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
PUM1	9698	broad.mit.edu	37	1	31467951	31467951	+	Silent	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31467951G>A	uc001bsi.1	-	6	950	c.837C>T	c.(835-837)ACC>ACT	p.T279T	PUM1_uc001bsf.1_5'Flank|PUM1_uc001bsg.1_Silent_p.T91T|PUM1_uc001bsh.1_Silent_p.T279T|PUM1_uc001bsj.1_Silent_p.T279T|PUM1_uc010oga.1_Silent_p.T183T|PUM1_uc001bsk.1_Silent_p.T315T|PUM1_uc010ogb.1_Silent_p.T219T	NM_014676	NP_055491	Q14671	PUM1_HUMAN	pumilio 1 isoform 2	279					cellular membrane organization|post-Golgi vesicle-mediated transport|regulation of translation	cytosol	RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		GTAAACCATTGGTCTTGTCCA	0.398													6	325	---	---	---	---	PASS
RAD54L	8438	broad.mit.edu	37	1	46738453	46738453	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46738453T>C	uc009vye.2	+	13	1468	c.1354T>C	c.(1354-1356)TCG>CCG	p.S452P	RAD54L_uc001cpl.2_Missense_Mutation_p.S452P|RAD54L_uc001cpm.1_Missense_Mutation_p.S272P	NM_001142548	NP_001136020	Q92698	RAD54_HUMAN	RAD54-like protein	452					meiosis	nucleus	ATP binding|DNA binding|helicase activity			ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)		TTCCATCACCTCGCTAAAGAA	0.502								Direct_reversal_of_damage|Homologous_recombination					6	234	---	---	---	---	PASS
IL23R	149233	broad.mit.edu	37	1	67666447	67666447	+	Silent	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67666447T>C	uc001ddo.2	+	5	604	c.519T>C	c.(517-519)TAT>TAC	p.Y173Y	IL23R_uc009waz.2_5'UTR|IL23R_uc001ddp.2_RNA|IL23R_uc010opi.1_RNA|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Silent_p.Y130Y|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_RNA|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Silent_p.Y18Y|IL23R_uc001ddr.2_RNA|IL23R_uc010opo.1_Silent_p.Y32Y|IL23R_uc010opp.1_RNA|IL23R_uc010opq.1_Silent_p.Y32Y|IL23R_uc010opr.1_RNA|IL23R_uc010ops.1_Intron|IL23R_uc010opt.1_5'UTR|IL23R_uc010opu.1_5'UTR|IL23R_uc010opv.1_Silent_p.Y32Y|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_5'UTR|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_5'UTR|IL23R_uc010oqb.1_Silent_p.Y32Y|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_Intron|IL23R_uc010oqf.1_Intron|IL23R_uc010oqg.1_5'UTR|IL23R_uc010oqh.1_Intron	NM_144701	NP_653302	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor precursor	173	Extracellular (Potential).|Fibronectin type-III 1.				inflammatory response|negative regulation of interleukin-10 production|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|response to interferon-gamma|response to lipopolysaccharide	interleukin-23 receptor complex	receptor activity				0						AGCAACAGTATCTCACCTCAA	0.313													6	149	---	---	---	---	PASS
SYDE2	84144	broad.mit.edu	37	1	85630328	85630328	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85630328T>C	uc009wcm.2	-	6	3015	c.2966A>G	c.(2965-2967)CAG>CGG	p.Q989R		NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	989	Rho-GAP.				activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)		CTCTTGCCTCTGACTTAATAA	0.383													44	145	---	---	---	---	PASS
DENND2C	163259	broad.mit.edu	37	1	115166246	115166246	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115166246C>A	uc001efd.1	-	5	1527	c.825G>T	c.(823-825)GAG>GAT	p.E275D	DENND2C_uc001eez.2_RNA|DENND2C_uc001efc.1_Missense_Mutation_p.E275D	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	275										skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCTGAATATCCTCAAATTCAA	0.289													36	122	---	---	---	---	PASS
PGLYRP3	114771	broad.mit.edu	37	1	153277480	153277480	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153277480G>C	uc001fbn.1	-	3	372	c.319C>G	c.(319-321)CAC>GAC	p.H107D		NM_052891	NP_443123	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3 precursor	107					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCCTGGGTGTGCAAGCCTTGG	0.498													24	107	---	---	---	---	PASS
SELP	6403	broad.mit.edu	37	1	169566355	169566355	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169566355G>T	uc001ggi.3	-	11	1830	c.1765C>A	c.(1765-1767)CGT>AGT	p.R589S	SELP_uc001ggh.2_Missense_Mutation_p.R424S|SELP_uc009wvr.2_Missense_Mutation_p.R589S	NM_003005	NP_002996	P16109	LYAM3_HUMAN	selectin P precursor	589	Extracellular (Potential).|Sushi 7.				platelet activation|platelet degranulation|positive regulation of platelet activation	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)|skin(2)	4	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)	AATTCTCCACGAGTGTCAGAA	0.473													8	16	---	---	---	---	PASS
CEP350	9857	broad.mit.edu	37	1	180063129	180063129	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180063129G>T	uc001gnt.2	+	34	8272	c.7889G>T	c.(7888-7890)AGT>ATT	p.S2630I	CEP350_uc009wxl.2_Missense_Mutation_p.S2629I|CEP350_uc001gnv.2_Missense_Mutation_p.S765I|CEP350_uc001gnw.1_Missense_Mutation_p.S387I|CEP350_uc001gnx.1_Missense_Mutation_p.S387I	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	2630						centrosome|nucleus|spindle				ovary(4)	4						GTTAATAGAAGTAGAAGCCTT	0.388													6	27	---	---	---	---	PASS
PFKFB2	5208	broad.mit.edu	37	1	207242844	207242844	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207242844A>G	uc001hfg.2	+	11	1172	c.1063A>G	c.(1063-1065)AAG>GAG	p.K355E	PFKFB2_uc010psc.1_Missense_Mutation_p.K257E|PFKFB2_uc001hfh.2_Missense_Mutation_p.K355E|PFKFB2_uc009xcc.2_Missense_Mutation_p.K313E|PFKFB2_uc010psd.1_Missense_Mutation_p.K169E	NM_006212	NP_006203	O60825	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,	355	Fructose-2,6-bisphosphatase.				fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity			ovary(1)	1	Prostate(682;0.19)					AGATCAAGAGAAGTATCTGTA	0.473													6	197	---	---	---	---	PASS
ARF1	375	broad.mit.edu	37	1	228285383	228285383	+	Silent	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228285383G>A	uc001hrr.2	+	4	579	c.351G>A	c.(349-351)CGG>CGA	p.R117R	ARF1_uc001hrs.2_Silent_p.R117R|ARF1_uc001hrt.2_Intron|ARF1_uc009xev.2_Intron|ARF1_uc001hru.2_Silent_p.R117R|ARF1_uc001hrv.2_Silent_p.R117R|ARF1_uc001hrw.2_Silent_p.R117R	NM_001024226	NP_001019397	P84077	ARF1_HUMAN	ADP-ribosylation factor 1	117					cellular copper ion homeostasis|COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|protein transport|regulation of defense response to virus by virus|retrograde vesicle-mediated transport, Golgi to ER|small GTPase mediated signal transduction|viral reproduction	cytosol|Golgi membrane|perinuclear region of cytoplasm|plasma membrane	GTP binding|GTPase activity|protein binding|receptor signaling protein activity				0		Prostate(94;0.0405)				ACGAGCTCCGGGATGCTGTCC	0.642													11	28	---	---	---	---	PASS
CRIPT	9419	broad.mit.edu	37	2	46850923	46850923	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46850923A>G	uc002rve.2	+	4	255	c.158A>G	c.(157-159)AAT>AGT	p.N53S		NM_014171	NP_054890	Q9P021	CRIPT_HUMAN	postsynaptic protein CRIPT	53						cell junction|cytoplasm|dendritic spine					0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			TATGGAAAGAATAAGTTCTCC	0.249													5	146	---	---	---	---	PASS
MSH2	4436	broad.mit.edu	37	2	47693828	47693828	+	Silent	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47693828T>C	uc002rvy.1	+	10	1610	c.1542T>C	c.(1540-1542)GAT>GAC	p.D514D	MSH2_uc010yoh.1_Silent_p.D448D|MSH2_uc002rvz.2_Silent_p.D514D|MSH2_uc010fbg.2_Silent_p.D324D|MSH2_uc010fbh.1_RNA|MSH2_uc010fbi.1_Intron	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2	514					B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding	p.?(2)		large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTAAACTGGATTCCAGTGCAC	0.333			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				5	165	---	---	---	---	PASS
C2orf63	130162	broad.mit.edu	37	2	55439899	55439899	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55439899T>C	uc002ryi.2	-	5	755	c.409A>G	c.(409-411)ATA>GTA	p.I137V	C2orf63_uc002ryh.2_Intron|C2orf63_uc002ryj.2_Missense_Mutation_p.I15V	NM_152385	NP_689598	Q8NHS4	CB063_HUMAN	hypothetical protein LOC130162 isoform 1	137							binding			ovary(2)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(58;0.179)|Lung(47;0.189)			ATGTGATCTATTTGAGATTGA	0.338													7	410	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141528493	141528493	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141528493A>G	uc002tvj.1	-	34	6555	c.5583T>C	c.(5581-5583)TGT>TGC	p.C1861C		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1861	Extracellular (Potential).|EGF-like 4.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATCCCACTGTACACATACAAG	0.373										TSP Lung(27;0.18)			4	98	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152348619	152348619	+	Silent	SNP	A	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152348619A>C	uc010fnx.2	-	145	19673	c.19482T>G	c.(19480-19482)ACT>ACG	p.T6494T	NEB_uc002txr.2_Silent_p.T2824T|RIF1_uc002txp.2_Intron|NEB_uc010zbz.1_Silent_p.T263T|NEB_uc002txq.2_Silent_p.T373T|NEB_uc010zca.1_Silent_p.T325T|NEB_uc010zcb.1_Silent_p.T263T	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	6494	Interaction with SVIL.				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)		TACCTGTAATAGTCTCCTGAT	0.413													43	131	---	---	---	---	PASS
SATB2	23314	broad.mit.edu	37	2	200213593	200213593	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200213593A>G	uc002uuy.1	-	7	1821	c.1004T>C	c.(1003-1005)ATC>ACC	p.I335T	SATB2_uc010fsq.1_Missense_Mutation_p.I217T|SATB2_uc002uuz.1_Missense_Mutation_p.I335T|SATB2_uc002uva.1_Missense_Mutation_p.I335T|SATB2_uc002uvb.1_Missense_Mutation_p.I78T	NM_015265	NP_056080	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	335						cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1						CTGCTGGTTGATGGCTTGAGG	0.517													6	231	---	---	---	---	PASS
RBM44	375316	broad.mit.edu	37	2	238742708	238742708	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238742708A>G	uc002vxi.3	+	14	3090	c.2958A>G	c.(2956-2958)ATA>ATG	p.I986M		NM_001080504	NP_001073973	Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	985							nucleotide binding|RNA binding			ovary(4)	4		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		TTCAATTCATACCTCCAAATA	0.328													4	129	---	---	---	---	PASS
COL6A6	131873	broad.mit.edu	37	3	130284103	130284103	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130284103A>G	uc010htl.2	+	3	958	c.927A>G	c.(925-927)GGA>GGG	p.G309G		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	309	Nonhelical region.|VWFA 2.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						CCTATACTGGAGCTGCCATCA	0.498													4	45	---	---	---	---	PASS
SENP2	59343	broad.mit.edu	37	3	185316760	185316760	+	Silent	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185316760T>C	uc003fpn.2	+	4	477	c.306T>C	c.(304-306)TCT>TCC	p.S102S	SENP2_uc011brv.1_Silent_p.S92S|SENP2_uc011brw.1_Intron	NM_021627	NP_067640	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific protease 2	102					mRNA transport|protein desumoylation|protein transport|proteolysis|regulation of Wnt receptor signaling pathway|transmembrane transport|Wnt receptor signaling pathway	cytoplasm|nuclear membrane|nuclear pore	protein binding|SUMO-specific protease activity				0	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			TTTCGAACTCTTCATCTTGTG	0.368													6	250	---	---	---	---	PASS
SDHAP2	727956	broad.mit.edu	37	3	195410627	195410627	+	Missense_Mutation	SNP	A	G	G	rs6583272	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195410627A>G	uc003fuw.2	+	13	1718	c.524A>G	c.(523-525)CAG>CGG	p.Q175R	SDHAP2_uc003fuv.2_RNA					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						CCTCAGGTGCAGATTGATGAG	0.473													16	162	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506597	195506597	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506597G>A	uc011bto.1	-	3	11930	c.11470C>T	c.(11470-11472)CCT>TCT	p.P3824S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGTGTCA	0.602													10	16	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506603	195506603	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506603T>C	uc011bto.1	-	3	11924	c.11464A>G	c.(11464-11466)ACC>GCC	p.T3822A	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGTGTCACCTGTG	0.592													10	16	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513806	195513806	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513806C>G	uc011bto.1	-	2	5105	c.4645G>C	c.(4645-4647)GAC>CAC	p.D1549H	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGTGTCACCTGTGGAT	0.582													7	47	---	---	---	---	PASS
RNF212	285498	broad.mit.edu	37	4	1075211	1075211	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1075211C>G	uc003gcj.2	-	7	790	c.460G>C	c.(460-462)GAC>CAC	p.D154H	RNF212_uc003gch.2_Intron|RNF212_uc003gci.2_Missense_Mutation_p.D154H|RNF212_uc010ibp.2_Intron|RNF212_uc010ibq.2_Intron	NM_001131034	NP_001124506	Q495C1	RN212_HUMAN	ring finger protein 212 isoform a	154							zinc ion binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (64;0.151)		ACACACCTGTCGGGGGCTGAT	0.577													51	153	---	---	---	---	PASS
DHX15	1665	broad.mit.edu	37	4	24557930	24557930	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24557930T>C	uc003gqx.2	-	4	973	c.805A>G	c.(805-807)ACA>GCA	p.T269A		NM_001358	NP_001349	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 15	269	Helicase ATP-binding.				mRNA processing	U12-type spliceosomal complex	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(1)	1		Breast(46;0.0503)				AGAATATCTGTAGCCAGTGTC	0.388													4	123	---	---	---	---	PASS
PCDH7	5099	broad.mit.edu	37	4	30725280	30725280	+	Nonsense_Mutation	SNP	A	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30725280A>T	uc003gsk.1	+	1	3244	c.2236A>T	c.(2236-2238)AAA>TAA	p.K746*	PCDH7_uc011bxw.1_Nonsense_Mutation_p.K699*|PCDH7_uc011bxx.1_Nonsense_Mutation_p.K746*	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	746	Extracellular (Potential).|Cadherin 7.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						TACCCTTCCCAAAAACATTTC	0.478													8	41	---	---	---	---	PASS
LOC401127	401127	broad.mit.edu	37	4	39482474	39482474	+	RNA	SNP	A	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39482474A>C	uc011byn.1	+	1		c.600A>C			LOC401127_uc011byo.1_RNA	NR_026854				Homo sapiens WD repeat domain 5 pseudogene (LOC401127), non-coding RNA.												0						GGGACACAGTAATTATGTCTT	0.448													67	198	---	---	---	---	PASS
EXOC1	55763	broad.mit.edu	37	4	56762947	56762947	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56762947C>T	uc003hbe.1	+	16	2176	c.2018C>T	c.(2017-2019)CCA>CTA	p.P673L	EXOC1_uc003hbf.1_Missense_Mutation_p.P673L|EXOC1_uc003hbg.1_Missense_Mutation_p.P658L	NM_018261	NP_060731	Q9NV70	EXOC1_HUMAN	exocyst complex component 1 isoform 1	673					exocytosis|protein transport	exocyst	protein binding			ovary(2)|skin(2)|lung(1)|central_nervous_system(1)	6	Glioma(25;0.08)|all_neural(26;0.101)					GGAATTCTTCCATTTGTTGCT	0.373													6	215	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16699579	16699579	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16699579T>C	uc003jft.3	-	26	4004	c.3536A>G	c.(3535-3537)CAC>CGC	p.H1179R	MYO10_uc011cnc.1_Missense_Mutation_p.H58R|MYO10_uc011cnd.1_Missense_Mutation_p.H536R|MYO10_uc011cne.1_Missense_Mutation_p.H536R|MYO10_uc010itx.2_Missense_Mutation_p.H802R	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1179					axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						CAGAAAGCTGTGGAAATACGG	0.507													39	76	---	---	---	---	PASS
ANKRD31	256006	broad.mit.edu	37	5	74518184	74518184	+	Splice_Site	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74518184C>A	uc003kdo.1	-	3	371	c.179_splice	c.e3-1	p.G60_splice				Q8N7Z5	ANR31_HUMAN	Homo sapiens cDNA FLJ40191 fis, clone TESTI2019280, weakly similar to Homo sapiens nasopharyngeal carcinoma susceptibility protein LZ16 mRNA.												0						GAAGGCATGCCTAGAGTGAAA	0.353													5	133	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	90085634	90085634	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90085634T>C	uc003kju.2	+	69	14105	c.14009T>C	c.(14008-14010)GTC>GCC	p.V4670A	GPR98_uc003kjt.2_Missense_Mutation_p.V2376A|GPR98_uc003kjw.2_Missense_Mutation_p.V331A	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	4670	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ACCTTCTTTGTCAGAAGAGTC	0.428													5	149	---	---	---	---	PASS
LMNB1	4001	broad.mit.edu	37	5	126172027	126172027	+	3'UTR	SNP	C	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126172027C>G	uc003kud.1	+	11					LMNB1_uc010jdb.1_RNA|LMNB1_uc011cxb.1_3'UTR	NM_005573	NP_005564	P20700	LMNB1_HUMAN	lamin B1						cellular component disassembly involved in apoptosis	lamin filament|nuclear inner membrane	protein binding|structural molecule activity			kidney(1)|central_nervous_system(1)	2		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		AGAGCCTTCTCAGAAGCACAG	0.318													39	157	---	---	---	---	PASS
RAD50	10111	broad.mit.edu	37	5	131977874	131977874	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131977874A>C	uc003kxi.2	+	25	4144	c.3757A>C	c.(3757-3759)ATA>CTA	p.I1253L	RAD50_uc003kxh.2_Missense_Mutation_p.I1114L	NM_005732	NP_005723	Q92878	RAD50_HUMAN	RAD50 homolog isoform 1	1253					DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTGCAGGATAATAAAAAGTCG	0.373								Homologous_recombination					129	158	---	---	---	---	PASS
LOC153328	153328	broad.mit.edu	37	5	135207183	135207183	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135207183C>A	uc003laz.1	+	5	627	c.455C>A	c.(454-456)CCT>CAT	p.P152H	LOC153328_uc003lba.2_Intron			Q6ZT89	S2548_HUMAN	RecName: Full=Putative mitochondrial carrier protein FLJ44862;	152	Solcar 2.				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCAGTGGCTCCTGCGGAGCAG	0.602													21	18	---	---	---	---	PASS
PCDHA8	56140	broad.mit.edu	37	5	140222015	140222015	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140222015C>T	uc003lhs.2	+	1	1109	c.1109C>T	c.(1108-1110)GCC>GTC	p.A370V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhr.1_Missense_Mutation_p.A370V	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	370	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTGTCATCGCCCTAATTAGC	0.488													13	81	---	---	---	---	PASS
PCDHB16	57717	broad.mit.edu	37	5	140564230	140564230	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140564230C>G	uc003liv.2	+	1	3251	c.2096C>G	c.(2095-2097)TCG>TGG	p.S699W	PCDHB9_uc003liw.1_5'Flank	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	699	Helical; (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCGGTGTCGTCGCTCTTCCTC	0.687													9	15	---	---	---	---	PASS
PCDHGA7	56108	broad.mit.edu	37	5	140762931	140762931	+	Silent	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140762931C>T	uc003lka.1	+	1	465	c.465C>T	c.(463-465)AGC>AGT	p.S155S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003ljz.1_Silent_p.S155S	NM_018920	NP_061743	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7 isoform 1	155	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCGTTAAGCGAGGCTGGGG	0.463													13	69	---	---	---	---	PASS
CNOT6	57472	broad.mit.edu	37	5	179998388	179998388	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179998388G>C	uc003mlx.2	+	11	1766	c.1417G>C	c.(1417-1419)GAG>CAG	p.E473Q	CNOT6_uc010jld.2_Missense_Mutation_p.E473Q|CNOT6_uc010jle.2_Missense_Mutation_p.E468Q	NM_015455	NP_056270	Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	473					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	exonuclease activity|metal ion binding|protein binding|RNA binding				0	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		GAGTGCCTATGAGAGTGGCCT	0.423													105	169	---	---	---	---	PASS
NQO2	4835	broad.mit.edu	37	6	3006757	3006757	+	5'UTR	SNP	T	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3006757T>A	uc003mus.2	+	2					NQO2_uc003mup.1_5'UTR|NQO2_uc003mut.2_5'UTR	NM_000904	NP_000895	P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2							cytoplasm|nucleus	coenzyme binding|dihydronicotinamide riboside quinone reductase activity|electron carrier activity|metal ion binding|NADPH dehydrogenase (quinone) activity			ovary(1)	1	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Menadione(DB00170)|NADH(DB00157)	ACCCATCAAATCAGAGAGAAG	0.418													43	156	---	---	---	---	PASS
BTN3A1	11119	broad.mit.edu	37	6	26413269	26413269	+	Intron	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26413269T>C	uc003nhv.2	+						BTN3A1_uc011dkj.1_3'UTR|BTN3A1_uc011dkk.1_Intron|BTN3A1_uc010jqj.2_3'UTR	NM_007048	NP_008979	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1 isoform a						lipid metabolic process	integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2						GAGTCACATTTAGGGCAGACT	0.532													6	13	---	---	---	---	PASS
DDR1	780	broad.mit.edu	37	6	30866860	30866860	+	Intron	SNP	A	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30866860A>T	uc003nrr.2	+						DDR1_uc010jse.2_Intron|DDR1_uc003nrq.2_Intron|DDR1_uc003nrs.2_Intron|DDR1_uc003nrt.2_Intron|DDR1_uc011dms.1_Intron|DDR1_uc003nru.2_Intron|DDR1_uc003nrv.2_Intron|DDR1_uc003nrz.1_Missense_Mutation_p.R208W	NM_013993	NP_054699	Q08345	DDR1_HUMAN	discoidin domain receptor family, member 1						cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to plasma membrane	ATP binding|protein binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|central_nervous_system(3)|large_intestine(1)|ovary(1)	9					Imatinib(DB00619)	GGGGGACAGAAGGGGCAGAGT	0.607													5	27	---	---	---	---	PASS
