD4A_uc001xba.2_Intron|SAMD4A_uc001xbc.2_Intron	NM_015589	NP_056404	Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0						CTGGAGAAAGCAAAAAAAAAAC	0.436													4	2	---	---	---	---	
SNAPC1	6617	broad.mit.edu	37	14	62243179	62243179	+	Intron	DEL	T	-	-	rs33967758		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62243179delT	uc001xft.2	+							NM_003082	NP_003073	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		ATGTATTTTCTTTTTTTTTTG	0.244													4	2	---	---	---	---	
TSHR	7253	broad.mit.edu	37	14	81589486	81589486	+	Intron	DEL	T	-	-	rs3783939		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81589486delT	uc001xvd.1	+							NM_000369	NP_000360	P16473	TSHR_HUMAN	thyroid stimulating hormone receptor isoform 1						cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity			thyroid(289)|ovary(5)|lung(3)|kidney(1)|skin(1)	299				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	aaaaaaaaaaTTAACACTTAA	0.174			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism 						2	4	---	---	---	---	
ATXN3	4287	broad.mit.edu	37	14	92537423	92537423	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92537423delT	uc001yac.3	-						ATXN3_uc010aug.2_Intron|ATXN3_uc001yad.3_Intron|ATXN3_uc010auh.2_Intron|ATXN3_uc001yae.3_Intron	NM_004993	NP_004984	P54252	ATX3_HUMAN	ataxin 3 reference isoform						cell death|nervous system development|nucleotide-excision repair|regulation of transcription, DNA-dependent|synaptic transmission|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		GTGAAGTATATTTAAAAAACA	0.244													4	2	---	---	---	---	
XRCC3	7517	broad.mit.edu	37	14	104177632	104177632	+	Intron	DEL	C	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104177632delC	uc001yny.3	-						XRCC3_uc001ynx.3_Intron|XRCC3_uc001ynz.3_Intron|XRCC3_uc001yoa.3_Intron|XRCC3_uc001yob.1_Intron	NM_005432	NP_005423	O43542	XRCC3_HUMAN	X-ray repair cross complementing protein 3						DNA recombination|DNA repair	mitochondrion|nucleus|perinuclear region of cytoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0		Melanoma(154;0.155)|all_epithelial(191;0.19)		Epithelial(152;0.239)		CTAGCTACATCTAGGGCAACA	0.498								Direct_reversal_of_damage|Homologous_recombination					4	2	---	---	---	---	
TDRD9	122402	broad.mit.edu	37	14	104508331	104508332	+	Intron	INS	-	T	T			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104508331_104508332insT	uc001yom.3	+						TDRD9_uc001yon.3_Intron	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9						cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				ACTCTGAATGCTATGAATTCTC	0.238													93	55	---	---	---	---	
GABRG3	2567	broad.mit.edu	37	15	27245425	27245425	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27245425delT	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		ttgagtatcattttggtgtat	0.000													4	2	---	---	---	---	
SORD	6652	broad.mit.edu	37	15	45323625	45323625	+	Intron	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45323625delG	uc001zul.3	+						SORD_uc010uel.1_Intron|SORD_uc001zum.3_Intron|SORD_uc010bdz.2_Intron	NM_003104	NP_003095	Q00796	DHSO_HUMAN	sorbitol dehydrogenase						fructose biosynthetic process|glucose metabolic process|L-xylitol catabolic process|sorbitol catabolic process|sperm motility	cilium|extracellular space|flagellum|membrane fraction|mitochondrial membrane|soluble fraction	L-iditol 2-dehydrogenase activity|NAD binding|sugar binding|zinc ion binding				0		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)	NADH(DB00157)	ACAACAAAGTGGGAGGAGTGT	0.483													4	2	---	---	---	---	
PDE8A	5151	broad.mit.edu	37	15	85645754	85645754	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85645754delT	uc002blh.2	+						PDE8A_uc002bli.2_Intron|PDE8A_uc010bnc.2_Intron|PDE8A_uc010bnd.2_Intron|PDE8A_uc002blj.2_Intron|PDE8A_uc002blk.2_Intron	NM_002605	NP_002596	O60658	PDE8A_HUMAN	phosphodiesterase 8A isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)			GTTGTAAGCATTTTTTTTTTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102069724	102069725	+	IGR	DEL	CA	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102069724_102069725delCA								PCSK6 (39537 upstream) : TM2D3 (103455 downstream)																							TTTCTGTGTTCACAGCATAGTT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8360292	8360292	+	IGR	DEL	C	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8360292delC								A2BP1 (596952 upstream) : TMEM114 (259211 downstream)																							AAAAATGAAACCCCCCAACCA	0.408													4	2	---	---	---	---	