MDGA1	266727	broad.mit.edu	37	6	37615095	37615095	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37615095C>T	uc003onu.1	-	10	3079	c.1900G>A	c.(1900-1902)GCC>ACC	p.A634T	MDGA1_uc003onv.1_5'UTR	NM_153487	NP_705691	Q8NFP4	MDGA1_HUMAN	MAM domain containing	634					brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2						GGGCTGTAGGCTTTGGCTAAG	0.468													6	23	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51612957	51612957	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51612957A>G	uc003pah.1	-	58	9733	c.9457T>C	c.(9457-9459)TTT>CTT	p.F3153L	PKHD1_uc010jzn.1_Missense_Mutation_p.F1136L|PKHD1_uc003pai.2_Missense_Mutation_p.F3153L	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3153	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					CCATAGTCAAAGTTCTTGAAA	0.413													17	45	---	---	---	---	PASS
DOPEY1	23033	broad.mit.edu	37	6	83823098	83823098	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83823098A>G	uc003pjs.1	+	7	998	c.738A>G	c.(736-738)ACA>ACG	p.T246T	DOPEY1_uc011dyy.1_Silent_p.T246T|DOPEY1_uc010kbl.1_Silent_p.T246T	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	246					protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		AGAGAAGCACACTGGACCTCA	0.373													29	100	---	---	---	---	PASS
LAMA4	3910	broad.mit.edu	37	6	112460350	112460350	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112460350T>C	uc003pvu.2	-	24	3563	c.3254A>G	c.(3253-3255)AAC>AGC	p.N1085S	LAMA4_uc003pvv.2_Missense_Mutation_p.N1078S|LAMA4_uc003pvt.2_Missense_Mutation_p.N1078S	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	1085	Laminin G-like 2.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		AATAAGGCCGTTGTCAGCTGG	0.448													5	96	---	---	---	---	PASS
C6orf72	116254	broad.mit.edu	37	6	149901111	149901111	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149901111A>G	uc003qmq.1	+	5	598	c.571A>G	c.(571-573)AAC>GAC	p.N191D	C6orf72_uc010kie.1_Missense_Mutation_p.N71D	NM_138785	NP_620140	Q9NU53	CF072_HUMAN	hypothetical protein LOC116254 precursor	191	Extracellular (Potential).					integral to membrane					0		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.66e-12)|GBM - Glioblastoma multiforme(68;0.171)		TACCCTTCCTAACCTCTCCAA	0.338													4	141	---	---	---	---	PASS
HGC6.3	100128124	broad.mit.edu	37	6	168376847	168376847	+	Silent	SNP	C	G	G	rs77867907	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168376847C>G	uc010kks.1	-	1	773	c.486G>C	c.(484-486)CTG>CTC	p.L162L		NM_001129895	NP_001123367	Q9UM08	Q9UM08_HUMAN	hypothetical protein LOC100128124	162											0						GTGTGGGGAGCAGGAGGCAGT	0.617													6	48	---	---	---	---	PASS
KLHL7	55975	broad.mit.edu	37	7	23214077	23214077	+	3'UTR	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23214077C>T	uc003svs.3	+	11					KLHL7_uc003svr.3_3'UTR|KLHL7_uc011jys.1_3'UTR|KLHL7_uc011jyt.1_3'UTR|KLHL7_uc003svt.2_3'UTR|KLHL7_uc011jyv.1_3'UTR	NM_001031710	NP_001026880	Q8IXQ5	KLHL7_HUMAN	kelch-like 7 isoform 1							Golgi apparatus|nucleolus|plasma membrane					0						ATATGGATTTCCTTAATTCAA	0.303													4	4	---	---	---	---	PASS
C7orf42	55069	broad.mit.edu	37	7	66416003	66416003	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66416003A>G	uc003tvk.2	+	5	925	c.661A>G	c.(661-663)ACT>GCT	p.T221A	C7orf42_uc010lah.2_Intron|C7orf42_uc003tvl.2_Missense_Mutation_p.T221A	NM_017994	NP_060464	Q9NWD8	CG042_HUMAN	hypothetical protein LOC55069	221						integral to membrane				ovary(1)	1						GATCTTCACAACTGCCAGAGA	0.488													6	260	---	---	---	---	PASS
AUTS2	26053	broad.mit.edu	37	7	70228160	70228160	+	Silent	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70228160G>A	uc003tvw.3	+	7	1790	c.1047G>A	c.(1045-1047)CAG>CAA	p.Q349Q	AUTS2_uc003tvx.3_Silent_p.Q349Q	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1	349										ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CTGAGGCCCAGCTCCAGCCTG	0.682													7	26	---	---	---	---	PASS
BAZ1B	9031	broad.mit.edu	37	7	72877401	72877401	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72877401G>C	uc003tyc.2	-	12	3445	c.3100C>G	c.(3100-3102)CTA>GTA	p.L1034V		NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	1034					ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)				TTCCGTGCTAGATGAATAGAG	0.373													101	185	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94038888	94038888	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94038888G>T	uc003ung.1	+	18	1375	c.904G>T	c.(904-906)GCA>TCA	p.A302S	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	302					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TAATCCTGGAGCAAACGGCCT	0.433										HNSCC(75;0.22)			155	274	---	---	---	---	PASS
ASNS	440	broad.mit.edu	37	7	97487671	97487671	+	Silent	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97487671C>A	uc003uot.3	-	7	1328	c.822G>T	c.(820-822)CTG>CTT	p.L274L	ASNS_uc011kin.1_Silent_p.L191L|ASNS_uc003uou.3_Silent_p.L274L|ASNS_uc003uov.3_Silent_p.L274L|ASNS_uc011kio.1_Silent_p.L253L|ASNS_uc003uow.3_Silent_p.L253L|ASNS_uc003uox.3_Silent_p.L191L	NM_133436	NP_597680	P08243	ASNS_HUMAN	asparagine synthetase	274	Asparagine synthetase.				cellular response to glucose starvation|glutamine metabolic process|negative regulation of apoptosis|positive regulation of mitotic cell cycle	cytosol|soluble fraction	asparagine synthase (glutamine-hydrolyzing) activity|ATP binding			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	GGGCTTCTTTCAGCTGCTTCA	0.493													23	83	---	---	---	---	PASS
KEL	3792	broad.mit.edu	37	7	142658954	142658954	+	Silent	SNP	A	G	G	rs8175960	byFrequency	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142658954A>G	uc003wcb.2	-	2	219	c.9T>C	c.(7-9)GGT>GGC	p.G3G		NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	3	Cytoplasmic (Potential).				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)					TTTGGTCCCCACCTTCCTGAA	0.547													6	149	---	---	---	---	PASS
RB1CC1	9821	broad.mit.edu	37	8	53568570	53568570	+	Silent	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53568570T>C	uc003xre.3	-	15	4377	c.3819A>G	c.(3817-3819)AAA>AAG	p.K1273K	RB1CC1_uc003xrf.3_Silent_p.K1273K	NM_014781	NP_055596	Q8TDY2	RBCC1_HUMAN	Rb1-inducible coiled coil protein 1 isoform 1	1273	Potential.				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)				ATTCTTACCTTTTTGCTATTT	0.289													5	138	---	---	---	---	PASS
LRRCC1	85444	broad.mit.edu	37	8	86050475	86050475	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86050475A>C	uc003ycw.2	+	16	2853	c.2699A>C	c.(2698-2700)TAC>TCC	p.Y900S	LRRCC1_uc010maa.1_Missense_Mutation_p.Y601S|LRRCC1_uc003ycx.2_Missense_Mutation_p.Y807S|LRRCC1_uc003ycy.2_Missense_Mutation_p.Y880S	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	900					cell division|mitosis	centriole|nucleus					0						AGAAAAGCTTACAGGTATTAT	0.294													41	96	---	---	---	---	PASS
DSCC1	79075	broad.mit.edu	37	8	120865387	120865387	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120865387T>C	uc003yov.2	-	2	386	c.251A>G	c.(250-252)AAG>AGG	p.K84R		NM_024094	NP_076999	Q9BVC3	DCC1_HUMAN	defective in sister chromatid cohesion 1	84					DNA replication|maintenance of mitotic sister chromatid cohesion|post-translational protein acetylation|regulation of DNA replication	chromatin|chromosome, centromeric region|nucleoplasm	DNA binding|protein binding			pancreas(1)	1	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GTCTGCTATCTTCAAGTCGTA	0.393													6	317	---	---	---	---	PASS
MFSD3	113655	broad.mit.edu	37	8	145735861	145735861	+	Silent	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145735861C>A	uc003zdi.1	+	2	966	c.801C>A	c.(799-801)TCC>TCA	p.S267S		NM_138431	NP_612440	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing	267	Leu-rich.|Helical; (Potential).				transmembrane transport	integral to membrane				central_nervous_system(2)	2	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CTGGCTCCTCCCTGGGTGGGA	0.617													28	89	---	---	---	---	PASS
PLAA	9373	broad.mit.edu	37	9	26910422	26910422	+	Missense_Mutation	SNP	C	A	A	rs141986086		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26910422C>A	uc003zqd.2	-	12	1996	c.1571G>T	c.(1570-1572)CGA>CTA	p.R524L	PLAA_uc003zqe.2_Missense_Mutation_p.R524L	NM_001031689	NP_001026859	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	524					phospholipid metabolic process|signal transduction		phospholipase A2 activator activity				0		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		TGCAGCTGATCGGTAGGCACT	0.313													6	234	---	---	---	---	PASS
PSAT1	29968	broad.mit.edu	37	9	80919858	80919858	+	Splice_Site	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80919858T>C	uc004ala.2	+	4	465	c.397_splice	c.e4+2	p.K133_splice	PSAT1_uc004alb.2_Splice_Site_p.K133_splice	NM_058179	NP_478059	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1 isoform 1						L-serine biosynthetic process|pyridoxine biosynthetic process		O-phospho-L-serine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)	1					L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)	GTTATACAAGTAAGTTCTGGG	0.478													4	95	---	---	---	---	PASS
RASEF	158158	broad.mit.edu	37	9	85630816	85630816	+	Splice_Site	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85630816C>A	uc004amo.1	-	4	931	c.670_splice	c.e4-1	p.E224_splice		NM_152573	NP_689786	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing						protein transport|small GTPase mediated signal transduction	perinuclear region of cytoplasm	calcium ion binding|GTP binding			upper_aerodigestive_tract(1)|lung(1)|breast(1)	3						TGCGTTTTTCCTAAAAGAAAA	0.383													5	113	---	---	---	---	PASS
UPF2	26019	broad.mit.edu	37	10	11985089	11985089	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11985089C>T	uc001ila.2	-	16	3727	c.3253G>A	c.(3253-3255)GAA>AAA	p.E1085K	UPF2_uc001ilb.2_Missense_Mutation_p.E1085K|UPF2_uc001ilc.2_Missense_Mutation_p.E1085K	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	1085	Sufficient for interaction with UPF1 C- terminus.|Glu-rich.|Sufficient for interaction with EIF4A1 and EIF1.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				GTTTCATTTTCCTTATTGGAA	0.328													123	353	---	---	---	---	PASS
UPF2	26019	broad.mit.edu	37	10	11998363	11998363	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11998363G>A	uc001ila.2	-	12	3004	c.2530C>T	c.(2530-2532)CAC>TAC	p.H844Y	UPF2_uc001ilb.2_Missense_Mutation_p.H844Y|UPF2_uc001ilc.2_Missense_Mutation_p.H844Y|UPF2_uc009xiz.1_Missense_Mutation_p.H844Y	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	844	Binds to UPF3B.|Sufficient for interaction with UPF3A and UPF3B.|MIF4G 3.|Sufficient for interaction with EIF4A1 and EIF1.			H -> Q (in Ref. 2; AAG48509 and 4; BAA92646).	mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				TCCACAACGTGGATCCCAACA	0.373													53	142	---	---	---	---	PASS
MPP7	143098	broad.mit.edu	37	10	28378668	28378668	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28378668G>T	uc001iua.1	-	14	1459	c.1055C>A	c.(1054-1056)CCC>CAC	p.P352H	MPP7_uc009xkz.1_RNA|MPP7_uc001iub.1_Missense_Mutation_p.P352H|MPP7_uc009xla.2_Missense_Mutation_p.P352H|MPP7_uc010qdv.1_RNA	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7	352					establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1						TTCGTATGTGGGTACGTCAGC	0.383													7	350	---	---	---	---	PASS
C10orf53	282966	broad.mit.edu	37	10	50902024	50902024	+	Intron	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50902024A>G	uc001jib.2	+						C10orf53_uc001jic.1_3'UTR|C10orf53_uc001jid.1_Intron	NM_001042427	NP_001035892	Q8N6V4	CJ053_HUMAN	chromosome 10 open reading frame 53 isoform b												0		all_neural(218;0.107)				TCAGTGTATCATGCCTGGATT	0.458													4	32	---	---	---	---	PASS
TTC18	118491	broad.mit.edu	37	10	75069951	75069951	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75069951C>A	uc009xrc.2	-	13	1552	c.1431G>T	c.(1429-1431)TTG>TTT	p.L477F	TTC18_uc001jty.2_Missense_Mutation_p.L477F|TTC18_uc009xrd.1_Missense_Mutation_p.L291F	NM_145170	NP_660153	Q5T0N1	TTC18_HUMAN	tetratricopeptide repeat domain 18	477							binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)					GCTTTGGAACCAAGGCTTTGT	0.363													5	133	---	---	---	---	PASS
C10orf118	55088	broad.mit.edu	37	10	115889683	115889683	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115889683C>A	uc001lbb.1	-	13	2801	c.2149G>T	c.(2149-2151)GTC>TTC	p.V717F	C10orf118_uc009xyd.1_Missense_Mutation_p.V315F|C10orf118_uc001lbc.1_Missense_Mutation_p.V717F|C10orf118_uc009xye.1_RNA	NM_018017	NP_060487	Q7Z3E2	CJ118_HUMAN	CTCL tumor antigen L14-2	717	Ser-rich.									ovary(2)	2		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)		ATGCTGCTGACTTCTTTGTCA	0.338													35	153	---	---	---	---	PASS
ATHL1	80162	broad.mit.edu	37	11	289868	289868	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:289868A>C	uc010qvu.1	+	2	167	c.52A>C	c.(52-54)AGT>CGT	p.S18R	ATHL1_uc001lor.3_Splice_Site|ATHL1_uc001los.1_Missense_Mutation_p.S18R	NM_025092	NP_079368	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1	18					carbohydrate metabolic process		hydrolase activity, acting on glycosyl bonds			liver(1)|central_nervous_system(1)|skin(1)	3		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		CTCTCTGCCCAGTGACCCCCG	0.672													11	40	---	---	---	---	PASS
B4GALNT4	338707	broad.mit.edu	37	11	375478	375478	+	Silent	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:375478C>T	uc001lpb.2	+	9	810	c.801C>T	c.(799-801)CCC>CCT	p.P267P		NM_178537	NP_848632	Q76KP1	B4GN4_HUMAN	beta	267	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTTTCCTGCCCGGCCTGAAGT	0.672													8	30	---	---	---	---	PASS
OR4P4	81300	broad.mit.edu	37	11	55406262	55406262	+	Silent	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55406262C>A	uc010rij.1	+	1	429	c.429C>A	c.(427-429)ATC>ATA	p.I143I		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	143	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1						ACACAATCATCATAGTTTGTT	0.428													13	40	---	---	---	---	PASS
MARK2	2011	broad.mit.edu	37	11	63670173	63670173	+	Silent	SNP	G	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63670173G>T	uc001nxw.2	+	13	1914	c.1335G>T	c.(1333-1335)CGG>CGT	p.R445R	MARK2_uc001nxx.2_Silent_p.R445R|MARK2_uc001nxy.2_Silent_p.R444R|MARK2_uc001nxv.3_Silent_p.R444R|MARK2_uc001nxz.3_Silent_p.R411R|MARK2_uc009yoy.2_Silent_p.R411R	NM_001039469	NP_001034558	Q7KZI7	MARK2_HUMAN	MAP/microtubule affinity-regulating kinase 2	445					cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress	plasma membrane	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3						AGTCAGGGCGGAAAGCCAGCA	0.612													11	49	---	---	---	---	PASS
MPZL2	10205	broad.mit.edu	37	11	118133354	118133354	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118133354A>G	uc001psn.2	-	3	376	c.235T>C	c.(235-237)TAC>CAC	p.Y79H	MPZL2_uc001pso.2_Missense_Mutation_p.Y79H|MPZL2_uc001psp.1_Missense_Mutation_p.Y79H	NM_005797	NP_005788	O60487	MPZL2_HUMAN	myelin protein zero-like 2 precursor	79	Extracellular (Potential).|Ig-like V-type.				anatomical structure morphogenesis|homophilic cell adhesion	cytoskeleton|integral to membrane				skin(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		TCTATGTGGTAGTAGAATACC	0.532													21	59	---	---	---	---	PASS
CD3G	917	broad.mit.edu	37	11	118221315	118221315	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118221315T>C	uc001psu.2	+	4	436	c.356T>C	c.(355-357)CTC>CCC	p.L119P	CD3G_uc009zaa.1_Missense_Mutation_p.L59P	NM_000073	NP_000064	P09693	CD3G_HUMAN	CD3G antigen, gamma polypeptide precursor	119	Helical; (Potential).				establishment or maintenance of cell polarity|protein complex assembly|protein transport|regulation of apoptosis|T cell activation|T cell costimulation|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	protein heterodimerization activity|receptor signaling complex scaffold activity|T cell receptor binding|transmembrane receptor activity				0	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		TCTGGCTTTCTCTTTGCTGAA	0.453													38	154	---	---	---	---	PASS
OR10G4	390264	broad.mit.edu	37	11	123887007	123887007	+	Silent	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123887007C>T	uc010sac.1	+	1	726	c.726C>T	c.(724-726)TCC>TCT	p.S242S		NM_001004462	NP_001004462	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G,	242	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CCTGTGCCTCCCACTGTATTG	0.522													10	146	---	---	---	---	PASS
ADAMTS15	170689	broad.mit.edu	37	11	130341137	130341137	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130341137C>T	uc010scd.1	+	7	1937	c.1937C>T	c.(1936-1938)ACC>ATC	p.T646I		NM_139055	NP_620686	Q8TE58	ATS15_HUMAN	a disintegrin-like and metalloprotease	646	Cys-rich.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|pancreas(1)|lung(1)|skin(1)	5	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		CCTGACTCCACCTCCGTCTGT	0.587													49	143	---	---	---	---	PASS
C1S	716	broad.mit.edu	37	12	7177661	7177661	+	Silent	SNP	T	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7177661T>G	uc001qsj.2	+	15	2492	c.1773T>G	c.(1771-1773)CCT>CCG	p.P591P	C1S_uc001qsk.2_Silent_p.P591P|C1S_uc001qsl.2_Silent_p.P591P|C1S_uc009zfr.2_Silent_p.P424P|C1S_uc009zfs.2_RNA	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent	591	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	CTGTAGCTCCTTTAAGAAAAT	0.517													19	40	---	---	---	---	PASS
IPO8	10526	broad.mit.edu	37	12	30827606	30827606	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30827606G>A	uc001rjd.2	-	7	981	c.811C>T	c.(811-813)CGG>TGG	p.R271W	IPO8_uc010sjt.1_Missense_Mutation_p.R66W	NM_006390	NP_006381	O15397	IPO8_HUMAN	importin 8	271					intracellular protein transport|signal transduction	cytoplasm|nucleus	protein transporter activity|Ran GTPase binding			skin(2)|central_nervous_system(1)	3	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TCAAAGAGCCGAGCTACAATA	0.418													5	187	---	---	---	---	PASS
COL2A1	1280	broad.mit.edu	37	12	48381066	48381066	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48381066C>G	uc001rqu.2	-	20	1433	c.1252G>C	c.(1252-1254)GCC>CCC	p.A418P	COL2A1_uc009zkw.2_RNA|COL2A1_uc001rqv.2_Missense_Mutation_p.A349P	NM_001844	NP_001835	P02458	CO2A1_HUMAN	collagen, type II, alpha 1 isoform 1 precursor	418	Triple-helical region.				axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	GATCCTTTGGCTCCAGGAATT	0.552													40	107	---	---	---	---	PASS
SMARCC2	6601	broad.mit.edu	37	12	56563619	56563619	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56563619T>C	uc001skb.2	-	23	2502	c.2396A>G	c.(2395-2397)GAG>GGG	p.E799G	SMARCC2_uc001skd.2_Missense_Mutation_p.E830G|SMARCC2_uc001ska.2_Missense_Mutation_p.E830G|SMARCC2_uc001skc.2_Missense_Mutation_p.E829G|SMARCC2_uc010sqf.1_Missense_Mutation_p.E719G	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	799	Glu-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)			TTTCCCTTTCTCCTCATCCTT	0.537													7	349	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88505102	88505102	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88505102A>G	uc001tar.2	-	22	2588	c.2244T>C	c.(2242-2244)AGT>AGC	p.S748S	CEP290_uc001tat.2_Silent_p.S541S|CEP290_uc009zsl.1_RNA	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	748	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						GTCGTAAAAGACTAGTTTCTT	0.343													5	74	---	---	---	---	PASS
USPL1	10208	broad.mit.edu	37	13	31195955	31195955	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31195955A>G	uc001utc.2	+	3	586	c.154A>G	c.(154-156)AAG>GAG	p.K52E	USPL1_uc001utb.2_5'UTR|USPL1_uc001utd.2_5'UTR	NM_005800	NP_005791	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	52					ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			pancreas(2)|skin(1)	3		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		TTGTAGAGAGAAGGGAAAGTT	0.303													5	153	---	---	---	---	PASS
OLFM4	10562	broad.mit.edu	37	13	53624673	53624673	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53624673T>C	uc001vhl.2	+	5	1300	c.1300T>C	c.(1300-1302)TTC>CTC	p.F434L	OLFM4_uc001vhk.1_3'UTR	NM_006418	NP_006409	Q6UX06	OLFM4_HUMAN	olfactomedin 4 precursor	434	Olfactomedin-like.				cell adhesion	extracellular space				skin(1)	1		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		TTCTAACGCCTTCATGGTATG	0.423													15	48	---	---	---	---	PASS
PIBF1	10464	broad.mit.edu	37	13	73482729	73482729	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73482729C>T	uc001vjc.2	+	12	1854	c.1549C>T	c.(1549-1551)CAA>TAA	p.Q517*	PIBF1_uc010aeo.1_RNA|PIBF1_uc001vjb.2_Nonsense_Mutation_p.Q517*|PIBF1_uc010aep.2_5'UTR	NM_006346	NP_006337	Q8WXW3	PIBF1_HUMAN	progesterone-induced blocking factor 1	517						centrosome				ovary(1)|breast(1)	2		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		TACTGAACTTCAAGCACAGAA	0.348													44	150	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44973708	44973708	+	3'UTR	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44973708C>A	uc001wvn.2	-	1						NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein							cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		TTAGGTACAACCTGACTACAG	0.383													14	117	---	---	---	---	PASS
PSMA3	5684	broad.mit.edu	37	14	58737676	58737676	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58737676T>C	uc001xdj.1	+	10	729	c.683T>C	c.(682-684)GTT>GCT	p.V228A	C14orf37_uc010tro.1_Intron|PSMA3_uc001xdk.1_Missense_Mutation_p.V221A|uc001xdl.2_Intron	NM_002788	NP_002779	P25788	PSA3_HUMAN	proteasome alpha 3 subunit isoform 1	228					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	protein binding|threonine-type endopeptidase activity				0						CATGAAATTGTTCCAAAAGAT	0.313													5	141	---	---	---	---	PASS
ZFYVE26	23503	broad.mit.edu	37	14	68274120	68274120	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68274120C>T	uc001xka.2	-	5	1020	c.881G>A	c.(880-882)GGA>GAA	p.G294E	ZFYVE26_uc010tsz.1_RNA|ZFYVE26_uc001xkc.3_Missense_Mutation_p.G294E|ZFYVE26_uc010tta.1_Missense_Mutation_p.G294E	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	294					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CACACCTTTTCCCGAGGCTGT	0.572													6	27	---	---	---	---	PASS
RBM25	58517	broad.mit.edu	37	14	73544104	73544104	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73544104G>T	uc001xno.2	+	4	392	c.184G>T	c.(184-186)GGA>TGA	p.G62*	RBM25_uc001xnn.3_Nonsense_Mutation_p.G62*|RBM25_uc010ttu.1_Nonsense_Mutation_p.G62*|RBM25_uc001xnp.2_5'UTR	NM_021239	NP_067062	P49756	RBM25_HUMAN	RNA binding motif protein 25	62					apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		GTCTATGGTTGGAAAGCATTT	0.363													6	347	---	---	---	---	PASS
RPS6KL1	83694	broad.mit.edu	37	14	75374134	75374134	+	Intron	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75374134T>C	uc010tux.1	-						RPS6KL1_uc001xqx.1_3'UTR|RPS6KL1_uc001xqw.2_Intron|RPS6KL1_uc010asd.1_Intron	NM_031464	NP_113652	Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1							ribosome	ATP binding|protein serine/threonine kinase activity			ovary(1)|stomach(1)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00658)		GGGCTACACCTCACCTCAGTC	0.637													4	45	---	---	---	---	PASS
VIPAR	63894	broad.mit.edu	37	14	77901629	77901629	+	Silent	SNP	G	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77901629G>T	uc001xtt.1	-	15	1358	c.1020C>A	c.(1018-1020)TCC>TCA	p.S340S	VIPAR_uc001xtu.1_Silent_p.S340S|VIPAR_uc010tvj.1_Silent_p.S291S|VIPAR_uc001xtv.1_Silent_p.S340S	NM_022067	NP_071350	Q9H9C1	VIPAR_HUMAN	hypothetical protein LOC63894	340					endosome to lysosome transport|intracellular protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	early endosome|late endosome|recycling endosome	protein binding			central_nervous_system(1)	1						GATAGAAGCAGGAGTAGAAAA	0.443													5	231	---	---	---	---	PASS
CCDC88C	440193	broad.mit.edu	37	14	91782078	91782078	+	Silent	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91782078C>T	uc010aty.2	-	14	1680	c.1581G>A	c.(1579-1581)CTG>CTA	p.L527L		NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE	527	Potential.				microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)				TGAGGGTCTCCAGATCTTGGT	0.527													7	378	---	---	---	---	PASS
KIAA1409	57578	broad.mit.edu	37	14	94008956	94008956	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94008956G>A	uc001ybv.1	+	11	1221	c.1138G>A	c.(1138-1140)GTC>ATC	p.V380I	KIAA1409_uc001ybs.1_Missense_Mutation_p.V380I	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	557						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		GCCTCAGTTTGTCACCAAATG	0.507													6	219	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106236827	106236827	+	RNA	SNP	G	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106236827G>T	uc010tyt.1	-	3613		c.57521C>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysh.1_RNA|uc001ysi.1_RNA					Parts of antibodies, mostly variable regions.												0						CCTGGGCACCGTGGGCACGGG	0.637													10	301	---	---	---	---	PASS
MAPKBP1	23005	broad.mit.edu	37	15	42107967	42107967	+	Missense_Mutation	SNP	T	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42107967T>A	uc001zok.3	+	13	1767	c.1481T>A	c.(1480-1482)CTA>CAA	p.L494Q	MAPKBP1_uc001zoj.3_Missense_Mutation_p.L488Q|MAPKBP1_uc010bcj.2_5'UTR|MAPKBP1_uc010bci.2_Missense_Mutation_p.L488Q|MAPKBP1_uc010udb.1_Missense_Mutation_p.L327Q|MAPKBP1_uc010bck.2_5'UTR|MAPKBP1_uc010bcl.2_5'UTR	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein	494	WD 7.									central_nervous_system(5)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	10		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		GGACAGCATCTAGCATCAGGG	0.572													30	71	---	---	---	---	PASS
MAPK6	5597	broad.mit.edu	37	15	52356581	52356581	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52356581A>G	uc002abp.2	+	6	2344	c.1550A>G	c.(1549-1551)AAA>AGA	p.K517R		NM_002748	NP_002739	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	517					cell cycle		ATP binding|MAP kinase activity			lung(3)|ovary(1)	4				all cancers(107;0.0028)		CTGGCTGGAAAAGAAAGGGAA	0.378													5	76	---	---	---	---	PASS
ZWILCH	55055	broad.mit.edu	37	15	66828309	66828309	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66828309G>T	uc002aqb.2	+	15	1626	c.1380G>T	c.(1378-1380)CAG>CAT	p.Q460H	ZWILCH_uc010bhu.1_Missense_Mutation_p.Q346H|ZWILCH_uc002aqa.2_Missense_Mutation_p.Q346H|ZWILCH_uc010bhv.2_Missense_Mutation_p.Q346H	NM_017975	NP_060445	Q9H900	ZWILC_HUMAN	Zwilch	460					cell division|mitotic cell cycle checkpoint|mitotic prometaphase	condensed chromosome kinetochore|cytosol	protein binding			ovary(1)	1						TACAAGAACAGGTTTATCGTG	0.328													6	322	---	---	---	---	PASS
UACA	55075	broad.mit.edu	37	15	70961034	70961034	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70961034T>G	uc002asr.2	-	16	2093	c.1989A>C	c.(1987-1989)GAA>GAC	p.E663D	UACA_uc010uke.1_Missense_Mutation_p.E554D|UACA_uc002asq.2_Missense_Mutation_p.E650D|UACA_uc010bin.1_Missense_Mutation_p.E638D	NM_018003	NP_060473	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and	663	Potential.					cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4						ACTGTCTAATTTCACTAAGTG	0.338													20	59	---	---	---	---	PASS
MAN2C1	4123	broad.mit.edu	37	15	75659878	75659878	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75659878C>G	uc002baf.2	-	3	342	c.325G>C	c.(325-327)GTG>CTG	p.V109L	MAN2C1_uc002bag.2_Missense_Mutation_p.V109L|MAN2C1_uc002bah.2_Missense_Mutation_p.V109L|MAN2C1_uc010bkk.2_Missense_Mutation_p.V109L|MAN2C1_uc010umi.1_Intron|MAN2C1_uc010umj.1_RNA|MAN2C1_uc010umk.1_RNA	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	109					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0						TCACGCCACACCAGACCTTCT	0.572													15	60	---	---	---	---	PASS
PSMA4	5685	broad.mit.edu	37	15	78834926	78834926	+	Missense_Mutation	SNP	C	A	A	rs149336836		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78834926C>A	uc002bdu.3	+	4	306	c.148C>A	c.(148-150)CGC>AGC	p.R50S	PSMA4_uc010blf.2_Missense_Mutation_p.R50S|PSMA4_uc002bdv.3_Intron|PSMA4_uc002bdw.3_Missense_Mutation_p.R26S|PSMA4_uc002bdx.3_Intron	NM_002789	NP_002780	P25789	PSA4_HUMAN	proteasome alpha 4 subunit isoform 1	50					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	identical protein binding|threonine-type endopeptidase activity				0						AGCAGAGAGACGCAACATCCA	0.358													52	160	---	---	---	---	PASS
CHD2	1106	broad.mit.edu	37	15	93489310	93489310	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93489310T>C	uc002bsp.2	+	12	1816	c.1241T>C	c.(1240-1242)CTA>CCA	p.L414P	CHD2_uc002bsn.2_Missense_Mutation_p.L414P|CHD2_uc002bso.1_Missense_Mutation_p.L414P|CHD2_uc010urb.1_Missense_Mutation_p.L427P|CHD2_uc010bof.1_RNA	NM_001271	NP_001262	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	414	Chromo 2.				regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			CCCGAATATCTATGTAAATGG	0.393													25	75	---	---	---	---	PASS
SRL	6345	broad.mit.edu	37	16	4245571	4245571	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4245571C>T	uc002cvz.3	-	5	606	c.593G>A	c.(592-594)CGC>CAC	p.R198H	SRL_uc002cvy.3_RNA	NM_001098814	NP_001092284	Q86TD4	SRCA_HUMAN	sarcalumenin	657						sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5						TTGCTGCTTGCGGTTCTCGAT	0.363													22	136	---	---	---	---	PASS
ATF7IP2	80063	broad.mit.edu	37	16	10567377	10567377	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10567377A>G	uc002czu.2	+	9	1695	c.1468A>G	c.(1468-1470)AAT>GAT	p.N490D	ATF7IP2_uc002czv.2_Missense_Mutation_p.N490D|ATF7IP2_uc010uyo.1_RNA|ATF7IP2_uc010uyp.1_Missense_Mutation_p.N34D|ATF7IP2_uc002czw.2_Missense_Mutation_p.N490D|ATF7IP2_uc010uyq.1_RNA	NM_024997	NP_079273	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting	490					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						CAATTCTCCCAATGCTGAAGT	0.284													28	118	---	---	---	---	PASS
C16orf62	57020	broad.mit.edu	37	16	19627466	19627466	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19627466G>C	uc002dgn.1	+	13	1066	c.1054G>C	c.(1054-1056)GAA>CAA	p.E352Q	C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Missense_Mutation_p.E101Q|C16orf62_uc002dgm.1_Missense_Mutation_p.E352Q	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020	352						integral to membrane				ovary(1)	1						ACATCTCAAAGAAACCCTAAA	0.358													54	187	---	---	---	---	PASS
RBBP6	5930	broad.mit.edu	37	16	24583192	24583192	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24583192A>G	uc002dmh.2	+	18	5845	c.4805A>G	c.(4804-4806)CAA>CGA	p.Q1602R	RBBP6_uc002dmi.2_Missense_Mutation_p.Q1568R|RBBP6_uc010bxr.2_Missense_Mutation_p.Q762R|RBBP6_uc002dmk.2_Missense_Mutation_p.Q1435R	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN	retinoblastoma-binding protein 6 isoform 1	1602					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0518)		GAAAAAGAGCAAATTACTGGG	0.388													14	75	---	---	---	---	PASS
SLC6A10P	386757	broad.mit.edu	37	16	32890622	32890622	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32890622T>G	uc002edh.1	-	5	440	c.264A>C	c.(262-264)AAA>AAC	p.K88N	SLC6A10P_uc002edi.1_RNA					RecName: Full=Transporter;												0						CGTTGGTGTTTTTGTAGACCA	0.512													5	35	---	---	---	---	PASS
RBL2	5934	broad.mit.edu	37	16	53498259	53498259	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53498259T>C	uc002ehi.3	+	12	1800	c.1682T>C	c.(1681-1683)CTT>CCT	p.L561P	RBL2_uc010vgv.1_Missense_Mutation_p.L487P|RBL2_uc002ehj.2_Missense_Mutation_p.L271P|RBL2_uc010vgw.1_Missense_Mutation_p.L345P	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)	561	Domain A.|Pocket; binds E1A.				cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						GATGTGCCTCTTTATCATTTT	0.343													6	294	---	---	---	---	PASS
GPR97	222487	broad.mit.edu	37	16	57707311	57707311	+	Missense_Mutation	SNP	A	G	G	rs144117124		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57707311A>G	uc002emh.2	+	2	240	c.137A>G	c.(136-138)GAC>GGC	p.D46G	GPR97_uc010cdc.2_Missense_Mutation_p.D46G|GPR97_uc010vhv.1_5'UTR|GPR97_uc010cdd.2_RNA	NM_170776	NP_740746	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97 precursor	46	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1						AACTTGAATGACAAGGCTTTG	0.547													5	122	---	---	---	---	PASS
CFDP1	10428	broad.mit.edu	37	16	75448541	75448541	+	Silent	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75448541C>A	uc002fdy.2	-	2	254	c.117G>T	c.(115-117)GTG>GTT	p.V39V	CFDP1_uc002fdz.2_5'UTR|CFDP1_uc002fea.1_Silent_p.V39V	NM_006324	NP_006315	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	39	Glu-rich.				multicellular organismal development					upper_aerodigestive_tract(1)	1						CTTCACCATCCACTTCATCTT	0.438													8	387	---	---	---	---	PASS
CNTNAP4	85445	broad.mit.edu	37	16	76461355	76461355	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76461355T>C	uc002feu.1	+	6	782	c.397T>C	c.(397-399)TCA>CCA	p.S133P	CNTNAP4_uc002fev.1_Missense_Mutation_p.S45P|CNTNAP4_uc010chb.1_Missense_Mutation_p.S108P|CNTNAP4_uc002fex.1_Missense_Mutation_p.S136P|CNTNAP4_uc002few.2_Missense_Mutation_p.S108P	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	133	Extracellular (Potential).|F5/8 type C.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						TTAGGGTTTTTCAGGAAATGC	0.418													4	54	---	---	---	---	PASS
PITPNA	5306	broad.mit.edu	37	17	1442229	1442229	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1442229A>G	uc002fst.3	-	6	646	c.390T>C	c.(388-390)CCT>CCC	p.P130P	PITPNA_uc010cjt.2_Silent_p.P14P|PITPNA_uc010cju.2_Silent_p.P28P	NM_006224	NP_006215	Q00169	PIPNA_HUMAN	phosphatidylinositol transfer protein, alpha	130					axon guidance|lipid metabolic process|visual perception	cytoplasm	phosphatidylcholine transmembrane transporter activity|phosphatidylinositol transporter activity|protein binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0845)		TCCACGCCTCAGGCTCCAGCT	0.483													6	215	---	---	---	---	PASS
RCVRN	5957	broad.mit.edu	37	17	9804495	9804495	+	Intron	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9804495C>T	uc002gme.1	-						RCVRN_uc002gmf.1_RNA	NM_002903	NP_002894	P35243	RECO_HUMAN	recoverin						visual perception		calcium ion binding|calcium sensitive guanylate cyclase activator activity				0						ACatcttacactgtacacaaa	0.199													10	43	---	---	---	---	PASS
MYO15A	51168	broad.mit.edu	37	17	18044110	18044110	+	Silent	SNP	C	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18044110C>T	uc010vxh.1	+	20	5708	c.5370C>T	c.(5368-5370)CCC>CCT	p.P1790P		NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	1790	Myosin head-like.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					GGTGCAACCCCTTGTTCATGC	0.512											OREG0024223	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	24	57	---	---	---	---	PASS
SSH2	85464	broad.mit.edu	37	17	27977810	27977810	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27977810T>C	uc002heo.1	-	12	1007	c.1007A>G	c.(1006-1008)TAT>TGT	p.Y336C	SSH2_uc010wbh.1_Missense_Mutation_p.Y363C|SSH2_uc002hep.1_Missense_Mutation_p.Y336C	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	336	Tyrosine-protein phosphatase.				actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						ATTCAAGATATACCGTACCCT	0.413													29	87	---	---	---	---	PASS
SLC4A1	6521	broad.mit.edu	37	17	42328875	42328875	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42328875G>A	uc002igf.3	-	18	2542	c.2393C>T	c.(2392-2394)ACG>ATG	p.T798M		NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member	798	Helical; (Potential).|Membrane (anion exchange).				bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GCTGAGCGACGTGACCCCCAT	0.597													30	94	---	---	---	---	PASS
ANKFN1	162282	broad.mit.edu	37	17	54452062	54452062	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54452062A>G	uc002iun.1	+	7	941	c.906A>G	c.(904-906)GTA>GTG	p.V302V		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	302	Fibronectin type-III.									large_intestine(1)|ovary(1)	2						CAGCTGTAGTAACCAGGTATA	0.443													34	67	---	---	---	---	PASS
NPLOC4	55666	broad.mit.edu	37	17	79589205	79589205	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79589205A>T	uc002kat.3	-	3	378	c.196T>A	c.(196-198)TTG>ATG	p.L66M	NPLOC4_uc002kau.3_Missense_Mutation_p.L66M|NPLOC4_uc010wur.1_Translation_Start_Site	NM_017921	NP_060391	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4	66					cellular membrane fusion|ER-associated protein catabolic process|Golgi organization	cytosol|endoplasmic reticulum|nuclear outer membrane-endoplasmic reticulum membrane network|nucleus	zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			ATTTTTAGCAAGTTGAGGGAT	0.468													62	171	---	---	---	---	PASS
C17orf101	79701	broad.mit.edu	37	17	80369360	80369360	+	Silent	SNP	G	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80369360G>T	uc002keu.1	-	3	452	c.351C>A	c.(349-351)ATC>ATA	p.I117I	C17orf101_uc002ket.1_Silent_p.I117I|C17orf101_uc010dip.1_RNA	NM_024648	NP_078924	Q6PK18	CQ101_HUMAN	hypothetical protein LOC79701 isoform 1	117	Lumenal (Potential).					integral to membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(1)	1						CCTCCCTGGTGATGACGACAT	0.632													7	41	---	---	---	---	PASS
EMILIN2	84034	broad.mit.edu	37	18	2891711	2891711	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2891711G>C	uc002kln.2	+	4	1745	c.1586G>C	c.(1585-1587)GGG>GCG	p.G529A		NM_032048	NP_114437	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2 precursor	529					cell adhesion	collagen	extracellular matrix constituent conferring elasticity|protein binding			skin(2)|ovary(1)	3				READ - Rectum adenocarcinoma(2;0.1)		GGAGTGTCAGGGTCAGGAGAT	0.527													19	65	---	---	---	---	PASS
GREB1L	80000	broad.mit.edu	37	18	19029597	19029597	+	Missense_Mutation	SNP	T	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19029597T>A	uc010xam.1	+	12	1791	c.1520T>A	c.(1519-1521)CTC>CAC	p.L507H	GREB1L_uc002ktf.1_Missense_Mutation_p.L507H|GREB1L_uc010dlp.1_Intron|GREB1L_uc010xan.1_5'Flank|GREB1L_uc010dlr.1_5'Flank	NM_001142966	NP_001136438	Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast	507						integral to membrane					0						CCAGGACAACTCCCCTGGCTT	0.473													36	114	---	---	---	---	PASS
KIAA1012	22878	broad.mit.edu	37	18	29454624	29454624	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29454624T>C	uc002kxc.3	-	13	2136	c.1772A>G	c.(1771-1773)TAC>TGC	p.Y591C	KIAA1012_uc002kxb.3_Missense_Mutation_p.Y537C|KIAA1012_uc002kxd.3_RNA|KIAA1012_uc002kxe.2_Missense_Mutation_p.Y591C	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878	591					ER to Golgi vesicle-mediated transport	cis-Golgi network					0						TTTTCCTTTGTAAACTTGCAT	0.358													5	119	---	---	---	---	PASS
GNG7	2788	broad.mit.edu	37	19	2514984	2514984	+	3'UTR	SNP	A	G	G	rs62121669		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2514984A>G	uc002lwd.2	-	5					GNG7_uc010dte.1_Intron	NM_052847	NP_443079	O60262	GBG7_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gagagagagaaagagagagag	0.303													6	43	---	---	---	---	PASS
TNPO2	30000	broad.mit.edu	37	19	12825662	12825662	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12825662T>C	uc002muo.2	-	9	1048	c.863A>G	c.(862-864)AAG>AGG	p.K288R	TNPO2_uc002mup.2_Missense_Mutation_p.K380R|TNPO2_uc002muq.2_Missense_Mutation_p.K288R|TNPO2_uc002mur.2_Missense_Mutation_p.K288R	NM_001136196	NP_001129668	O14787	TNPO2_HUMAN	transportin 2 (importin 3, karyopherin beta 2b)	288					intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1						CAGGACTTCCTTGCAGATGGG	0.602													5	102	---	---	---	---	PASS
ZNF529	57711	broad.mit.edu	37	19	37038540	37038540	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37038540T>C	uc002oeh.3	-	5	1122	c.920A>G	c.(919-921)GAG>GGG	p.E307G	ZNF529_uc010xth.1_Missense_Mutation_p.E307G|ZNF529_uc010xti.1_Missense_Mutation_p.E289G|ZNF529_uc002oeg.3_Missense_Mutation_p.E202G	NM_020951	NP_066002	Q6P280	ZN529_HUMAN	zinc finger protein 529 isoform a	274					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	Esophageal squamous(110;0.198)					GTAAGTTTTCTCATCAGTATG	0.388													5	112	---	---	---	---	PASS
TTC9B	148014	broad.mit.edu	37	19	40723224	40723224	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40723224A>G	uc002onc.2	-	2	498	c.480T>C	c.(478-480)TGT>TGC	p.C160C		NM_152479	NP_689692	Q8N6N2	TTC9B_HUMAN	tetratricopeptide repeat domain 9B	160							binding				0						GTACCTTGAGACAGTACTCGC	0.657													4	33	---	---	---	---	PASS
C19orf61	56006	broad.mit.edu	37	19	44237823	44237823	+	Silent	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44237823G>A	uc002oxj.2	-	11	1508	c.1165C>T	c.(1165-1167)CTG>TTG	p.L389L	C19orf61_uc002oxk.2_Silent_p.L389L	NM_019108	NP_061981	Q9H0W8	SMG9_HUMAN	SMG9 protein	389					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	intracellular	protein binding				0		Prostate(69;0.0352)				TCAATCATCAGGTGCATCTGC	0.567													24	78	---	---	---	---	PASS
ERCC2	2068	broad.mit.edu	37	19	45871971	45871971	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45871971A>G	uc002pbj.2	-	5	324	c.277T>C	c.(277-279)TTC>CTC	p.F93L	ERCC2_uc010ejz.2_Missense_Mutation_p.F93L|ERCC2_uc002pbk.2_Missense_Mutation_p.F69L|ERCC2_uc002pbl.3_Missense_Mutation_p.F69L|ERCC2_uc010xxj.1_RNA	NM_000400	NP_000391	P18074	ERCC2_HUMAN	excision repair cross-complementing rodent	93	Helicase ATP-binding.				cell cycle checkpoint|chromosome segregation|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|UV protection|viral reproduction	cytoplasm|holo TFIIH complex|MMXD complex	5'-3' DNA helicase activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding|protein C-terminus binding|protein N-terminus binding			lung(2)|pancreas(1)	3		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TTCTCATAGAAGTTGAGCAAC	0.552			Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				5	67	---	---	---	---	PASS
SULT2B1	6820	broad.mit.edu	37	19	49094973	49094973	+	Silent	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49094973G>A	uc002pjl.2	+	4	612	c.531G>A	c.(529-531)AGG>AGA	p.R177R	SULT2B1_uc002pjm.2_Silent_p.R162R	NM_177973	NP_814444	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	177					3'-phosphoadenosine 5'-phosphosulfate metabolic process|steroid metabolic process|xenobiotic metabolic process	cytosol	alcohol sulfotransferase activity|protein binding|steroid sulfotransferase activity			skin(1)	1		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		AGTTCCTGAGGGACTTCCTCA	0.637													5	73	---	---	---	---	PASS
JAG1	182	broad.mit.edu	37	20	10623159	10623159	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10623159T>C	uc002wnw.2	-	21	3065	c.2549A>G	c.(2548-2550)CAC>CGC	p.H850R	JAG1_uc010gcd.1_Missense_Mutation_p.H408R	NM_000214	NP_000205	P78504	JAG1_HUMAN	jagged 1 precursor	850	Extracellular (Potential).|EGF-like 16; calcium-binding (Potential).				angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1)	9						GGCACCACTGTGCCCTGGAGG	0.537									Alagille_Syndrome				6	99	---	---	---	---	PASS