CPPED1	55313	broad.mit.edu	37	16	12875830	12875830	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12875830delA	uc002dca.3	-						CPPED1_uc002dcb.3_Intron	NM_018340	NP_060810	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0						AATGTGGGAGAAAAAAAAAAG	0.428													4	3	---	---	---	---	
ABCC1	4363	broad.mit.edu	37	16	16225792	16225795	+	Splice_Site	DEL	GGTG	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16225792_16225795delGGTG	uc010bvi.2	+	27	4141	c.3966_splice	c.e27+1	p.K1322_splice	ABCC1_uc010bvj.2_Splice_Site_p.K1263_splice|ABCC1_uc010bvk.2_Splice_Site_p.K1266_splice|ABCC1_uc010bvl.2_Splice_Site_p.K1322_splice|ABCC1_uc010bvm.2_Splice_Site_p.K1207_splice|ABCC1_uc002del.3_Splice_Site_p.K1216_splice	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	GGGGAGAAAAGGTGGGTACACATC	0.598													7	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	19371601	19371601	+	IGR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19371601delT								LOC728276 (55885 upstream) : TMC5 (50260 downstream)																							TGTGCTTGACTTtttttttta	0.114													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32479576	32479576	+	IGR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32479576delT								HERC2P4 (315702 upstream) : TP53TG3B (205265 downstream)																							ATCCTGTCTCTTTATTTGGAA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33518772	33518772	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33518772delG								SLC6A10P (622309 upstream) : MIR1826 (446736 downstream)																							tacaataggtggccttttgtg	0.000													4	2	---	---	---	---	
NAE1	8883	broad.mit.edu	37	16	66839541	66839541	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66839541delA	uc002eqf.2	-						NAE1_uc002eqe.2_Intron|NAE1_uc002eqg.2_Intron|NAE1_uc010cdv.2_Intron	NM_003905	NP_003896	Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1 isoform a						apoptosis|cell cycle|DNA replication|mitotic cell cycle DNA replication checkpoint|protein neddylation|signal transduction	cytoplasm|insoluble fraction|plasma membrane	catalytic activity|protein heterodimerization activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)	actgcgtctcaaaaaaaaaaa	0.124													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	1124174	1124174	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1124174delA								ABR (33558 upstream) : TUSC5 (58783 downstream)																							TGTGGGAGAGAAAAGGGGTCT	0.483													4	2	---	---	---	---	
MNT	4335	broad.mit.edu	37	17	2299593	2299593	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2299593delT	uc002fur.2	-							NM_020310	NP_064706	Q99583	MNT_HUMAN	MAX binding protein						multicellular organismal development|negative regulation of cell proliferation|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			skin(1)	1				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		TTTCCCCAAATCCCCAACATC	0.547													4	2	---	---	---	---	
ZBTB4	57659	broad.mit.edu	37	17	7363094	7363094	+	3'UTR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7363094delA	uc002ghc.3	-	5					ZBTB4_uc002ghd.3_3'UTR	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		CATATTTAAGAAAAAAAAAAT	0.358													10	5	---	---	---	---	
TMEM220	388335	broad.mit.edu	37	17	10619038	10619039	+	Intron	DEL	AT	-	-	rs66790439		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10619038_10619039delAT	uc002gmx.2	-						TMEM220_uc002gmy.2_Intron	NM_001004313	NP_001004313	Q6QAJ8	TM220_HUMAN	transmembrane protein 220							integral to membrane					0						GAAATATAACattgatttatag	0.129													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21566171	21566172	+	IGR	DEL	AC	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21566171_21566172delAC								C17orf51 (88440 upstream) : FAM27L (259198 downstream)																							GCTACAAATAACCCACTTTACT	0.376													4	2	---	---	---	---	