CPNE1	8904	broad.mit.edu	37	20	34214664	34214664	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34214664T>G	uc002xdf.2	-	17	1661	c.1298A>C	c.(1297-1299)GAG>GCG	p.E433A	CPNE1_uc002xdc.2_Missense_Mutation_p.E95A|CPNE1_uc010zvj.1_Missense_Mutation_p.E438A|CPNE1_uc002xde.2_Missense_Mutation_p.E409A|CPNE1_uc002xdg.2_Missense_Mutation_p.E433A|CPNE1_uc010gfi.2_RNA|CPNE1_uc010gfj.2_RNA|CPNE1_uc002xdh.2_Missense_Mutation_p.E433A|CPNE1_uc002xdi.2_Missense_Mutation_p.E433A|CPNE1_uc002xdj.2_Missense_Mutation_p.E433A|CPNE1_uc002xdk.2_Missense_Mutation_p.E433A|CPNE1_uc002xdl.2_Missense_Mutation_p.E433A|CPNE1_uc002xdm.2_Missense_Mutation_p.E433A	NM_152931	NP_690908	Q99829	CPNE1_HUMAN	copine I isoform a	433	VWFA.				lipid metabolic process|vesicle-mediated transport		calcium-dependent phospholipid binding|phosphatidylserine binding|transporter activity			upper_aerodigestive_tract(1)	1	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			CACCACAGCCTCACGTGTGGC	0.567													17	56	---	---	---	---	PASS
RALGAPB	57148	broad.mit.edu	37	20	37144892	37144892	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37144892A>C	uc002xiw.2	+	7	1187	c.930A>C	c.(928-930)GAA>GAC	p.E310D	RALGAPB_uc010zvz.1_Missense_Mutation_p.E310D|RALGAPB_uc002xix.2_Missense_Mutation_p.E310D|RALGAPB_uc002xiy.1_Missense_Mutation_p.E310D|RALGAPB_uc002xiz.2_Missense_Mutation_p.E88D|RALGAPB_uc002xja.1_Missense_Mutation_p.E37D	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit	310					activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2						AATTTCAGGAACAGTTCTTGA	0.373													8	121	---	---	---	---	PASS
KRTAP10-6	386674	broad.mit.edu	37	21	46012291	46012291	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46012291A>G	uc002zfm.2	-	1	96	c.75T>C	c.(73-75)TGT>TGC	p.C25C	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198688	NP_941961	P60371	KR106_HUMAN	keratin associated protein 10-6	25						keratin filament					0						AGCAAGAGTCACAGGAACCAG	0.677													6	14	---	---	---	---	PASS
SEPT5	5413	broad.mit.edu	37	22	19707850	19707850	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19707850C>G	uc002zpv.1	+	6	495	c.370C>G	c.(370-372)CCC>GCC	p.P124A	SEPT5_uc002zpw.1_RNA|SEPT5_uc002zpx.1_RNA|SEPT5_uc002zpy.1_5'Flank	NM_002688	NP_002679	Q99719	SEPT5_HUMAN	septin 5	124					cell cycle|cytokinesis|regulation of exocytosis|synaptic vesicle targeting	plasma membrane|septin complex|synaptic vesicle	GTP binding|GTPase activity|protein binding|structural molecule activity			lung(1)	1	Colorectal(54;0.0993)					CAGCTGGAAGCCCATCACCGA	0.597													33	78	---	---	---	---	PASS
SLC2A11	66035	broad.mit.edu	37	22	24226915	24226915	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24226915C>A	uc002zyn.3	+	12	1469	c.1370C>A	c.(1369-1371)CCT>CAT	p.P457H	SLC2A11_uc002zym.3_Missense_Mutation_p.P464H|SLC2A11_uc002zyo.3_RNA|SLC2A11_uc011ajc.1_Missense_Mutation_p.L464M|SLC2A11_uc002zyp.3_Missense_Mutation_p.P460H	NM_001024938	NP_001020109	Q9BYW1	GTR11_HUMAN	glucose transporter protein 10 isoform c	457	Cytoplasmic (Potential).					integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1						CTGTTCCTTCCTGAGACCAAA	0.562													59	190	---	---	---	---	PASS
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	C	C	rs142470496	byFrequency	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29091840T>C	uc003adu.1	-	11	1189	c.1117A>G	c.(1117-1119)AAG>GAG	p.K373E	CHEK2_uc003ads.1_Missense_Mutation_p.K152E|CHEK2_uc010gvh.1_Missense_Mutation_p.K282E|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Missense_Mutation_p.K416E|CHEK2_uc003adv.1_Missense_Mutation_p.K344E|CHEK2_uc003adw.1_Missense_Mutation_p.K373E|CHEK2_uc003adx.1_Missense_Mutation_p.K152E|CHEK2_uc003ady.1_Missense_Mutation_p.K373E|CHEK2_uc003adz.1_Missense_Mutation_p.K177E	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a	373	Protein kinase.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.K373E(2)		central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				5	74	---	---	---	---	PASS
C22orf30	253143	broad.mit.edu	37	22	32112375	32112375	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32112375G>C	uc003alp.3	-	4	1643	c.1450C>G	c.(1450-1452)CAA>GAA	p.Q484E	C22orf30_uc003alo.1_Missense_Mutation_p.Q283E|C22orf30_uc010gwj.1_Missense_Mutation_p.Q283E	NM_173566	NP_775837	Q5THK1	PR14L_HUMAN	hypothetical protein LOC253143	484											0						AAGTTACCTTGAACGTGTACA	0.368											OREG0003537	type=REGULATORY REGION|Gene=NM_032234|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	21	61	---	---	---	---	PASS
CYP2D7P1	1564	broad.mit.edu	37	22	42540454	42540454	+	5'UTR	SNP	T	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42540454T>C	uc003bci.2	-	1					CYP2D7P1_uc003bcg.2_5'Flank|CYP2D7P1_uc003bch.2_5'Flank|CYP2D7P1_uc010gyv.2_5'Flank|CYP2D7P1_uc010gyw.2_RNA|CYP2D7P1_uc010gyx.1_5'UTR	NR_002570				SubName: Full=Cytochrome P450 2D6;          EC=1.14.14.1;												0						GCACCAGTGCTTCTAGCCCCA	0.652													4	27	---	---	---	---	PASS
PARVG	64098	broad.mit.edu	37	22	44602306	44602306	+	Nonstop_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44602306A>G	uc011aqe.1	+	14	1420	c.996A>G	c.(994-996)TGA>TGG	p.*332W	PARVG_uc003bep.2_Nonstop_Mutation_p.*332W|PARVG_uc011aqf.1_Nonstop_Mutation_p.*332W|PARVG_uc003beq.2_RNA|PARVG_uc003ber.2_RNA	NM_001137605	NP_001131077	Q9HBI0	PARVG_HUMAN	parvin, gamma	332					cell-matrix adhesion	cytoplasm|cytoskeleton|focal adhesion	actin binding				0		Ovarian(80;0.024)|all_neural(38;0.0299)				CCCCGAATTGACCCTCACTGC	0.617													4	48	---	---	---	---	PASS
PKDREJ	10343	broad.mit.edu	37	22	46654831	46654831	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46654831A>G	uc003bhh.2	-	1	4389	c.4389T>C	c.(4387-4389)TCT>TCC	p.S1463S		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	1463	Cytoplasmic (Potential).				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		GCTTTTGAGGAGATACCTCCT	0.428													5	53	---	---	---	---	PASS
FLJ44635	392490	broad.mit.edu	37	X	71380009	71380009	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71380009A>G	uc004eal.1	+	2	678	c.330A>G	c.(328-330)GAA>GAG	p.E110E		NM_207422	NP_997305	Q56UQ5	TPT1L_HUMAN	hypothetical protein LOC392490	110										lung(1)	1	Renal(35;0.156)					AACTGGAAGAACAGAGACCAA	0.373													5	92	---	---	---	---	PASS
TMLHE	55217	broad.mit.edu	37	X	154754204	154754204	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154754204G>A	uc004fnn.2	-	3	437	c.271C>T	c.(271-273)CAC>TAC	p.H91Y	TMLHE_uc004fno.2_Missense_Mutation_p.H91Y|TMLHE_uc004fnp.3_Missense_Mutation_p.H91Y	NM_018196	NP_060666	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	91					carnitine biosynthetic process	mitochondrial matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|trimethyllysine dioxygenase activity			ovary(1)	1	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	CTGCGCTGGTGAGTCTTAGAG	0.488													27	45	---	---	---	---	PASS
TMLHE	55217	broad.mit.edu	37	X	154754205	154754205	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154754205A>G	uc004fnn.2	-	3	436	c.270T>C	c.(268-270)ACT>ACC	p.T90T	TMLHE_uc004fno.2_Silent_p.T90T|TMLHE_uc004fnp.3_Silent_p.T90T	NM_018196	NP_060666	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	90					carnitine biosynthetic process	mitochondrial matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|trimethyllysine dioxygenase activity			ovary(1)	1	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	TGCGCTGGTGAGTCTTAGAGT	0.483													27	46	---	---	---	---	PASS
WDTC1	23038	broad.mit.edu	37	1	27623579	27623579	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27623579C>A	uc009vst.2	+	11	1525	c.990C>A	c.(988-990)AAC>AAA	p.N330K	WDTC1_uc001bno.2_Missense_Mutation_p.N329K|WDTC1_uc001bnp.1_RNA|WDTC1_uc001bnq.2_Missense_Mutation_p.N8K	NM_015023	NP_055838	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	330							protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		gtgtgtccaacggtgtgtcca	0.473											OREG0013279	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	85	---	---	---	---	PASS
SMAP2	64744	broad.mit.edu	37	1	40887783	40887783	+	3'UTR	SNP	A	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40887783A>C	uc001cfj.2	+	10					SMAP2_uc001cfk.2_3'UTR|SMAP2_uc010oji.1_3'UTR|SMAP2_uc010ojj.1_3'UTR	NM_022733	NP_073570	Q8WU79	SMAP2_HUMAN	small ArfGAP2						regulation of ARF GTPase activity	cytoplasm|nucleus	ARF GTPase activator activity|zinc ion binding				0	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			AAAACAAAACACCTGTATGGC	0.493													6	27	---	---	---	---	PASS
SYDE2	84144	broad.mit.edu	37	1	85630328	85630328	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85630328T>C	uc009wcm.2	-	6	3015	c.2966A>G	c.(2965-2967)CAG>CGG	p.Q989R		NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	989	Rho-GAP.				activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)		CTCTTGCCTCTGACTTAATAA	0.383													5	19	---	---	---	---	PASS
DENND2C	163259	broad.mit.edu	37	1	115166246	115166246	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115166246C>A	uc001efd.1	-	5	1527	c.825G>T	c.(823-825)GAG>GAT	p.E275D	DENND2C_uc001eez.2_RNA|DENND2C_uc001efc.1_Missense_Mutation_p.E275D	NM_198459	NP_940861	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	275										skin(3)	3	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCTGAATATCCTCAAATTCAA	0.289													13	70	---	---	---	---	PASS
ANXA9	8416	broad.mit.edu	37	1	150956864	150956864	+	Silent	SNP	T	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150956864T>C	uc001ewa.2	+	6	845	c.375T>C	c.(373-375)GCT>GCC	p.A125A		NM_003568	NP_003559	O76027	ANXA9_HUMAN	annexin A9	125	Annexin 2.				cell-cell adhesion	cell surface|cytosol	acetylcholine receptor activity|calcium ion binding|calcium-dependent phospholipid binding|phosphatidylserine binding|protein homodimerization activity				0	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TGAGGACAGCTCTGAAGGTAG	0.582													7	151	---	---	---	---	PASS
PGLYRP3	114771	broad.mit.edu	37	1	153277480	153277480	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153277480G>C	uc001fbn.1	-	3	372	c.319C>G	c.(319-321)CAC>GAC	p.H107D		NM_052891	NP_443123	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3 precursor	107					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCCTGGGTGTGCAAGCCTTGG	0.498													10	84	---	---	---	---	PASS
SELP	6403	broad.mit.edu	37	1	169566355	169566355	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169566355G>T	uc001ggi.3	-	11	1830	c.1765C>A	c.(1765-1767)CGT>AGT	p.R589S	SELP_uc001ggh.2_Missense_Mutation_p.R424S|SELP_uc009wvr.2_Missense_Mutation_p.R589S	NM_003005	NP_002996	P16109	LYAM3_HUMAN	selectin P precursor	589	Extracellular (Potential).|Sushi 7.				platelet activation|platelet degranulation|positive regulation of platelet activation	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)|skin(2)	4	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)	AATTCTCCACGAGTGTCAGAA	0.473													17	71	---	---	---	---	PASS
CEP350	9857	broad.mit.edu	37	1	180063129	180063129	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180063129G>T	uc001gnt.2	+	34	8272	c.7889G>T	c.(7888-7890)AGT>ATT	p.S2630I	CEP350_uc009wxl.2_Missense_Mutation_p.S2629I|CEP350_uc001gnv.2_Missense_Mutation_p.S765I|CEP350_uc001gnw.1_Missense_Mutation_p.S387I|CEP350_uc001gnx.1_Missense_Mutation_p.S387I	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	2630						centrosome|nucleus|spindle				ovary(4)	4						GTTAATAGAAGTAGAAGCCTT	0.388													8	39	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214781973	214781973	+	Intron	SNP	T	C	C	rs140032572	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214781973T>C	uc001hkm.2	+						uc001hkn.1_Missense_Mutation_p.T71A	NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F						cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GCGCGCTCCGTCAGGTGCAGC	0.721													7	68	---	---	---	---	PASS
ARF1	375	broad.mit.edu	37	1	228285383	228285383	+	Silent	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228285383G>A	uc001hrr.2	+	4	579	c.351G>A	c.(349-351)CGG>CGA	p.R117R	ARF1_uc001hrs.2_Silent_p.R117R|ARF1_uc001hrt.2_Intron|ARF1_uc009xev.2_Intron|ARF1_uc001hru.2_Silent_p.R117R|ARF1_uc001hrv.2_Silent_p.R117R|ARF1_uc001hrw.2_Silent_p.R117R	NM_001024226	NP_001019397	P84077	ARF1_HUMAN	ADP-ribosylation factor 1	117					cellular copper ion homeostasis|COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|protein transport|regulation of defense response to virus by virus|retrograde vesicle-mediated transport, Golgi to ER|small GTPase mediated signal transduction|viral reproduction	cytosol|Golgi membrane|perinuclear region of cytoplasm|plasma membrane	GTP binding|GTPase activity|protein binding|receptor signaling protein activity				0		Prostate(94;0.0405)				ACGAGCTCCGGGATGCTGTCC	0.642													21	84	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90139477	90139477	+	RNA	SNP	G	A	A	rs2848291	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90139477G>A	uc010fhm.2	+	18		c.2270G>A								Parts of antibodies, mostly variable regions.																		GTCCCATCAAGGTTCAGCGGC	0.483													4	106	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152348619	152348619	+	Silent	SNP	A	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152348619A>C	uc010fnx.2	-	145	19673	c.19482T>G	c.(19480-19482)ACT>ACG	p.T6494T	NEB_uc002txr.2_Silent_p.T2824T|RIF1_uc002txp.2_Intron|NEB_uc010zbz.1_Silent_p.T263T|NEB_uc002txq.2_Silent_p.T373T|NEB_uc010zca.1_Silent_p.T325T|NEB_uc010zcb.1_Silent_p.T263T	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	6494	Interaction with SVIL.				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)		TACCTGTAATAGTCTCCTGAT	0.413													90	286	---	---	---	---	PASS
MYO1B	4430	broad.mit.edu	37	2	192250811	192250811	+	Splice_Site	SNP	G	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192250811G>T	uc010fsg.2	+	16	1809	c.1554_splice	c.e16+1	p.K518_splice	MYO1B_uc002usq.2_Splice_Site_p.K518_splice|MYO1B_uc002usr.2_Splice_Site_p.K518_splice|MYO1B_uc002ust.1_Splice_Site_p.K156_splice	NM_001130158	NP_001123630	O43795	MYO1B_HUMAN	myosin IB isoform 1							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			TGCTGGAAAGGTATGGGGGAG	0.547													63	142	---	---	---	---	PASS
ANKZF1	55139	broad.mit.edu	37	2	220095115	220095115	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220095115A>G	uc002vkg.2	+	2	310	c.136A>G	c.(136-138)ACT>GCT	p.T46A	ATG9A_uc002vke.1_5'Flank|ATG9A_uc002vkf.1_5'Flank|ANKZF1_uc010zkv.1_Intron|ANKZF1_uc010zkw.1_Intron|ANKZF1_uc002vkh.2_Intron|ANKZF1_uc002vki.2_Missense_Mutation_p.T46A|ANKZF1_uc002vkj.1_5'Flank	NM_018089	NP_060559	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing	46						intracellular	zinc ion binding			ovary(2)	2		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGCTCCGCGTACTTCCTGTTC	0.587													3	110	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10183725	10183725	+	Nonsense_Mutation	SNP	C	A	A	rs5030826		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183725C>A	uc003bvc.2	+	1	407	c.194C>A	c.(193-195)TCG>TAG	p.S65*	VHL_uc003bvd.2_Nonsense_Mutation_p.S65*	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	65			S -> L (in VHLD; type I).|S -> A (in pheochromocytoma).|S -> W (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.S65*(8)|p.S65L(8)|p.S65S(2)|p.S65W(2)|p.S65fs*2(2)|p.S65P(1)|p.E52_S65del(1)|p.S65fs*92(1)|p.R60fs*35(1)|p.S65>Q(1)|p.S65_N67del(1)|p.P61fs*61(1)|p.R64fs*63(1)|p.V62fs*1(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)		GTGCTGCGCTCGGTGAACTCG	0.721		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				6	4	---	---	---	---	PASS
BSN	8927	broad.mit.edu	37	3	49662500	49662500	+	Missense_Mutation	SNP	A	G	G	rs140305957	byFrequency	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49662500A>G	uc003cxe.3	+	2	431	c.317A>G	c.(316-318)CAT>CGT	p.H106R		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	106					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		ACTCCTGGCCATGAGAGCCCC	0.622													22	32	---	---	---	---	PASS
NT5DC2	64943	broad.mit.edu	37	3	52558701	52558701	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52558701G>A	uc003deo.2	-	14	1772	c.1348C>T	c.(1348-1350)CGC>TGC	p.R450C	NT5DC2_uc003dem.2_Missense_Mutation_p.R320C|NT5DC2_uc003den.2_Missense_Mutation_p.R487C|NT5DC2_uc010hmi.2_Missense_Mutation_p.R462C|NT5DC2_uc010hmj.2_Missense_Mutation_p.R266C	NM_022908	NP_075059	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2 isoform 2	450							hydrolase activity|metal ion binding				0				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)		TGGAAGGTGCGGAAGATGCTG	0.622													3	53	---	---	---	---	PASS
RNF212	285498	broad.mit.edu	37	4	1075211	1075211	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1075211C>G	uc003gcj.2	-	7	790	c.460G>C	c.(460-462)GAC>CAC	p.D154H	RNF212_uc003gch.2_Intron|RNF212_uc003gci.2_Missense_Mutation_p.D154H|RNF212_uc010ibp.2_Intron|RNF212_uc010ibq.2_Intron	NM_001131034	NP_001124506	Q495C1	RN212_HUMAN	ring finger protein 212 isoform a	154							zinc ion binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (64;0.151)		ACACACCTGTCGGGGGCTGAT	0.577													41	223	---	---	---	---	PASS
PCDH7	5099	broad.mit.edu	37	4	30725280	30725280	+	Nonsense_Mutation	SNP	A	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30725280A>T	uc003gsk.1	+	1	3244	c.2236A>T	c.(2236-2238)AAA>TAA	p.K746*	PCDH7_uc011bxw.1_Nonsense_Mutation_p.K699*|PCDH7_uc011bxx.1_Nonsense_Mutation_p.K746*	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	746	Extracellular (Potential).|Cadherin 7.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						TACCCTTCCCAAAAACATTTC	0.478													40	100	---	---	---	---	PASS
LOC401127	401127	broad.mit.edu	37	4	39482474	39482474	+	RNA	SNP	A	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39482474A>C	uc011byn.1	+	1		c.600A>C			LOC401127_uc011byo.1_RNA	NR_026854				Homo sapiens WD repeat domain 5 pseudogene (LOC401127), non-coding RNA.												0						GGGACACAGTAATTATGTCTT	0.448													30	100	---	---	---	---	PASS
PAPSS1	9061	broad.mit.edu	37	4	108641417	108641417	+	5'UTR	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108641417G>A	uc003hyk.2	-	1					PAPSS1_uc011cfh.1_RNA	NM_005443	NP_005434	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		GCGGGGCGGGGCTGGAGGGCG	0.766													10	19	---	---	---	---	PASS
FGB	2244	broad.mit.edu	37	4	155491695	155491695	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155491695G>A	uc003ioa.3	+	8	1408	c.1369G>A	c.(1369-1371)GCA>ACA	p.A457T	FGB_uc003iob.3_3'UTR|FGB_uc010ipv.2_Missense_Mutation_p.A395T|FGB_uc010ipw.2_3'UTR|FGB_uc003ioc.3_Missense_Mutation_p.A238T	NM_005141	NP_005132	P02675	FIBB_HUMAN	fibrinogen, beta chain preproprotein	457	Fibrinogen C-terminal.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen|soluble fraction	chaperone binding|eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	CTGGGACATGGCAAAGCATGG	0.478													4	147	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16699579	16699579	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16699579T>C	uc003jft.3	-	26	4004	c.3536A>G	c.(3535-3537)CAC>CGC	p.H1179R	MYO10_uc011cnc.1_Missense_Mutation_p.H58R|MYO10_uc011cnd.1_Missense_Mutation_p.H536R|MYO10_uc011cne.1_Missense_Mutation_p.H536R|MYO10_uc010itx.2_Missense_Mutation_p.H802R	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1179					axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						CAGAAAGCTGTGGAAATACGG	0.507													17	31	---	---	---	---	PASS
HAPLN1	1404	broad.mit.edu	37	5	82940357	82940357	+	Silent	SNP	G	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82940357G>T	uc003kim.2	-	3	671	c.600C>A	c.(598-600)GGC>GGA	p.G200G	HAPLN1_uc003kin.2_Silent_p.G200G	NM_001884	NP_001875	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	200	Link 1.				cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding			large_intestine(3)|ovary(1)|skin(1)	5		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)		AGTCCAGCCCGCCCCGCCAGG	0.622													22	82	---	---	---	---	PASS
LMNB1	4001	broad.mit.edu	37	5	126172027	126172027	+	3'UTR	SNP	C	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126172027C>G	uc003kud.1	+	11					LMNB1_uc010jdb.1_RNA|LMNB1_uc011cxb.1_3'UTR	NM_005573	NP_005564	P20700	LMNB1_HUMAN	lamin B1						cellular component disassembly involved in apoptosis	lamin filament|nuclear inner membrane	protein binding|structural molecule activity			kidney(1)|central_nervous_system(1)	2		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		AGAGCCTTCTCAGAAGCACAG	0.318													33	140	---	---	---	---	PASS
RAD50	10111	broad.mit.edu	37	5	131977874	131977874	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131977874A>C	uc003kxi.2	+	25	4144	c.3757A>C	c.(3757-3759)ATA>CTA	p.I1253L	RAD50_uc003kxh.2_Missense_Mutation_p.I1114L	NM_005732	NP_005723	Q92878	RAD50_HUMAN	RAD50 homolog isoform 1	1253					DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTGCAGGATAATAAAAAGTCG	0.373								Homologous_recombination					72	106	---	---	---	---	PASS
LOC153328	153328	broad.mit.edu	37	5	135207183	135207183	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135207183C>A	uc003laz.1	+	5	627	c.455C>A	c.(454-456)CCT>CAT	p.P152H	LOC153328_uc003lba.2_Intron			Q6ZT89	S2548_HUMAN	RecName: Full=Putative mitochondrial carrier protein FLJ44862;	152	Solcar 2.				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCAGTGGCTCCTGCGGAGCAG	0.602													85	98	---	---	---	---	PASS
PCDHA8	56140	broad.mit.edu	37	5	140222015	140222015	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140222015C>T	uc003lhs.2	+	1	1109	c.1109C>T	c.(1108-1110)GCC>GTC	p.A370V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhr.1_Missense_Mutation_p.A370V	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	370	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTGTCATCGCCCTAATTAGC	0.488													41	285	---	---	---	---	PASS
PCDHB5	26167	broad.mit.edu	37	5	140516605	140516605	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140516605T>G	uc003liq.2	+	1	1806	c.1589T>G	c.(1588-1590)GTG>GGG	p.V530G		NM_015669	NP_056484	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5 precursor	530	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding|protein binding			skin(3)|ovary(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAGTTCCGCGTGGGAGCCACA	0.687													6	125	---	---	---	---	PASS
PCDHB16	57717	broad.mit.edu	37	5	140564230	140564230	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140564230C>G	uc003liv.2	+	1	3251	c.2096C>G	c.(2095-2097)TCG>TGG	p.S699W	PCDHB9_uc003liw.1_5'Flank	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	699	Helical; (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCGGTGTCGTCGCTCTTCCTC	0.687													53	291	---	---	---	---	PASS
PCDHGA7	56108	broad.mit.edu	37	5	140762931	140762931	+	Silent	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140762931C>T	uc003lka.1	+	1	465	c.465C>T	c.(463-465)AGC>AGT	p.S155S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003ljz.1_Silent_p.S155S	NM_018920	NP_061743	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7 isoform 1	155	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCGTTAAGCGAGGCTGGGG	0.463													17	76	---	---	---	---	PASS
CNOT6	57472	broad.mit.edu	37	5	179998388	179998388	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179998388G>C	uc003mlx.2	+	11	1766	c.1417G>C	c.(1417-1419)GAG>CAG	p.E473Q	CNOT6_uc010jld.2_Missense_Mutation_p.E473Q|CNOT6_uc010jle.2_Missense_Mutation_p.E468Q	NM_015455	NP_056270	Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	473					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	exonuclease activity|metal ion binding|protein binding|RNA binding				0	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		GAGTGCCTATGAGAGTGGCCT	0.423													66	107	---	---	---	---	PASS
NQO2	4835	broad.mit.edu	37	6	3006757	3006757	+	5'UTR	SNP	T	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3006757T>A	uc003mus.2	+	2					NQO2_uc003mup.1_5'UTR|NQO2_uc003mut.2_5'UTR	NM_000904	NP_000895	P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2							cytoplasm|nucleus	coenzyme binding|dihydronicotinamide riboside quinone reductase activity|electron carrier activity|metal ion binding|NADPH dehydrogenase (quinone) activity			ovary(1)	1	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Menadione(DB00170)|NADH(DB00157)	ACCCATCAAATCAGAGAGAAG	0.418													11	30	---	---	---	---	PASS
BTN3A1	11119	broad.mit.edu	37	6	26413269	26413269	+	Intron	SNP	T	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26413269T>C	uc003nhv.2	+						BTN3A1_uc011dkj.1_3'UTR|BTN3A1_uc011dkk.1_Intron|BTN3A1_uc010jqj.2_3'UTR	NM_007048	NP_008979	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1 isoform a						lipid metabolic process	integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2						GAGTCACATTTAGGGCAGACT	0.532													13	19	---	---	---	---	PASS
DDR1	780	broad.mit.edu	37	6	30866860	30866860	+	Intron	SNP	A	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30866860A>T	uc003nrr.2	+						DDR1_uc010jse.2_Intron|DDR1_uc003nrq.2_Intron|DDR1_uc003nrs.2_Intron|DDR1_uc003nrt.2_Intron|DDR1_uc011dms.1_Intron|DDR1_uc003nru.2_Intron|DDR1_uc003nrv.2_Intron|DDR1_uc003nrz.1_Missense_Mutation_p.R208W	NM_013993	NP_054699	Q08345	DDR1_HUMAN	discoidin domain receptor family, member 1						cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to plasma membrane	ATP binding|protein binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|central_nervous_system(3)|large_intestine(1)|ovary(1)	9					Imatinib(DB00619)	GGGGGACAGAAGGGGCAGAGT	0.607													52	150	---	---	---	---	PASS
PBX2	5089	broad.mit.edu	37	6	32156280	32156280	+	Silent	SNP	G	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32156280G>T	uc003oav.1	-	3	568	c.297C>A	c.(295-297)GGC>GGA	p.G99G	PBX2_uc003oaw.2_Silent_p.G99G	NM_002586	NP_002577	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	99							transcription factor binding			ovary(1)	1						GAATGCTGAGGCCTAGCATGC	0.612													8	79	---	---	---	---	PASS
POLH	5429	broad.mit.edu	37	6	43554942	43554942	+	Intron	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43554942A>G	uc003ovq.3	+						POLH_uc010jyu.2_Intron|POLH_uc011dvl.1_Intron|POLH_uc003ovr.3_5'UTR	NM_006502	NP_006493	Q9Y253	POLH_HUMAN	DNA-directed DNA polymerase eta						DNA replication|DNA synthesis involved in DNA repair|regulation of DNA repair|response to UV-C	cytoplasm|nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			breast(2)	2	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			GCAGGGTGGGAGTGGAGCAGA	0.373								DNA_polymerases_(catalytic_subunits)	Xeroderma_Pigmentosum				8	28	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51612957	51612957	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51612957A>G	uc003pah.1	-	58	9733	c.9457T>C	c.(9457-9459)TTT>CTT	p.F3153L	PKHD1_uc010jzn.1_Missense_Mutation_p.F1136L|PKHD1_uc003pai.2_Missense_Mutation_p.F3153L	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3153	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					CCATAGTCAAAGTTCTTGAAA	0.413													131	346	---	---	---	---	PASS
KCNQ5	56479	broad.mit.edu	37	6	73787159	73787159	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73787159G>A	uc003pgk.2	+	4	1078	c.731G>A	c.(730-732)CGC>CAC	p.R244H	KCNQ5_uc003pgj.3_Missense_Mutation_p.R244H|KCNQ5_uc011dyh.1_Missense_Mutation_p.R244H|KCNQ5_uc011dyi.1_Missense_Mutation_p.R244H|KCNQ5_uc010kat.2_Missense_Mutation_p.R244H|KCNQ5_uc011dyj.1_Missense_Mutation_p.R244H|KCNQ5_uc011dyk.1_Missense_Mutation_p.R3H	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	244	Helical; Voltage-sensor; Name=Segment S4; (Potential).		R -> C (in a colorectal cancer sample; somatic mutation).		protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity	p.R244C(1)		ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		CGCATGGTGCGCATGGACCGA	0.438													4	126	---	---	---	---	PASS
DOPEY1	23033	broad.mit.edu	37	6	83823098	83823098	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83823098A>G	uc003pjs.1	+	7	998	c.738A>G	c.(736-738)ACA>ACG	p.T246T	DOPEY1_uc011dyy.1_Silent_p.T246T|DOPEY1_uc010kbl.1_Silent_p.T246T	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	246					protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		AGAGAAGCACACTGGACCTCA	0.373													37	115	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90503860	90503860	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90503860C>G	uc003pnn.1	-	4	737	c.621G>C	c.(619-621)AAG>AAC	p.K207N	MDN1_uc003pnp.1_Missense_Mutation_p.K207N	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	207					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TAAATATCTTCTTAAGAAATG	0.328													3	109	---	---	---	---	PASS
BCLAF1	9774	broad.mit.edu	37	6	136589503	136589503	+	Intron	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136589503G>A	uc003qgx.1	-						BCLAF1_uc011edb.1_Missense_Mutation_p.H60Y|BCLAF1_uc003qgw.1_Intron|BCLAF1_uc003qgy.1_Intron|BCLAF1_uc011edc.1_Intron|BCLAF1_uc011edd.1_Intron|BCLAF1_uc011ede.1_Intron	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1 isoform						induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		AACAAAAAATGTGATACTTTT	0.318													7	24	---	---	---	---	PASS
AUTS2	26053	broad.mit.edu	37	7	70228160	70228160	+	Silent	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70228160G>A	uc003tvw.3	+	7	1790	c.1047G>A	c.(1045-1047)CAG>CAA	p.Q349Q	AUTS2_uc003tvx.3_Silent_p.Q349Q	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1	349										ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CTGAGGCCCAGCTCCAGCCTG	0.682													70	70	---	---	---	---	PASS
BAZ1B	9031	broad.mit.edu	37	7	72877401	72877401	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72877401G>C	uc003tyc.2	-	12	3445	c.3100C>G	c.(3100-3102)CTA>GTA	p.L1034V		NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	1034					ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)				TTCCGTGCTAGATGAATAGAG	0.373													202	303	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94038888	94038888	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94038888G>T	uc003ung.1	+	18	1375	c.904G>T	c.(904-906)GCA>TCA	p.A302S	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	302					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TAATCCTGGAGCAAACGGCCT	0.433										HNSCC(75;0.22)			72	116	---	---	---	---	PASS
ASNS	440	broad.mit.edu	37	7	97487671	97487671	+	Silent	SNP	C	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97487671C>A	uc003uot.3	-	7	1328	c.822G>T	c.(820-822)CTG>CTT	p.L274L	ASNS_uc011kin.1_Silent_p.L191L|ASNS_uc003uou.3_Silent_p.L274L|ASNS_uc003uov.3_Silent_p.L274L|ASNS_uc011kio.1_Silent_p.L253L|ASNS_uc003uow.3_Silent_p.L253L|ASNS_uc003uox.3_Silent_p.L191L	NM_133436	NP_597680	P08243	ASNS_HUMAN	asparagine synthetase	274	Asparagine synthetase.				cellular response to glucose starvation|glutamine metabolic process|negative regulation of apoptosis|positive regulation of mitotic cell cycle	cytosol|soluble fraction	asparagine synthase (glutamine-hydrolyzing) activity|ATP binding			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	GGGCTTCTTTCAGCTGCTTCA	0.493													19	76	---	---	---	---	PASS
SPAM1	6677	broad.mit.edu	37	7	123594295	123594295	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123594295G>T	uc003vld.2	+	4	1073	c.671G>T	c.(670-672)TGT>TTT	p.C224F	SPAM1_uc003vle.2_Missense_Mutation_p.C224F|SPAM1_uc011koa.1_5'Flank|SPAM1_uc003vlf.3_Missense_Mutation_p.C224F|SPAM1_uc010lku.2_Missense_Mutation_p.C224F	NM_153189	NP_694859	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 2	224					binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)	TTTCCGGATTGTTACAACCAT	0.373													5	294	---	---	---	---	PASS
LRRCC1	85444	broad.mit.edu	37	8	86050475	86050475	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86050475A>C	uc003ycw.2	+	16	2853	c.2699A>C	c.(2698-2700)TAC>TCC	p.Y900S	LRRCC1_uc010maa.1_Missense_Mutation_p.Y601S|LRRCC1_uc003ycx.2_Missense_Mutation_p.Y807S|LRRCC1_uc003ycy.2_Missense_Mutation_p.Y880S	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	900					cell division|mitosis	centriole|nucleus					0						AGAAAAGCTTACAGGTATTAT	0.294													16	47	---	---	---	---	PASS
NAPRT1	93100	broad.mit.edu	37	8	144657686	144657686	+	Missense_Mutation	SNP	C	A	A	rs148462517	byFrequency	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144657686C>A	uc003yym.3	-	10	1223	c.1198G>T	c.(1198-1200)GTG>TTG	p.V400L	C8orf73_uc010mff.2_5'Flank|C8orf73_uc010mfg.1_5'Flank|NAPRT1_uc003yyn.3_Missense_Mutation_p.V400L|NAPRT1_uc011lkh.1_Missense_Mutation_p.V400L|NAPRT1_uc003yyo.3_Missense_Mutation_p.V400L	NM_145201	NP_660202	Q6XQN6	PNCB_HUMAN	nicotinate phosphoribosyltransferase domain	400					nicotinamide metabolic process|nicotinate nucleotide salvage|response to oxidative stress|water-soluble vitamin metabolic process	cytosol|Golgi apparatus|nucleus	nicotinate phosphoribosyltransferase activity|nicotinate-nucleotide diphosphorylase (carboxylating) activity			ovary(1)	1	all_cancers(97;6.49e-11)|all_epithelial(106;4.73e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.014)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.146)			TGGCCCCCCACGGCCACCAGC	0.672													18	48	---	---	---	---	PASS
MFSD3	113655	broad.mit.edu	37	8	145735861	145735861	+	Silent	SNP	C	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145735861C>A	uc003zdi.1	+	2	966	c.801C>A	c.(799-801)TCC>TCA	p.S267S		NM_138431	NP_612440	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing	267	Leu-rich.|Helical; (Potential).				transmembrane transport	integral to membrane				central_nervous_system(2)	2	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CTGGCTCCTCCCTGGGTGGGA	0.617													51	165	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66499867	66499867	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66499867T>C	uc004aee.1	+	1	677	c.677T>C	c.(676-678)CTG>CCG	p.L226P	LOC442421_uc004aed.1_RNA					Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).												0						TTCACTTTGCTGGTGAGCCAG	0.567													5	55	---	---	---	---	PASS
UPF2	26019	broad.mit.edu	37	10	11985089	11985089	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11985089C>T	uc001ila.2	-	16	3727	c.3253G>A	c.(3253-3255)GAA>AAA	p.E1085K	UPF2_uc001ilb.2_Missense_Mutation_p.E1085K|UPF2_uc001ilc.2_Missense_Mutation_p.E1085K	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	1085	Sufficient for interaction with UPF1 C- terminus.|Glu-rich.|Sufficient for interaction with EIF4A1 and EIF1.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				GTTTCATTTTCCTTATTGGAA	0.328													32	117	---	---	---	---	PASS
UPF2	26019	broad.mit.edu	37	10	11998363	11998363	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11998363G>A	uc001ila.2	-	12	3004	c.2530C>T	c.(2530-2532)CAC>TAC	p.H844Y	UPF2_uc001ilb.2_Missense_Mutation_p.H844Y|UPF2_uc001ilc.2_Missense_Mutation_p.H844Y|UPF2_uc009xiz.1_Missense_Mutation_p.H844Y	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	844	Binds to UPF3B.|Sufficient for interaction with UPF3A and UPF3B.|MIF4G 3.|Sufficient for interaction with EIF4A1 and EIF1.			H -> Q (in Ref. 2; AAG48509 and 4; BAA92646).	mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				TCCACAACGTGGATCCCAACA	0.373													68	180	---	---	---	---	PASS
CC2D2B	387707	broad.mit.edu	37	10	97779664	97779664	+	Intron	SNP	T	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97779664T>G	uc001kll.2	+						uc001klg.1_Intron|uc001klj.1_Intron|CC2D2B_uc001klk.2_Intron|CC2D2B_uc010qop.1_Intron|uc009xvb.1_RNA	NM_001001732	NP_001001732	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B isoform											ovary(1)	1		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		TCTTATTATGTTTTATAGTTG	0.343													23	62	---	---	---	---	PASS
C10orf118	55088	broad.mit.edu	37	10	115889683	115889683	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115889683C>A	uc001lbb.1	-	13	2801	c.2149G>T	c.(2149-2151)GTC>TTC	p.V717F	C10orf118_uc009xyd.1_Missense_Mutation_p.V315F|C10orf118_uc001lbc.1_Missense_Mutation_p.V717F|C10orf118_uc009xye.1_RNA	NM_018017	NP_060487	Q7Z3E2	CJ118_HUMAN	CTCL tumor antigen L14-2	717	Ser-rich.									ovary(2)	2		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)		ATGCTGCTGACTTCTTTGTCA	0.338													30	147	---	---	---	---	PASS
B4GALNT4	338707	broad.mit.edu	37	11	375478	375478	+	Silent	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:375478C>T	uc001lpb.2	+	9	810	c.801C>T	c.(799-801)CCC>CCT	p.P267P		NM_178537	NP_848632	Q76KP1	B4GN4_HUMAN	beta	267	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTTTCCTGCCCGGCCTGAAGT	0.672													70	242	---	---	---	---	PASS
LOC650368	650368	broad.mit.edu	37	11	3427765	3427765	+	RNA	SNP	G	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3427765G>C	uc010qxs.1	+	9		c.758G>C			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						CACACGTCCTGCAGTGGCCTG	0.602													4	86	---	---	---	---	PASS
OR4P4	81300	broad.mit.edu	37	11	55406262	55406262	+	Silent	SNP	C	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55406262C>A	uc010rij.1	+	1	429	c.429C>A	c.(427-429)ATC>ATA	p.I143I		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	143	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1						ACACAATCATCATAGTTTGTT	0.428													57	136	---	---	---	---	PASS
MARK2	2011	broad.mit.edu	37	11	63670173	63670173	+	Silent	SNP	G	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63670173G>T	uc001nxw.2	+	13	1914	c.1335G>T	c.(1333-1335)CGG>CGT	p.R445R	MARK2_uc001nxx.2_Silent_p.R445R|MARK2_uc001nxy.2_Silent_p.R444R|MARK2_uc001nxv.3_Silent_p.R444R|MARK2_uc001nxz.3_Silent_p.R411R|MARK2_uc009yoy.2_Silent_p.R411R	NM_001039469	NP_001034558	Q7KZI7	MARK2_HUMAN	MAP/microtubule affinity-regulating kinase 2	445					cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress	plasma membrane	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3						AGTCAGGGCGGAAAGCCAGCA	0.612													21	53	---	---	---	---	PASS
MPZL2	10205	broad.mit.edu	37	11	118133354	118133354	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118133354A>G	uc001psn.2	-	3	376	c.235T>C	c.(235-237)TAC>CAC	p.Y79H	MPZL2_uc001pso.2_Missense_Mutation_p.Y79H|MPZL2_uc001psp.1_Missense_Mutation_p.Y79H	NM_005797	NP_005788	O60487	MPZL2_HUMAN	myelin protein zero-like 2 precursor	79	Extracellular (Potential).|Ig-like V-type.				anatomical structure morphogenesis|homophilic cell adhesion	cytoskeleton|integral to membrane				skin(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		TCTATGTGGTAGTAGAATACC	0.532													9	41	---	---	---	---	PASS
CD3G	917	broad.mit.edu	37	11	118221315	118221315	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118221315T>C	uc001psu.2	+	4	436	c.356T>C	c.(355-357)CTC>CCC	p.L119P	CD3G_uc009zaa.1_Missense_Mutation_p.L59P	NM_000073	NP_000064	P09693	CD3G_HUMAN	CD3G antigen, gamma polypeptide precursor	119	Helical; (Potential).				establishment or maintenance of cell polarity|protein complex assembly|protein transport|regulation of apoptosis|T cell activation|T cell costimulation|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	protein heterodimerization activity|receptor signaling complex scaffold activity|T cell receptor binding|transmembrane receptor activity				0	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		TCTGGCTTTCTCTTTGCTGAA	0.453													19	106	---	---	---	---	PASS
OR10G4	390264	broad.mit.edu	37	11	123887007	123887007	+	Silent	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123887007C>T	uc010sac.1	+	1	726	c.726C>T	c.(724-726)TCC>TCT	p.S242S		NM_001004462	NP_001004462	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G,	242	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CCTGTGCCTCCCACTGTATTG	0.522													10	119	---	---	---	---	PASS
FLI1	2313	broad.mit.edu	37	11	128680779	128680779	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128680779G>A	uc010sbu.1	+	9	1596	c.1255G>A	c.(1255-1257)GCA>ACA	p.A419T	FLI1_uc010sbt.1_Missense_Mutation_p.A226T|FLI1_uc010sbv.1_Missense_Mutation_p.A386T|FLI1_uc009zci.2_Missense_Mutation_p.A353T	NM_002017	NP_002008	Q01543	FLI1_HUMAN	Friend leukemia virus integration 1	419					hemostasis|organ morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2266)	bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2)	2273	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		CTTTGGAGCCGCATCACAATA	0.577			T	EWSR1	Ewing sarcoma								4	104	---	---	---	---	PASS
ADAMTS15	170689	broad.mit.edu	37	11	130341137	130341137	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130341137C>T	uc010scd.1	+	7	1937	c.1937C>T	c.(1936-1938)ACC>ATC	p.T646I		NM_139055	NP_620686	Q8TE58	ATS15_HUMAN	a disintegrin-like and metalloprotease	646	Cys-rich.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|pancreas(1)|lung(1)|skin(1)	5	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		CCTGACTCCACCTCCGTCTGT	0.587													15	62	---	---	---	---	PASS
C1S	716	broad.mit.edu	37	12	7177661	7177661	+	Silent	SNP	T	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7177661T>G	uc001qsj.2	+	15	2492	c.1773T>G	c.(1771-1773)CCT>CCG	p.P591P	C1S_uc001qsk.2_Silent_p.P591P|C1S_uc001qsl.2_Silent_p.P591P|C1S_uc009zfr.2_Silent_p.P424P|C1S_uc009zfs.2_RNA	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent	591	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	CTGTAGCTCCTTTAAGAAAAT	0.517													51	114	---	---	---	---	PASS
COL2A1	1280	broad.mit.edu	37	12	48381066	48381066	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48381066C>G	uc001rqu.2	-	20	1433	c.1252G>C	c.(1252-1254)GCC>CCC	p.A418P	COL2A1_uc009zkw.2_RNA|COL2A1_uc001rqv.2_Missense_Mutation_p.A349P	NM_001844	NP_001835	P02458	CO2A1_HUMAN	collagen, type II, alpha 1 isoform 1 precursor	418	Triple-helical region.				axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	GATCCTTTGGCTCCAGGAATT	0.552													11	48	---	---	---	---	PASS
TSC22D1	8848	broad.mit.edu	37	13	45008837	45008837	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45008837A>G	uc001uzn.3	-	3	3638	c.3147T>C	c.(3145-3147)CCT>CCC	p.P1049P	TSC22D1_uc001uzo.1_Intron|TSC22D1_uc001uzm.3_Silent_p.P120P	NM_183422	NP_904358	Q15714	T22D1_HUMAN	TSC22 domain family, member 1 isoform 1	1049					transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		GGGTGGTGGCAGGGGGGGAGC	0.642													4	22	---	---	---	---	PASS
OLFM4	10562	broad.mit.edu	37	13	53624673	53624673	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53624673T>C	uc001vhl.2	+	5	1300	c.1300T>C	c.(1300-1302)TTC>CTC	p.F434L	OLFM4_uc001vhk.1_3'UTR	NM_006418	NP_006409	Q6UX06	OLFM4_HUMAN	olfactomedin 4 precursor	434	Olfactomedin-like.				cell adhesion	extracellular space				skin(1)	1		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		TTCTAACGCCTTCATGGTATG	0.423													62	155	---	---	---	---	PASS