STAT3	6774	broad.mit.edu	37	17	40497378	40497378	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40497378delT	uc002hzl.1	-						STAT3_uc002hzk.1_Intron|STAT3_uc002hzm.1_Intron|STAT3_uc010wgh.1_Intron|STAT3_uc002hzn.1_Intron	NM_139276	NP_644805	P40763	STAT3_HUMAN	signal transducer and activator of transcription						cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		TGGAACTTTCTTTTTTTTAGA	0.219									Hyperimmunoglobulin_E_Recurrent_Infection_Syndrome				5	3	---	---	---	---	
FASN	2194	broad.mit.edu	37	17	80040057	80040057	+	Intron	DEL	C	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80040057delC	uc002kdu.2	-						FASN_uc002kdv.1_5'Flank	NM_004104	NP_004095	P49327	FAS_HUMAN	fatty acid synthase						energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	cytosol|Golgi apparatus|melanosome|plasma membrane	3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339)	GCGTGTCACTCCCCATTGGCC	0.652													6	6	---	---	---	---	
NOL4	8715	broad.mit.edu	37	18	31537664	31537664	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31537664delA	uc010dmi.2	-						NOL4_uc010xbs.1_Intron|NOL4_uc002kxr.3_Intron|NOL4_uc010xbt.1_Intron|NOL4_uc010dmh.2_Intron|NOL4_uc010xbu.1_Intron|NOL4_uc002kxt.3_Intron|NOL4_uc010xbv.1_Intron	NM_003787	NP_003778	O94818	NOL4_HUMAN	nucleolar protein 4							nucleolus	RNA binding			ovary(3)	3						TGGTTGGATTAAAAAATAGag	0.249													4	2	---	---	---	---	
CCDC123	84902	broad.mit.edu	37	19	33414830	33414830	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33414830delA	uc002nty.2	-						CCDC123_uc002ntx.2_Intron|CCDC123_uc010edg.2_Intron|CCDC123_uc002ntz.1_Intron	NM_032816	NP_116205	Q96ST8	CEP89_HUMAN	coiled-coil domain containing 123							centrosome|spindle pole					0	Esophageal squamous(110;0.137)					TTTTTAATATAAAAAATAAGA	0.343													4	2	---	---	---	---	
NUMBL	9253	broad.mit.edu	37	19	41173395	41173395	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41173395delT	uc002oon.2	-	10	1976	c.1808delA	c.(1807-1809)AAGfs	p.K603fs	NUMBL_uc010xvq.1_Frame_Shift_Del_p.K562fs|NUMBL_uc002ooo.2_Frame_Shift_Del_p.K602fs|NUMBL_uc010xvr.1_Frame_Shift_Del_p.K562fs	NM_004756	NP_004747	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	603					cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process	cytoplasm	protein binding			lung(3)|ovary(1)|breast(1)	5			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			CTCGAATGTCTTTTGCAGGTC	0.597													4	2	---	---	---	---	
IRF2BP1	26145	broad.mit.edu	37	19	46389712	46389712	+	5'Flank	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46389712delT	uc002pds.1	-							NM_015649	NP_056464	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		gctgtgcagctttaggcaaaa	0.234													4	2	---	---	---	---	
PRR12	57479	broad.mit.edu	37	19	50128756	50128756	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50128756delG	uc002poo.3	+	14	6003	c.6003delG	c.(6001-6003)CAGfs	p.Q2001fs		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	1180							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)		ACCTGGGCCAGGAGGAGGTGG	0.677													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	809760	809760	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:809760delA								C20orf54 (60532 upstream) : FAM110A (4596 downstream)																							GCTGAGTGGCAAAAATACTGC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22843317	22843317	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22843317delA								FOXA2 (277216 upstream) : SSTR4 (172740 downstream)																							GATGATCATTAAACACACAGA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23430690	23430690	+	IGR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23430690delT								CSTL1 (5124 upstream) : CST11 (351 downstream)																							tatttcacactttaggtaagg	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	30758611	30758611	+	IGR	DEL	C	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30758611delC								TM9SF4 (3550 upstream) : TSPYL3 (18338 downstream)																							CCACGTGGGTCCCCACCGACC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31545692	31545692	+	Intron	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31545692delT	uc010zub.1	+							NM_001143967	NP_001137439			EF-hand calcium binding domain 8																		tttccagtgattttttttttt	0.000													4	2	---	---	---	---	
TAF4	6874	broad.mit.edu	37	20	60557124	60557124	+	Intron	DEL	C	-	-	rs112352725		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60557124delC	uc002ybs.2	-							NM_003185	NP_003176	O00268	TAF4_HUMAN	TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			CAAACCCACACCCCACCCGAG	0.577													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	18096826	18096826	+	IGR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18096826delT								C21orf34 (114732 upstream) : CXADR (788504 downstream)																							GCTCTGGCCATTTTTTTGATC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	20360251	20360256	+	IGR	DEL	GAGTGT	-	-	rs143927554		TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20360251_20360256delGAGTGT								TMPRSS15 (584281 upstream) : None (None downstream)																							gttgagggcagagtgtgagtgtgagt	0.044													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	28773469	28773470	+	Intron	INS	-	T	T	rs145131559	by1000genomes	TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28773469_28773470insT	uc002ymh.2	-											Homo sapiens, clone IMAGE:5227164, mRNA.																		GTGCTGAGTTGTTTTTTTTTCT	0.327													4	2	---	---	---	---	
GCFC1	94104	broad.mit.edu	37	21	34120605	34120605	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34120605delA	uc002yqn.2	-						GCFC1_uc002yql.2_Intron|GCFC1_uc002yqm.2_Intron|GCFC1_uc002yqo.2_Intron|GCFC1_uc002yqp.2_Intron	NM_016631	NP_057715	Q9Y5B6	GCFC1_HUMAN	GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						CAACAACAACAAAAAAAACAC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	21592250	21592250	+	IGR	DEL	T	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21592250delT								LOC400891 (173795 upstream) : POM121L8P (44464 downstream)																							TCAATCAACATTTTTTTCAGT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	36535116	36535116	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36535116delG								RBM9 (110531 upstream) : APOL3 (1256 downstream)																							aggatgggcagggatagtggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47770776	47770776	+	IGR	DEL	C	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47770776delC								TBC1D22A (201054 upstream) : None (None downstream)																							AGCCCTCTGTCCTGTTTCTGA	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49446306	49446306	+	IGR	DEL	G	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49446306delG								FAM19A5 (298564 upstream) : C22orf34 (361870 downstream)																							taagccaggcggagttagatt	0.000													4	2	---	---	---	---	
ARSE	415	broad.mit.edu	37	X	2854634	2854634	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2854634delA	uc004crc.3	-						ARSE_uc011mhi.1_Intron|ARSE_uc011mhh.1_Intron	NM_000047	NP_000038	P51690	ARSE_HUMAN	arylsulfatase E precursor						skeletal system development	Golgi stack	arylsulfatase activity|metal ion binding			ovary(1)|central_nervous_system(1)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AACTAAATTTAAAAAGCTCGT	0.473													4	2	---	---	---	---	
FAM9B	171483	broad.mit.edu	37	X	8994167	8994167	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8994167delA	uc011mhu.1	-						FAM9B_uc011mhv.1_Intron|FAM9B_uc004csh.2_Intron	NM_205849	NP_995321	Q8IZU0	FAM9B_HUMAN	family with sequence similarity 9, member B							nucleus					0		Hepatocellular(5;0.219)				ATGAATACACAATCTTCCGTA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13433457	13433458	+	IGR	DEL	AG	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13433457_13433458delAG								None (None upstream) : None (None downstream)																							agaaaaaGAAAGAAAACCAGAA	0.153													4	2	---	---	---	---	
DAZ3	57054	broad.mit.edu	37	Y	26942265	26942265	+	Intron	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:26942265delA	uc004fwk.2	-						DAZ3_uc004fwl.2_Intron|DAZ3_uc011nbt.1_Intron	NM_020364	NP_065097	Q9NR90	DAZ3_HUMAN	deleted in azoospermia 3						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleotide binding|RNA binding				0						AAGGTTCCAGAAAAAAATGAA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58856003	58856003	+	IGR	DEL	A	-	-			TCGA-B8-5549-01A-01D-1534-10	TCGA-B8-5549-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58856003delA								None (None upstream) : None (None downstream)																							actccattctatgcgatttca	0.070													4	2	---	---	---	---	