PIBF1	10464	broad.mit.edu	37	13	73482729	73482729	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73482729C>T	uc001vjc.2	+	12	1854	c.1549C>T	c.(1549-1551)CAA>TAA	p.Q517*	PIBF1_uc010aeo.1_RNA|PIBF1_uc001vjb.2_Nonsense_Mutation_p.Q517*|PIBF1_uc010aep.2_5'UTR	NM_006346	NP_006337	Q8WXW3	PIBF1_HUMAN	progesterone-induced blocking factor 1	517						centrosome				ovary(1)|breast(1)	2		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		TACTGAACTTCAAGCACAGAA	0.348													30	87	---	---	---	---	PASS
TEP1	7011	broad.mit.edu	37	14	20872832	20872832	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20872832G>A	uc001vxe.2	-	5	1010	c.970C>T	c.(970-972)CGA>TGA	p.R324*	TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Intron	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	324	TROVE.				telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CAGAAATATCGTCGCAGGTGG	0.552													6	145	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44973708	44973708	+	3'UTR	SNP	C	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44973708C>A	uc001wvn.2	-	1						NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein							cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		TTAGGTACAACCTGACTACAG	0.383													7	100	---	---	---	---	PASS
ZFYVE26	23503	broad.mit.edu	37	14	68274120	68274120	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68274120C>T	uc001xka.2	-	5	1020	c.881G>A	c.(880-882)GGA>GAA	p.G294E	ZFYVE26_uc010tsz.1_RNA|ZFYVE26_uc001xkc.3_Missense_Mutation_p.G294E|ZFYVE26_uc010tta.1_Missense_Mutation_p.G294E	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	294					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CACACCTTTTCCCGAGGCTGT	0.572													20	73	---	---	---	---	PASS
APBA2	321	broad.mit.edu	37	15	29346528	29346528	+	Silent	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29346528G>A	uc001zck.2	+	3	648	c.441G>A	c.(439-441)CCG>CCA	p.P147P	APBA2_uc010azj.2_Silent_p.P147P|APBA2_uc010uat.1_Silent_p.P147P|APBA2_uc001zcl.2_Silent_p.P147P|APBA2_uc010uas.1_Silent_p.P147P	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,	147					nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CGGCGGGCCCGCACCCCCACG	0.672													14	48	---	---	---	---	PASS
APBA2	321	broad.mit.edu	37	15	29409434	29409434	+	3'UTR	SNP	G	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29409434G>T	uc001zck.2	+	14					APBA2_uc010uat.1_3'UTR|APBA2_uc001zcl.2_3'UTR	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CGACGCCACAGCCCAGCCACG	0.637													4	7	---	---	---	---	PASS
MAPKBP1	23005	broad.mit.edu	37	15	42107967	42107967	+	Missense_Mutation	SNP	T	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42107967T>A	uc001zok.3	+	13	1767	c.1481T>A	c.(1480-1482)CTA>CAA	p.L494Q	MAPKBP1_uc001zoj.3_Missense_Mutation_p.L488Q|MAPKBP1_uc010bcj.2_5'UTR|MAPKBP1_uc010bci.2_Missense_Mutation_p.L488Q|MAPKBP1_uc010udb.1_Missense_Mutation_p.L327Q|MAPKBP1_uc010bck.2_5'UTR|MAPKBP1_uc010bcl.2_5'UTR	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein	494	WD 7.									central_nervous_system(5)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	10		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		GGACAGCATCTAGCATCAGGG	0.572													20	68	---	---	---	---	PASS
UACA	55075	broad.mit.edu	37	15	70961034	70961034	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70961034T>G	uc002asr.2	-	16	2093	c.1989A>C	c.(1987-1989)GAA>GAC	p.E663D	UACA_uc010uke.1_Missense_Mutation_p.E554D|UACA_uc002asq.2_Missense_Mutation_p.E650D|UACA_uc010bin.1_Missense_Mutation_p.E638D	NM_018003	NP_060473	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and	663	Potential.					cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4						ACTGTCTAATTTCACTAAGTG	0.338													57	164	---	---	---	---	PASS
MAN2C1	4123	broad.mit.edu	37	15	75659878	75659878	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75659878C>G	uc002baf.2	-	3	342	c.325G>C	c.(325-327)GTG>CTG	p.V109L	MAN2C1_uc002bag.2_Missense_Mutation_p.V109L|MAN2C1_uc002bah.2_Missense_Mutation_p.V109L|MAN2C1_uc010bkk.2_Missense_Mutation_p.V109L|MAN2C1_uc010umi.1_Intron|MAN2C1_uc010umj.1_RNA|MAN2C1_uc010umk.1_RNA	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	109					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0						TCACGCCACACCAGACCTTCT	0.572													54	164	---	---	---	---	PASS
PSMA4	5685	broad.mit.edu	37	15	78834926	78834926	+	Missense_Mutation	SNP	C	A	A	rs149336836		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78834926C>A	uc002bdu.3	+	4	306	c.148C>A	c.(148-150)CGC>AGC	p.R50S	PSMA4_uc010blf.2_Missense_Mutation_p.R50S|PSMA4_uc002bdv.3_Intron|PSMA4_uc002bdw.3_Missense_Mutation_p.R26S|PSMA4_uc002bdx.3_Intron	NM_002789	NP_002780	P25789	PSA4_HUMAN	proteasome alpha 4 subunit isoform 1	50					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	identical protein binding|threonine-type endopeptidase activity				0						AGCAGAGAGACGCAACATCCA	0.358													59	256	---	---	---	---	PASS
CHD2	1106	broad.mit.edu	37	15	93489310	93489310	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93489310T>C	uc002bsp.2	+	12	1816	c.1241T>C	c.(1240-1242)CTA>CCA	p.L414P	CHD2_uc002bsn.2_Missense_Mutation_p.L414P|CHD2_uc002bso.1_Missense_Mutation_p.L414P|CHD2_uc010urb.1_Missense_Mutation_p.L427P|CHD2_uc010bof.1_RNA	NM_001271	NP_001262	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	414	Chromo 2.				regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			CCCGAATATCTATGTAAATGG	0.393													30	102	---	---	---	---	PASS
SRL	6345	broad.mit.edu	37	16	4245571	4245571	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4245571C>T	uc002cvz.3	-	5	606	c.593G>A	c.(592-594)CGC>CAC	p.R198H	SRL_uc002cvy.3_RNA	NM_001098814	NP_001092284	Q86TD4	SRCA_HUMAN	sarcalumenin	657						sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5						TTGCTGCTTGCGGTTCTCGAT	0.363													40	209	---	---	---	---	PASS
ATF7IP2	80063	broad.mit.edu	37	16	10567377	10567377	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10567377A>G	uc002czu.2	+	9	1695	c.1468A>G	c.(1468-1470)AAT>GAT	p.N490D	ATF7IP2_uc002czv.2_Missense_Mutation_p.N490D|ATF7IP2_uc010uyo.1_RNA|ATF7IP2_uc010uyp.1_Missense_Mutation_p.N34D|ATF7IP2_uc002czw.2_Missense_Mutation_p.N490D|ATF7IP2_uc010uyq.1_RNA	NM_024997	NP_079273	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting	490					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						CAATTCTCCCAATGCTGAAGT	0.284													50	149	---	---	---	---	PASS
C16orf62	57020	broad.mit.edu	37	16	19627466	19627466	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19627466G>C	uc002dgn.1	+	13	1066	c.1054G>C	c.(1054-1056)GAA>CAA	p.E352Q	C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Missense_Mutation_p.E101Q|C16orf62_uc002dgm.1_Missense_Mutation_p.E352Q	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020	352						integral to membrane				ovary(1)	1						ACATCTCAAAGAAACCCTAAA	0.358													29	93	---	---	---	---	PASS
RBBP6	5930	broad.mit.edu	37	16	24583192	24583192	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24583192A>G	uc002dmh.2	+	18	5845	c.4805A>G	c.(4804-4806)CAA>CGA	p.Q1602R	RBBP6_uc002dmi.2_Missense_Mutation_p.Q1568R|RBBP6_uc010bxr.2_Missense_Mutation_p.Q762R|RBBP6_uc002dmk.2_Missense_Mutation_p.Q1435R	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN	retinoblastoma-binding protein 6 isoform 1	1602					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0518)		GAAAAAGAGCAAATTACTGGG	0.388													30	119	---	---	---	---	PASS
SEPHS2	22928	broad.mit.edu	37	16	30455564	30455564	+	3'UTR	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30455564A>G	uc010ves.1	-	2					SEPHS2_uc002dyh.1_3'UTR|SEPHS2_uc010vet.1_3'UTR	NM_012248	NP_036380	Q99611	SPS2_HUMAN	selenophosphate synthetase 2						selenocysteine biosynthetic process		ATP binding|selenide, water dikinase activity			breast(2)	2						AGATGGGCTGATTCCAATCAC	0.443													9	9	---	---	---	---	PASS
C17orf97	400566	broad.mit.edu	37	17	263712	263712	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:263712G>A	uc002frh.2	+	3	1124	c.1108G>A	c.(1108-1110)GAG>AAG	p.E370K	C17orf97_uc010vpz.1_RNA	NM_001013672	NP_001013694	Q6ZQX7	CQ097_HUMAN	hypothetical protein LOC400566	390	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.|19.									ovary(1)	1						CCCCGACCCCGAGGCCCTCAA	0.682													4	94	---	---	---	---	PASS
RCVRN	5957	broad.mit.edu	37	17	9804495	9804495	+	Intron	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9804495C>T	uc002gme.1	-						RCVRN_uc002gmf.1_RNA	NM_002903	NP_002894	P35243	RECO_HUMAN	recoverin						visual perception		calcium ion binding|calcium sensitive guanylate cyclase activator activity				0						ACatcttacactgtacacaaa	0.199													12	17	---	---	---	---	PASS
MYO15A	51168	broad.mit.edu	37	17	18044110	18044110	+	Silent	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18044110C>T	uc010vxh.1	+	20	5708	c.5370C>T	c.(5368-5370)CCC>CCT	p.P1790P		NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	1790	Myosin head-like.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					GGTGCAACCCCTTGTTCATGC	0.512											OREG0024223	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	28	104	---	---	---	---	PASS
SSH2	85464	broad.mit.edu	37	17	27977810	27977810	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27977810T>C	uc002heo.1	-	12	1007	c.1007A>G	c.(1006-1008)TAT>TGT	p.Y336C	SSH2_uc010wbh.1_Missense_Mutation_p.Y363C|SSH2_uc002hep.1_Missense_Mutation_p.Y336C	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	336	Tyrosine-protein phosphatase.				actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						ATTCAAGATATACCGTACCCT	0.413													62	151	---	---	---	---	PASS
SLC4A1	6521	broad.mit.edu	37	17	42328875	42328875	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42328875G>A	uc002igf.3	-	18	2542	c.2393C>T	c.(2392-2394)ACG>ATG	p.T798M		NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member	798	Helical; (Potential).|Membrane (anion exchange).				bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GCTGAGCGACGTGACCCCCAT	0.597													31	107	---	---	---	---	PASS
ANKFN1	162282	broad.mit.edu	37	17	54452062	54452062	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54452062A>G	uc002iun.1	+	7	941	c.906A>G	c.(904-906)GTA>GTG	p.V302V		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	302	Fibronectin type-III.									large_intestine(1)|ovary(1)	2						CAGCTGTAGTAACCAGGTATA	0.443													41	137	---	---	---	---	PASS
NPLOC4	55666	broad.mit.edu	37	17	79589205	79589205	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79589205A>T	uc002kat.3	-	3	378	c.196T>A	c.(196-198)TTG>ATG	p.L66M	NPLOC4_uc002kau.3_Missense_Mutation_p.L66M|NPLOC4_uc010wur.1_Translation_Start_Site	NM_017921	NP_060391	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4	66					cellular membrane fusion|ER-associated protein catabolic process|Golgi organization	cytosol|endoplasmic reticulum|nuclear outer membrane-endoplasmic reticulum membrane network|nucleus	zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			ATTTTTAGCAAGTTGAGGGAT	0.468													36	131	---	---	---	---	PASS
C17orf101	79701	broad.mit.edu	37	17	80369360	80369360	+	Silent	SNP	G	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80369360G>T	uc002keu.1	-	3	452	c.351C>A	c.(349-351)ATC>ATA	p.I117I	C17orf101_uc002ket.1_Silent_p.I117I|C17orf101_uc010dip.1_RNA	NM_024648	NP_078924	Q6PK18	CQ101_HUMAN	hypothetical protein LOC79701 isoform 1	117	Lumenal (Potential).					integral to membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(1)	1						CCTCCCTGGTGATGACGACAT	0.632													17	42	---	---	---	---	PASS
EMILIN2	84034	broad.mit.edu	37	18	2891711	2891711	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2891711G>C	uc002kln.2	+	4	1745	c.1586G>C	c.(1585-1587)GGG>GCG	p.G529A		NM_032048	NP_114437	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2 precursor	529					cell adhesion	collagen	extracellular matrix constituent conferring elasticity|protein binding			skin(2)|ovary(1)	3				READ - Rectum adenocarcinoma(2;0.1)		GGAGTGTCAGGGTCAGGAGAT	0.527													24	90	---	---	---	---	PASS
MALT1	10892	broad.mit.edu	37	18	56414872	56414872	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56414872A>T	uc002lhm.1	+	17	2531	c.2273A>T	c.(2272-2274)CAT>CTT	p.H758L	MALT1_uc002lhn.1_Missense_Mutation_p.H747L	NM_006785	NP_006776	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma	758					activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|lung(1)|central_nervous_system(1)	4						GACCCATTCCATGGTGTTTAC	0.448			T	BIRC3	MALT								6	366	---	---	---	---	PASS
GPI	2821	broad.mit.edu	37	19	34859595	34859595	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34859595G>C	uc002nvg.1	+	4	493	c.390G>C	c.(388-390)AAG>AAC	p.K130N	GPI_uc002nvf.2_Missense_Mutation_p.K169N|GPI_uc010xrv.1_Missense_Mutation_p.K169N|GPI_uc010xrw.1_Missense_Mutation_p.K130N|GPI_uc010edl.1_Missense_Mutation_p.K130N|GPI_uc002nvh.1_3'UTR	NM_000175	NP_000166	P06744	G6PI_HUMAN	glucose phosphate isomerase	130					angiogenesis|gluconeogenesis|glycolysis|hemostasis|humoral immune response	cytosol|extracellular space|nucleus|plasma membrane	cytokine activity|glucose-6-phosphate isomerase activity|growth factor activity			ovary(1)|kidney(1)	2	Esophageal squamous(110;0.162)					ACAAGATGAAGTCTTTCTGCC	0.567													4	87	---	---	---	---	PASS
C19orf61	56006	broad.mit.edu	37	19	44237823	44237823	+	Silent	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44237823G>A	uc002oxj.2	-	11	1508	c.1165C>T	c.(1165-1167)CTG>TTG	p.L389L	C19orf61_uc002oxk.2_Silent_p.L389L	NM_019108	NP_061981	Q9H0W8	SMG9_HUMAN	SMG9 protein	389					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	intracellular	protein binding				0		Prostate(69;0.0352)				TCAATCATCAGGTGCATCTGC	0.567													14	58	---	---	---	---	PASS
CPNE1	8904	broad.mit.edu	37	20	34214664	34214664	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34214664T>G	uc002xdf.2	-	17	1661	c.1298A>C	c.(1297-1299)GAG>GCG	p.E433A	CPNE1_uc002xdc.2_Missense_Mutation_p.E95A|CPNE1_uc010zvj.1_Missense_Mutation_p.E438A|CPNE1_uc002xde.2_Missense_Mutation_p.E409A|CPNE1_uc002xdg.2_Missense_Mutation_p.E433A|CPNE1_uc010gfi.2_RNA|CPNE1_uc010gfj.2_RNA|CPNE1_uc002xdh.2_Missense_Mutation_p.E433A|CPNE1_uc002xdi.2_Missense_Mutation_p.E433A|CPNE1_uc002xdj.2_Missense_Mutation_p.E433A|CPNE1_uc002xdk.2_Missense_Mutation_p.E433A|CPNE1_uc002xdl.2_Missense_Mutation_p.E433A|CPNE1_uc002xdm.2_Missense_Mutation_p.E433A	NM_152931	NP_690908	Q99829	CPNE1_HUMAN	copine I isoform a	433	VWFA.				lipid metabolic process|vesicle-mediated transport		calcium-dependent phospholipid binding|phosphatidylserine binding|transporter activity			upper_aerodigestive_tract(1)	1	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			CACCACAGCCTCACGTGTGGC	0.567													17	47	---	---	---	---	PASS
RALGAPB	57148	broad.mit.edu	37	20	37144892	37144892	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37144892A>C	uc002xiw.2	+	7	1187	c.930A>C	c.(928-930)GAA>GAC	p.E310D	RALGAPB_uc010zvz.1_Missense_Mutation_p.E310D|RALGAPB_uc002xix.2_Missense_Mutation_p.E310D|RALGAPB_uc002xiy.1_Missense_Mutation_p.E310D|RALGAPB_uc002xiz.2_Missense_Mutation_p.E88D|RALGAPB_uc002xja.1_Missense_Mutation_p.E37D	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit	310					activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2						AATTTCAGGAACAGTTCTTGA	0.373													11	260	---	---	---	---	PASS
TMEM189-UBE2V1	387522	broad.mit.edu	37	20	48760154	48760154	+	Silent	SNP	C	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48760154C>T	uc002xvf.2	-	2	287	c.126G>A	c.(124-126)AAG>AAA	p.K42K	TMEM189_uc010zyq.1_RNA|TMEM189_uc002xvg.2_Silent_p.K42K|TMEM189_uc010gif.2_Silent_p.K42K	NM_199203	NP_954673	Q13404	UB2V1_HUMAN	TMEM189-UBE2V1 readthrough transcript	Error:Variant_position_missing_in_Q13404_after_alignment					cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein K63-linked ubiquitination|regulation of DNA repair|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus|UBC13-UEV1A complex|ubiquitin ligase complex	acid-amino acid ligase activity|protein binding				0			BRCA - Breast invasive adenocarcinoma(9;8.29e-07)			CCTGGAGGCGCTTGCCTGCAG	0.557													13	41	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	11014987	11014987	+	RNA	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11014987A>G	uc002yis.1	-	7		c.1459T>C						P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CTATAGTTTCAATAGCAGACT	0.388													3	59	---	---	---	---	PASS
KRTAP10-6	386674	broad.mit.edu	37	21	46012291	46012291	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46012291A>G	uc002zfm.2	-	1	96	c.75T>C	c.(73-75)TGT>TGC	p.C25C	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198688	NP_941961	P60371	KR106_HUMAN	keratin associated protein 10-6	25						keratin filament					0						AGCAAGAGTCACAGGAACCAG	0.677													6	41	---	---	---	---	PASS
SEPT5	5413	broad.mit.edu	37	22	19707850	19707850	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19707850C>G	uc002zpv.1	+	6	495	c.370C>G	c.(370-372)CCC>GCC	p.P124A	SEPT5_uc002zpw.1_RNA|SEPT5_uc002zpx.1_RNA|SEPT5_uc002zpy.1_5'Flank	NM_002688	NP_002679	Q99719	SEPT5_HUMAN	septin 5	124					cell cycle|cytokinesis|regulation of exocytosis|synaptic vesicle targeting	plasma membrane|septin complex|synaptic vesicle	GTP binding|GTPase activity|protein binding|structural molecule activity			lung(1)	1	Colorectal(54;0.0993)					CAGCTGGAAGCCCATCACCGA	0.597													15	43	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22664606	22664606	+	RNA	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22664606A>G	uc011aim.1	+	31		c.2121A>G			LOC96610_uc011aiq.1_RNA					Parts of antibodies, mostly variable regions.												0						GTCTTCATGCAAACTTGGTAT	0.398													3	53	---	---	---	---	PASS
SLC2A11	66035	broad.mit.edu	37	22	24226915	24226915	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24226915C>A	uc002zyn.3	+	12	1469	c.1370C>A	c.(1369-1371)CCT>CAT	p.P457H	SLC2A11_uc002zym.3_Missense_Mutation_p.P464H|SLC2A11_uc002zyo.3_RNA|SLC2A11_uc011ajc.1_Missense_Mutation_p.L464M|SLC2A11_uc002zyp.3_Missense_Mutation_p.P460H	NM_001024938	NP_001020109	Q9BYW1	GTR11_HUMAN	glucose transporter protein 10 isoform c	457	Cytoplasmic (Potential).					integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1						CTGTTCCTTCCTGAGACCAAA	0.562													93	227	---	---	---	---	PASS
ASPHD2	57168	broad.mit.edu	37	22	26830026	26830026	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26830026A>G	uc003acg.2	+	2	842	c.445A>G	c.(445-447)ATC>GTC	p.I149V		NM_020437	NP_065170	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	149	Lumenal (Potential).				peptidyl-amino acid modification	integral to endoplasmic reticulum membrane	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity			ovary(1)	1						CCACAAGGGCATCCGCGAGCA	0.647													5	52	---	---	---	---	PASS
DCX	1641	broad.mit.edu	37	X	110644391	110644391	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110644391G>A	uc004epd.2	-	3	947	c.775C>T	c.(775-777)CGC>TGC	p.R259C	DCX_uc011msv.1_Missense_Mutation_p.R259C|DCX_uc004epe.2_Missense_Mutation_p.R178C|DCX_uc004epf.2_Missense_Mutation_p.R178C|DCX_uc004epg.2_Missense_Mutation_p.R178C	NM_000555	NP_000546	O43602	DCX_HUMAN	doublecortin isoform a	259			R -> L (in SBHX).|R -> C (in SBHX).		axon guidance|central nervous system development|intracellular signal transduction	cytosol|microtubule associated complex	microtubule binding			central_nervous_system(2)|lung(1)|skin(1)	4						AGCTTGGGGCGCACAAAGTCC	0.537													4	95	---	---	---	---	PASS
TMLHE	55217	broad.mit.edu	37	X	154754204	154754204	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154754204G>A	uc004fnn.2	-	3	437	c.271C>T	c.(271-273)CAC>TAC	p.H91Y	TMLHE_uc004fno.2_Missense_Mutation_p.H91Y|TMLHE_uc004fnp.3_Missense_Mutation_p.H91Y	NM_018196	NP_060666	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	91					carnitine biosynthetic process	mitochondrial matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|trimethyllysine dioxygenase activity			ovary(1)	1	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	CTGCGCTGGTGAGTCTTAGAG	0.488													91	85	---	---	---	---	PASS
TMLHE	55217	broad.mit.edu	37	X	154754205	154754205	+	Silent	SNP	A	G	G			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154754205A>G	uc004fnn.2	-	3	436	c.270T>C	c.(268-270)ACT>ACC	p.T90T	TMLHE_uc004fno.2_Silent_p.T90T|TMLHE_uc004fnp.3_Silent_p.T90T	NM_018196	NP_060666	Q9NVH6	TMLH_HUMAN	trimethyllysine hydroxylase, epsilon	90					carnitine biosynthetic process	mitochondrial matrix	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|trimethyllysine dioxygenase activity			ovary(1)	1	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Succinic acid(DB00139)|Vitamin C(DB00126)	TGCGCTGGTGAGTCTTAGAGT	0.483													90	83	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	2774577	2774577	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2774577delT								MMEL1 (210096 upstream) : ACTRT2 (163469 downstream)																							ccacagccccttttttaggat	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2893075	2893075	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2893075delG								MMEL1 (328594 upstream) : ACTRT2 (44971 downstream)																							GATGGAtggtggggtgctggt	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	8138368	8138370	+	IGR	DEL	TGT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8138368_8138370delTGT								ERRFI1 (51975 upstream) : SLC45A1 (246020 downstream)																							TTGGGGAAGGTGTTGTTGAAAAG	0.443													4	2	---	---	---	---	
DFFA	1676	broad.mit.edu	37	1	10521380	10521380	+	3'UTR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10521380delA	uc001arj.2	-	6					DFFA_uc001ark.2_3'UTR	NM_004401	NP_004392	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha						DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction|negative regulation of apoptosis	cytosol|mitochondrion|nucleoplasm|plasma membrane	deoxyribonuclease activity|identical protein binding				0	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		TGGTGGGGCTAAAAAAAAAAT	0.433													4	2	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15146202	15146203	+	Intron	INS	-	TT	TT	rs12131142		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15146202_15146203insTT	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						gaaaaaaaatcttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	15936559	15936560	+	IGR	DEL	AC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15936559_15936560delAC								DNAJC16 (17687 upstream) : DDI2 (7510 downstream)																							ATCAAAGCATACACACACAAAT	0.312													4	2	---	---	---	---	
PLA2G5	5322	broad.mit.edu	37	1	20413894	20413894	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20413894delT	uc001bcy.2	+						PLA2G5_uc001bcw.2_Intron|PLA2G5_uc001bcx.2_Intron	NM_000929	NP_000920	P39877	PA2G5_HUMAN	phospholipase A2, group V precursor						lipid catabolic process	extracellular region	calcium ion binding|calcium-dependent phospholipase A2 activity			skin(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)		GATCATATACttttttttttt	0.025													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25828682	25828683	+	IGR	INS	-	CGT	CGT	rs146841318	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25828682_25828683insCGT								TMEM57 (1986 upstream) : LDLRAP1 (41393 downstream)																							CCCATCCTGAGCTGACTTTCCT	0.198													3	3	---	---	---	---	
GPN2	54707	broad.mit.edu	37	1	27215784	27215784	+	Intron	DEL	C	-	-	rs910048	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27215784delC	uc001bnd.1	-							NM_018066	NP_060536	Q9H9Y4	GPN2_HUMAN	ATP binding domain 1 family, member B								GTP binding				0						TAGGAGTCATCTTTTTTTTCT	0.443													4	2	---	---	---	---	
RCC1	1104	broad.mit.edu	37	1	28863600	28863600	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28863600delT	uc001bqg.1	+						SNHG3-RCC1_uc001bqa.1_Intron|SNHG3-RCC1_uc001bqb.1_Intron|SNHG3-RCC1_uc001bqc.1_Intron|RCC1_uc001bqe.1_Intron|RCC1_uc001bqf.1_Intron	NM_001269	NP_001260	P18754	RCC1_HUMAN	regulator of chromosome condensation 1 isoform						cell division|chromosome segregation|G1/S transition of mitotic cell cycle|mitosis|mitotic spindle organization|regulation of mitosis|regulation of S phase of mitotic cell cycle|spindle assembly|viral reproduction	condensed nuclear chromosome|cytoplasm|nuclear chromatin|nuclear membrane|nucleoplasm	histone binding|nucleosomal DNA binding|Ran guanyl-nucleotide exchange factor activity			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		ACACAAATTATTTTAGTAAAG	0.378													6	3	---	---	---	---	
GJA4	2701	broad.mit.edu	37	1	35256465	35256465	+	5'Flank	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35256465delG	uc009vul.2	+							NM_002060	NP_002051	P35212	CXA4_HUMAN	connexin 37						cell-cell junction assembly	integral to plasma membrane				central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TTGGAAGGGTGGGGCTAGAGG	0.562													4	2	---	---	---	---	
EIF2C1	26523	broad.mit.edu	37	1	36338845	36338845	+	Intron	DEL	T	-	-	rs74394911		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36338845delT	uc001bzk.2	+							NM_012199	NP_036331	Q9UL18	AGO1_HUMAN	eukaryotic translation initiation factor 2C, 1						negative regulation of translation involved in gene silencing by miRNA|nuclear-transcribed mRNA catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|polysome	protein binding|RNA binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AATCTCTCTCTTTTTTTTTGG	0.219													4	2	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42358193	42358193	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42358193delA	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron|HIVEP3_uc001chb.1_Intron	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GGAAGAGAAGAAAAAAAGACC	0.473													4	2	---	---	---	---	
CCDC30	728621	broad.mit.edu	37	1	42989825	42989825	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42989825delT	uc001chn.2	+						CCDC30_uc001chm.2_Intron|CCDC30_uc010oju.1_Intron	NM_001080850	NP_001074319	Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30												0						tttctttgtatttttttttct	0.000													4	3	---	---	---	---	
ERMAP	114625	broad.mit.edu	37	1	43291626	43291626	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43291626delG	uc001cic.1	+						ERMAP_uc010ojw.1_Intron|ERMAP_uc001cid.1_Intron|ERMAP_uc001cie.1_Intron	NM_001017922	NP_001017922	Q96PL5	ERMAP_HUMAN	erythroblast membrane-associated protein							integral to membrane|plasma membrane				ovary(1)	1	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AAGTAGTATTGTCATCATTAT	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	43610216	43610216	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43610216delC	uc009vwn.1	+											Homo sapiens cDNA, FLJ99785.																		ATCCAGCCCTCCTTTCTGCTG	0.453													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49119930	49119931	+	Intron	INS	-	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49119930_49119931insC	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		aacagccaccacctatgaaatg	0.050													3	3	---	---	---	---	
FAM159A	348378	broad.mit.edu	37	1	53115801	53115801	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53115801delG	uc001cuf.2	+						FAM159A_uc001cug.1_Intron|FAM159A_uc001cuh.2_Intron	NM_001042693	NP_001036158	Q6UWV7	F159A_HUMAN	hypothetical protein LOC348378							integral to membrane					0						TGTCACCCCAGAGCCCACTGC	0.403													4	2	---	---	---	---	
USP24	23358	broad.mit.edu	37	1	55541339	55541339	+	Intron	DEL	C	-	-	rs60526291		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55541339delC	uc001cyg.3	-							NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						acaacaacaacaCCACCACCA	0.154													6	3	---	---	---	---	
USP24	23358	broad.mit.edu	37	1	55541341	55541348	+	Intron	DEL	CCACCACC	-	-	rs61579636		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55541341_55541348delCCACCACC	uc001cyg.3	-							NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						aacaacaacaCCACCACCACCAATACAg	0.144													6	3	---	---	---	---	
C1orf168	199920	broad.mit.edu	37	1	57251907	57251907	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57251907delC	uc001cym.3	-						C1orf168_uc009vzu.1_Intron	NM_001004303	NP_001004303	Q5VWT5	CA168_HUMAN	hypothetical protein LOC199920											ovary(3)|skin(2)	5						ctgaccccagCCCAGATCAGC	0.184													4	2	---	---	---	---	
HOOK1	51361	broad.mit.edu	37	1	60305823	60305823	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60305823delT	uc009wad.2	+						HOOK1_uc001czo.2_Intron|HOOK1_uc001czp.2_Intron|HOOK1_uc010oor.1_Intron	NM_015888	NP_056972	Q9UJC3	HOOK1_HUMAN	hook homolog 1						early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|multicellular organismal development|protein transport	FHF complex|microtubule	identical protein binding			ovary(1)|breast(1)	2	all_cancers(7;0.000129)					taaaattctcttttttttgtt	0.109													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	68101494	68101494	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68101494delC								SERBP1 (205371 upstream) : GADD45A (49389 downstream)																							CTCCGCACTTCCCCAGCCCTT	0.527													4	2	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	85885735	85885736	+	Intron	DEL	TC	-	-	rs145432410	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85885735_85885736delTC	uc001dlb.2	-						DDAH1_uc001dlc.2_Intron|DDAH1_uc009wco.2_Intron	NM_012137	NP_036269	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	gagctgcggttcgacctgggct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	103769193	103769194	+	IGR	DEL	GA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103769193_103769194delGA								COL11A1 (195141 upstream) : RNPC3 (299384 downstream)																							GAATATTCTTGAACGTGTCACC	0.450													4	2	---	---	---	---	
GSTM4	2948	broad.mit.edu	37	1	110196277	110196277	+	5'Flank	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110196277delA	uc001dyf.2	+						GSTM4_uc009wfi.2_5'Flank|GSTM4_uc001dyg.2_5'Flank|GSTM4_uc009wfj.2_5'Flank|GSTM4_uc001dyh.2_5'Flank|GSTM2_uc001dyi.2_5'Flank	NM_000850	NP_000841	Q03013	GSTM4_HUMAN	glutathione S-transferase mu 4 isoform 1						xenobiotic metabolic process	endoplasmic reticulum membrane	glutathione transferase activity				0		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0123)|Colorectal(144;0.0129)|Epithelial(280;0.0147)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.0471)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)	GTGCTCCACTAAAATCCTGTT	0.358													4	2	---	---	---	---	
HSD3B1	3283	broad.mit.edu	37	1	120056196	120056197	+	Intron	DEL	AC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120056196_120056197delAC	uc001ehv.1	+						HSD3B1_uc001ehw.2_Intron	NM_000862	NP_000853	P14060	3BHS1_HUMAN	3 beta-hydroxysteroid dehydrogenase 1						androgen biosynthetic process|estrogen biosynthetic process|glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process	integral to membrane|microsome|mitochondrial inner membrane|mitochondrial intermembrane space|smooth endoplasmic reticulum membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|steroid delta-isomerase activity			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	NADH(DB00157)|Trilostane(DB01108)	aaattaaagtacacacacacac	0.114													4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145330541	145330541	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145330541delA	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron|NBPF10_uc001enc.2_Intron|NBPF10_uc010oym.1_Intron|NBPF10_uc010oyn.1_Intron|NBPF10_uc010oyo.1_Intron|NBPF10_uc010oyp.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GTCCCATCATAAAGGCAATAA	0.333													4	2	---	---	---	---	
CRTC2	200186	broad.mit.edu	37	1	153926532	153926532	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153926532delC	uc010ped.1	-						CRTC2_uc001fde.3_Intron|CRTC2_uc001fdf.3_Intron	NM_181715	NP_859066	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)	2	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGAGGCTTGACCACTAGTGTC	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157380057	157380057	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157380057delG								ETV3 (271674 upstream) : FCRL5 (103111 downstream)																							TGTGAGATGTGGGAGGAGGAC	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159193310	159193310	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159193310delC								DARC (17022 upstream) : FCER1A (66196 downstream)																							GCAAAGTGTGCCCCTCCTCCA	0.423													4	2	---	---	---	---	
CCDC19	25790	broad.mit.edu	37	1	159891275	159891276	+	Intron	INS	-	C	C	rs145000097	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159891275_159891276insC	uc001ful.2	-						TAGLN2_uc001fum.1_5'Flank|TAGLN2_uc001fun.1_Intron|TAGLN2_uc001fuo.1_Intron|TAGLN2_uc010piy.1_Intron	NM_012337	NP_036469	Q9UL16	CCD19_HUMAN	nasopharyngeal epithelium specific protein 1							mitochondrion|soluble fraction				ovary(1)	1	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			tcacccaaaaaccccagaagga	0.000													5	7	---	---	---	---	
KLHDC9	126823	broad.mit.edu	37	1	161067022	161067025	+	5'Flank	DEL	TTTC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161067022_161067025delTTTC	uc001fxr.2	+						KLHDC9_uc001fxq.2_5'Flank|KLHDC9_uc001fxs.2_5'Flank	NM_152366	NP_689579	Q8NEP7	KLDC9_HUMAN	kelch/ankyrin repeat containing cyclin A1												0	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			cttttctttttttctttctttctt	0.221													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163373447	163373447	+	IGR	DEL	G	-	-	rs115984645	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163373447delG								NUF2 (47894 upstream) : None (None downstream)																							tttgtccagtgggctgcagtc	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168554078	168554078	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168554078delA								XCL1 (2763 upstream) : DPT (110629 downstream)																							AATTTGGAGGAAAATGGTTGA	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	182023445	182023446	+	IGR	DEL	TT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182023445_182023446delTT								CACNA1E (252732 upstream) : ZNF648 (261 downstream)																							TTTCTGCCTATTAACAAGTACG	0.347													4	2	---	---	---	---	
NEK7	140609	broad.mit.edu	37	1	198290067	198290068	+	3'UTR	DEL	CC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198290067_198290068delCC	uc001gun.3	+	10						NM_133494	NP_598001	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7							cytoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|lung(1)|ovary(1)	4						GATGTGTTTTCCCTGAATGCTT	0.421													4	2	---	---	---	---	
SHISA4	149345	broad.mit.edu	37	1	201855890	201855890	+	5'Flank	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201855890delC	uc001gxa.2	+							NM_198149	NP_937792	Q96DD7	SHSA4_HUMAN	shisa homolog 4 precursor							integral to membrane					0						CATAAGCTAGCCCCAGCTCTC	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209460696	209460699	+	IGR	DEL	TCTC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209460696_209460699delTCTC								None (None upstream) : LOC642587 (141469 downstream)																							AACCCAGTCATCTCTCTCTCTCTC	0.451													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213628880	213628884	+	IGR	DEL	GAGTG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213628880_213628884delGAGTG								RPS6KC1 (182073 upstream) : PROX1 (532402 downstream)																							ataagcagttgagtggatgaggttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213868325	213868325	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213868325delT								RPS6KC1 (421518 upstream) : PROX1 (292961 downstream)																							acagagATTGTTGGGGAATTG	0.159													4	2	---	---	---	---	
ENAH	55740	broad.mit.edu	37	1	225718042	225718042	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225718042delA	uc001hpc.1	-						ENAH_uc001hpd.1_Intron	NM_001008493	NP_001008493	Q8N8S7	ENAH_HUMAN	enabled homolog isoform a						axon guidance|intracellular transport|T cell receptor signaling pathway	cytosol|filopodium|focal adhesion|lamellipodium|synapse	actin binding|SH3 domain binding|WW domain binding			ovary(1)|skin(1)	2	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)		TAATTTTTACAAAAAAAAACA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238726005	238726006	+	IGR	DEL	TT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238726005_238726006delTT								LOC339535 (76688 upstream) : CHRM3 (823859 downstream)																							AGAGATTCTCTTTTTTTAATTA	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244264257	244264257	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244264257delA								ZNF238 (43481 upstream) : C1orf100 (251680 downstream)																							TTTAAGCCTTAAAAAAAAAGA	0.458													4	2	---	---	---	---	
PPPDE1	51029	broad.mit.edu	37	1	244820709	244820709	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244820709delC	uc001iao.2	+						PPPDE1_uc001iap.2_Intron	NM_016076	NP_057160	Q9BSY9	PPDE1_HUMAN	PPPDE peptidase domain containing 1											breast(3)	3						CTTCCTCTTGCCCCATGCCAC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8718642	8718642	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8718642delG								LOC339788 (601665 upstream) : ID2 (100698 downstream)																							gtgggactctggcaaatcaac	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8738018	8738019	+	IGR	INS	-	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8738018_8738019insA								LOC339788 (621041 upstream) : ID2 (81321 downstream)																							GGGGCAGAGGGCAAATCCAGTT	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10075452	10075452	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10075452delA								TAF1B (909 upstream) : GRHL1 (16340 downstream)																							gcagccatccagggggagatc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12582213	12582214	+	Intron	DEL	CT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12582213_12582214delCT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		tcctctctccctctctctccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21122532	21122532	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21122532delA								C2orf43 (99705 upstream) : APOB (101770 downstream)																							CCTGCGATGGAATGTCACAGA	0.567													4	2	---	---	---	---	
DTNB	1838	broad.mit.edu	37	2	25769726	25769726	+	Intron	DEL	C	-	-	rs78459048		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25769726delC	uc002rgh.2	-						DTNB_uc010yko.1_Intron|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707	O60941	DTNB_HUMAN	dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ttttttttttctttttggaga	0.164													4	2	---	---	---	---	
PLB1	151056	broad.mit.edu	37	2	28788429	28788429	+	Intron	DEL	G	-	-	rs67312105		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28788429delG	uc002rmb.1	+						PLB1_uc010ezj.1_Intron|PLB1_uc002rmc.2_Intron|PLB1_uc002rmd.1_5'Flank	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)					CCTTGAGCCAGGAATCCAGGA	0.373													3	4	---	---	---	---	
LTBP1	4052	broad.mit.edu	37	2	33482144	33482145	+	Intron	INS	-	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33482144_33482145insA	uc002ros.2	+						LTBP1_uc002rot.2_Intron|LTBP1_uc002rou.2_Intron|LTBP1_uc002rov.2_Intron|LTBP1_uc010ymz.1_Intron|LTBP1_uc010yna.1_Intron	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AAATGTTTAGTAAAAAAAAAGT	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42152348	42152349	+	IGR	DEL	GA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42152348_42152349delGA								None (None upstream) : PKDCC (122812 downstream)																							CAACCATGAGGAGACAAGAGCA	0.272													4	2	---	---	---	---	
THADA	63892	broad.mit.edu	37	2	43697981	43697981	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43697981delT	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron|THADA_uc010fat.1_Intron|THADA_uc002rta.2_Intron	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TTCACTAGACTTAGCTAACCT	0.403													4	2	---	---	---	---	
LRPPRC	10128	broad.mit.edu	37	2	44172277	44172277	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44172277delA	uc002rtr.2	-						LRPPRC_uc010yob.1_Intron	NM_133259	NP_573566	P42704	LPPRC_HUMAN	leucine-rich PPR motif-containing protein						mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GTGCAAATGTAAATGACAAGC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64486789	64486789	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64486789delA								PELI1 (115184 upstream) : HSPC159 (194538 downstream)																							GCACCAAGTTAAAAAAAAAAA	0.453													4	3	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71708825	71708826	+	Intron	INS	-	ATCC	ATCC	rs75288288	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71708825_71708826insATCC	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						GGTCTTcatctatccatccatc	0.248													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	72085172	72085172	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72085172delA								DYSF (171280 upstream) : CYP26B1 (271195 downstream)																							GGTACCTCCCAAATCAGAGCC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73534519	73534520	+	IGR	DEL	GA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73534519_73534520delGA								EGR4 (13690 upstream) : ALMS1 (78366 downstream)																							AAGGTGGTCTGAGAATTGGTGT	0.480													4	2	---	---	---	---	
SLC4A5	57835	broad.mit.edu	37	2	74486406	74486406	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74486406delC	uc002sko.1	-						SLC4A5_uc002skl.2_Intron|SLC4A5_uc002skn.2_Intron|SLC4A5_uc010ffc.1_Intron|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a							apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	9						ATAGATGAAGCCATGTGTGCT	0.522													4	2	---	---	---	---	
TTC31	64427	broad.mit.edu	37	2	74716530	74716530	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74716530delG	uc002slt.2	+						TTC31_uc002sls.2_Intron|TTC31_uc010yrv.1_Intron|TTC31_uc002slu.2_Intron	NM_022492	NP_071937	Q49AM3	TTC31_HUMAN	tetratricopeptide repeat domain 31								binding				0						CAGTGAAGCAGGGGAGGATTA	0.562													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	79742588	79742589	+	Intron	INS	-	TT	TT			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79742588_79742589insTT	uc010yse.1	+						CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						GGGCTTTGCTCTTTCTTTGTTG	0.465													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87571069	87571070	+	Intron	DEL	TC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87571069_87571070delTC	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						ATCATCCGGATCATCAAAAGAT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92188299	92188299	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92188299delA								FKSG73 (57805 upstream) : None (None downstream)																							ATGGGTGGTTAAAAAAAACCT	0.438													4	2	---	---	---	---	
TSGA10	80705	broad.mit.edu	37	2	99719429	99719429	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99719429delA	uc002szg.3	-						TSGA10_uc002szh.3_Intron|TSGA10_uc002szi.3_Intron|TSGA10_uc010fin.1_Intron|TSGA10_uc010yvn.1_Intron	NM_182911	NP_878915	Q9BZW7	TSG10_HUMAN	testis specific, 10						spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2						AACTTTTTGTAAAATGTTCTG	0.244													4	2	---	---	---	---	
ERCC3	2071	broad.mit.edu	37	2	128029350	128029350	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128029350delT	uc002toh.1	-						ERCC3_uc002toe.1_Intron|ERCC3_uc002tof.1_Intron|ERCC3_uc002tog.1_Intron	NM_000122	NP_000113	P19447	ERCC3_HUMAN	excision repair cross-complementing rodent						cell cycle checkpoint|DNA topological change|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA duplex unwinding|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein localization|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	3'-5' DNA helicase activity|ATP binding|damaged DNA binding|protein C-terminus binding|protein N-terminus binding|transcription factor binding			ovary(2)|lung(2)|breast(2)|kidney(1)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		GAGTCATTCATTTTTTTGGCT	0.488			Mis|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130006022	130006023	+	Intron	DEL	GC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130006022_130006023delGC	uc002tpv.1	-											Homo sapiens cDNA FLJ32036 fis, clone NTONG2000492.																		ttcctTAACTGCAAGAAGAAAG	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131611213	131611213	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131611213delG	uc002try.1	+											Homo sapiens cDNA FLJ45181 fis, clone BRAWH3047644, highly  similar to Homo sapiens Rho guanine nucleotide exchange factor (GEF) 4 (ARHGEF4).																		TCGGTGTCCAGGAAGAGCAAC	0.637													4	2	---	---	---	---	
CCDC74A	90557	broad.mit.edu	37	2	132288575	132288576	+	Intron	INS	-	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132288575_132288576insG	uc002tta.2	+						CCDC74A_uc002ttb.2_Intron	NM_138770	NP_620125	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A											skin(1)	1						GAGGGGATTAAGGGGGGGTGGG	0.668													4	2	---	---	---	---	
LASS6	253782	broad.mit.edu	37	2	169436564	169436564	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169436564delT	uc002ueb.1	+						LASS6_uc002uec.1_Intron	NM_203463	NP_982288	Q6ZMG9	CERS6_HUMAN	longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1						atccttgccatttaacaagta	0.020													4	2	---	---	---	---	
PPIG	9360	broad.mit.edu	37	2	170463838	170463839	+	Intron	INS	-	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170463838_170463839insA	uc002uez.2	+						PPIG_uc010fpx.2_Intron|PPIG_uc010fpy.2_Intron|PPIG_uc002ufa.2_Intron|PPIG_uc002ufb.2_Intron|PPIG_uc002ufc.1_Intron|PPIG_uc002ufd.2_Intron	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G						protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)	GGTATTTTTTCTTCTTAGGACA	0.292													4	2	---	---	---	---	
UBR3	130507	broad.mit.edu	37	2	170789263	170789263	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170789263delA	uc010zdi.1	+						UBR3_uc002ufr.3_5'Flank	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3						sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0						TTTGACTTAGAAAAGTAATCA	0.294													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	202777030	202777030	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202777030delA								CDK15 (18767 upstream) : FZD7 (122280 downstream)																							ggcgctgaggagaggatctgg	0.179													4	2	---	---	---	---	
CD28	940	broad.mit.edu	37	2	204571164	204571164	+	5'Flank	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204571164delA	uc002vah.3	+						CD28_uc002vag.1_5'Flank|CD28_uc010zio.1_5'Flank|CD28_uc010ftx.2_5'Flank|CD28_uc002vaj.3_5'Flank	NM_006139	NP_006130	P10747	CD28_HUMAN	CD28 antigen precursor						cell surface receptor linked signaling pathway|cytokine biosynthetic process|humoral immune response|positive regulation of anti-apoptosis|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation of translation|positive regulation of viral genome replication|regulation of defense response to virus by virus|regulatory T cell differentiation|T cell costimulation|viral reproduction	cytosol|external side of plasma membrane|integral to plasma membrane	coreceptor activity|protease binding|SH3/SH2 adaptor activity				0						TTTCAGTGACAAAAAAAAAGT	0.358													4	4	---	---	---	---	
PTPRN	5798	broad.mit.edu	37	2	220166061	220166061	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220166061delG	uc002vkz.2	-						PTPRN_uc010zlc.1_Intron|PTPRN_uc002vla.2_Intron	NM_002846	NP_002837	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N						response to reactive oxygen species	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|lung(1)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		CCTTTTCCCTGCTCACACCCT	0.502													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	236844396	236844396	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236844396delT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						AAGCCTGTAATTTTTTTTGAT	0.428													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	237026424	237026424	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237026424delT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						GTTTAATACATTTTAAATAAG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	240552659	240552659	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240552659delT								HDAC4 (229313 upstream) : NDUFA10 (347499 downstream)																							CTGTTCTGTATTTTTTTGTTG	0.448													3	4	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2396402	2396403	+	Intron	INS	-	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2396402_2396403insA	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TGGTATTGCAGAAAAAAAAAAT	0.436													4	2	---	---	---	---	
LOC285375	285375	broad.mit.edu	37	3	13716251	13716251	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13716251delG	uc003byd.1	+							NR_027103				Homo sapiens, clone IMAGE:5742174, mRNA.												0						aaatatgcttggcttgtttac	0.000													4	2	---	---	---	---	
THRB	7068	broad.mit.edu	37	3	24185426	24185430	+	Intron	DEL	CAAAA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24185426_24185430delCAAAA	uc003ccx.3	-						THRB_uc010hfe.2_Intron|THRB_uc003ccy.3_Intron|THRB_uc003ccz.3_Intron	NM_001128176	NP_001121648	P10828	THB_HUMAN	thyroid hormone receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)	GCCAGCTTTTCAAAACAAAGTCCCC	0.488													4	2	---	---	---	---	
CRTAP	10491	broad.mit.edu	37	3	33183639	33183639	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33183639delG	uc003cfl.3	+						CRTAP_uc010hfz.2_Intron|CRTAP_uc003cfm.2_Intron|CRTAP_uc003cfn.2_Intron	NM_006371	NP_006362	O75718	CRTAP_HUMAN	cartilage associated protein precursor							proteinaceous extracellular matrix	binding				0						TTCACAGGCTGGGCTGTCCGC	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	34397673	34397674	+	IGR	DEL	GA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34397673_34397674delGA								PDCD6IP (486479 upstream) : None (None downstream)																							TCAAATGTCTGAGAGCCAGCTT	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	43256952	43256952	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43256952delC								C3orf39 (109387 upstream) : SNRK (71052 downstream)																							ATCTGACTATCCAGACCAAAG	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	46693219	46693220	+	IGR	INS	-	AC	AC			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46693219_46693220insAC								TDGF1 (69269 upstream) : ALS2CL (17459 downstream)																							aggtgcaaaaatcttcaacaaa	0.000													4	2	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54872838	54872838	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54872838delT	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		ATTTAAAAGGTTTTTTTTTTA	0.318													4	3	---	---	---	---	
PTPRG	5793	broad.mit.edu	37	3	62268432	62268432	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62268432delC	uc003dlb.2	+	28	4662	c.3943delC	c.(3943-3945)CAGfs	p.Q1315fs	PTPRG_uc003dlc.2_Frame_Shift_Del_p.Q1286fs|PTPRG_uc011bfi.1_Frame_Shift_Del_p.Q561fs|uc010hno.2_Intron|uc003dld.3_Intron|uc010hnp.2_Intron|uc003dle.3_Intron	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	1315	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TCGGCACTTTCAGTGTCCCAA	0.423													41	29	---	---	---	---	
IGSF11	152404	broad.mit.edu	37	3	118864633	118864633	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118864633delG	uc003eby.2	-						IGSF11_uc003ebz.2_Intron|IGSF11_uc010hqs.2_Intron|C3orf30_uc011biw.1_5'Flank|C3orf30_uc003ecb.1_5'Flank	NM_152538	NP_689751	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11 isoform a						cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0						GAGGTGCGGTGGGGGATGTTA	0.512											OREG0015728	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	120076659	120076659	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120076659delA								LRRC58 (8473 upstream) : FSTL1 (36403 downstream)																							GTGTCCCTTCAAAGACATGCT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	124464447	124464447	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124464447delC								UMPS (409 upstream) : ITGB5 (17349 downstream)																							GGCTTCATGTCCCCAGTGCTG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	133519591	133519591	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133519591delC								TF (21956 upstream) : SRPRB (5086 downstream)																							AGGAGGATGTCAGACAGGAGC	0.348													4	2	---	---	---	---	
MME	4311	broad.mit.edu	37	3	154816685	154816685	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154816685delG	uc010hvr.1	+						MME_uc003fab.1_Intron|MME_uc003fac.1_Intron|MME_uc003fad.1_Intron|MME_uc003fae.1_Intron	NM_007289	NP_009220	P08473	NEP_HUMAN	membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)	GAACTTATGTGGAAGGGCAGA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	175535291	175535291	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175535291delA								NAALADL2 (11865 upstream) : None (None downstream)																							gccactctggaaaaaaatgtg	0.015													4	2	---	---	---	---	
FGF12	2257	broad.mit.edu	37	3	192282430	192282430	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192282430delA	uc003fsy.2	-							NM_004113	NP_004104	P61328	FGF12_HUMAN	fibroblast growth factor 12 isoform 2						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		AGTGCAACAGAAACCAGTGAT	0.423													4	2	---	---	---	---	
ATP13A3	79572	broad.mit.edu	37	3	194157630	194157630	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194157630delA	uc003fty.3	-						ATP13A3_uc003ftz.1_Intron	NM_024524	NP_078800	Q9H7F0	AT133_HUMAN	ATPase type 13A3						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)	1	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		actgtctctcaaaaaaaaaCC	0.144													4	3	---	---	---	---	
SDHAP1	255812	broad.mit.edu	37	3	195709193	195709193	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195709193delA	uc011btq.1	-						SDHAP1_uc003fvx.3_Intron|SDHAP1_uc011btp.1_Intron					SubName: Full=cDNA FLJ56858, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						TAAAAGAAAGAAAAAAAAAGG	0.423													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49719	49719	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49719delT								None (None upstream) : ZNF595 (3508 downstream)																							CTCAATACGGTTTTACTCAGA	0.373													4	2	---	---	---	---	
ZNF141	7700	broad.mit.edu	37	4	368604	368604	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:368604delT	uc003gab.2	+							NM_003441	NP_003432	Q15928	ZN141_HUMAN	zinc finger protein 141						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding				0						TTCCTCAGTCTTTTCTAATCA	0.353													4	2	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7225405	7225405	+	Intron	DEL	C	-	-	rs6816930		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7225405delC	uc003gkb.3	+							NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						CACAGCATGGCCCGTGTGTGC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	8312022	8312025	+	IGR	DEL	TGAT	-	-	rs33941522		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8312022_8312025delTGAT								HTRA3 (3192 upstream) : ACOX3 (55985 downstream)																							ccagacaaactgattgtagactct	0.015													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13821245	13821245	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13821245delT	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																		TCACTGGTCGTTTTTTCTTCT	0.368													4	2	---	---	---	---	
CC2D2A	57545	broad.mit.edu	37	4	15538886	15538886	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15538886delA	uc010idv.2	+						CC2D2A_uc003gnx.2_Intron|CC2D2A_uc003gnz.1_Intron|CC2D2A_uc003goa.1_5'Flank	NM_001080522	NP_001073991	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A isoform						cell projection organization	cilium|microtubule basal body				pancreas(2)|ovary(1)	3						GCATTTGCTTAAAAAGCCACC	0.463													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	20905532	20905532	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20905532delC	uc003gqe.2	-						KCNIP4_uc003gqf.1_Intron|KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_147182	NP_671711	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				TCCTCTGAAGCCCTACTTGCT	0.438													4	2	---	---	---	---	
FAM114A1	92689	broad.mit.edu	37	4	38880181	38880182	+	Intron	INS	-	TGTGT	TGTGT	rs142950595	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38880181_38880182insTGTGT	uc003gtn.2	+						FAM114A1_uc011byh.1_Intron	NM_138389	NP_612398	Q8IWE2	NXP20_HUMAN	hypothetical protein LOC92689							cytoplasm				ovary(1)	1						GTCATCAGAAATGTGTAGTGAG	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49246086	49246087	+	IGR	DEL	AC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49246086_49246087delAC								CWH43 (181993 upstream) : None (None downstream)																							ACAAAAACAAACAAAAAAAAAT	0.252													4	2	---	---	---	---	
AASDH	132949	broad.mit.edu	37	4	57226432	57226433	+	Intron	DEL	CT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57226432_57226433delCT	uc003hbn.2	-						AASDH_uc010ihb.2_Intron|AASDH_uc011caa.1_Intron|AASDH_uc003hbo.2_Intron|AASDH_uc011cab.1_Intron|AASDH_uc010ihc.2_Intron|AASDH_uc003hbp.2_Intron	NM_181806	NP_861522	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase						fatty acid metabolic process		acid-thiol ligase activity|acyl carrier activity|ATP binding|cofactor binding			ovary(4)	4	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TGAGTGCAACCTCAGCCAGGAA	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	78539223	78539223	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78539223delT								CXCL13 (6237 upstream) : CNOT6L (95319 downstream)																							CTATTCATGCTTTCCATCCCC	0.343													4	2	---	---	---	---	
ALPK1	80216	broad.mit.edu	37	4	113362552	113362552	+	3'UTR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113362552delG	uc003iap.3	+	16					ALPK1_uc003ian.3_3'UTR|ALPK1_uc011cfx.1_3'UTR|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_3'UTR	NM_025144	NP_079420	Q96QP1	ALPK1_HUMAN	alpha-kinase 1								ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		cgctgcttctgggcataagtc	0.000													4	2	---	---	---	---	
NDST4	64579	broad.mit.edu	37	4	115896107	115896107	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115896107delG	uc003ibu.2	-						NDST4_uc010imw.2_Intron	NM_022569	NP_072091	Q9H3R1	NDST4_HUMAN	heparan sulfate N-deacetylase/N-sulfotransferase							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		AGATCATTCTGGGAGAGAACA	0.443													4	2	---	---	---	---	
AADAT	51166	broad.mit.edu	37	4	170982318	170982319	+	Intron	INS	-	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170982318_170982319insT	uc003isr.2	-						AADAT_uc003iss.2_Intron|AADAT_uc003ist.2_Intron	NM_016228	NP_057312	Q8N5Z0	AADAT_HUMAN	kynurenine aminotransferase II						2-oxoglutarate metabolic process|biosynthetic process|glutamate metabolic process|lysine catabolic process	mitochondrial matrix	2-aminoadipate transaminase activity|kynurenine-oxoglutarate transaminase activity|protein homodimerization activity				0		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	AGTACATCAGATTTTCAGGATT	0.327													4	2	---	---	---	---	
DCTD	1635	broad.mit.edu	37	4	183825916	183825925	+	Intron	DEL	CTCCACCGGA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183825916_183825925delCTCCACCGGA	uc003ivf.2	-						DCTD_uc003ivg.2_Intron|DCTD_uc010irw.2_Intron|DCTD_uc003ivh.2_Intron	NM_001921	NP_001912	P32321	DCTD_HUMAN	dCMP deaminase isoform b						nucleotide biosynthetic process|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide metabolic process	cytosol	dCMP deaminase activity|zinc ion binding				0		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)		accctgcttcctccaccggaatggtgcaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	191032542	191032542	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:191032542delG								LOC653545 (22366 upstream) : None (None downstream)																							gttagcatgcgccatctgcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1830989	1830989	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1830989delG								NDUFS6 (14826 upstream) : IRX4 (46552 downstream)																							TCTAATATGTGTGGACCTGAC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2009360	2009360	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2009360delT								IRX4 (126480 upstream) : IRX2 (736921 downstream)																							CACAGCCCCCTTGAGAGAGCC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4485452	4485452	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4485452delA								IRX1 (883936 upstream) : LOC340094 (549020 downstream)																							attcgaaagcaaaaaaaaatc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6677286	6677286	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6677286delG								SRD5A1 (7613 upstream) : PAPD7 (37432 downstream)																							caagacatctggcaaatggtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6865713	6865713	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6865713delC								PAPD7 (108552 upstream) : ADCY2 (530630 downstream)																							TGGCCCAGGTCCCAATGCATA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	15201563	15201563	+	IGR	DEL	T	-	-	rs141450656		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15201563delT								ANKH (329676 upstream) : FBXL7 (298742 downstream)																							catactgatcttttttttttt	0.000													5	6	---	---	---	---	
NPR3	4883	broad.mit.edu	37	5	32739295	32739296	+	Intron	INS	-	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32739295_32739296insC	uc003jhv.2	+						NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Intron	NM_000908	NP_000899	P17342	ANPRC_HUMAN	natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)	GTGTGTTTTTTTTTTTTCCTTT	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	39433419	39433422	+	IGR	DEL	TGTT	-	-	rs71606526		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39433419_39433422delTGTT								DAB2 (8084 upstream) : None (None downstream)																							TCTCAGTCTCTGTTGGTGAAAGGA	0.436													4	7	---	---	---	---	
MGC42105	167359	broad.mit.edu	37	5	43273303	43273303	+	Intron	DEL	T	-	-	rs113748798		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43273303delT	uc003jno.2	+							NM_153361	NP_699192	Q8IY84	NIM1_HUMAN	serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9						GCCAGAGTGCttttttttttt	0.279													5	3	---	---	---	---	
SKIV2L2	23517	broad.mit.edu	37	5	54719019	54719020	+	Intron	DEL	CG	-	-	rs142533410	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54719019_54719020delCG	uc003jpy.3	+						SKIV2L2_uc011cqi.1_Intron	NM_015360	NP_056175	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2						maturation of 5.8S rRNA	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)|skin(1)	2		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				attaattgtacgctaactacat	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56334038	56334039	+	IGR	DEL	AG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56334038_56334039delAG								MIER3 (66537 upstream) : GPBP1 (135736 downstream)																							AGTTCGCCACAGAGAGAGagag	0.054													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	60625017	60625018	+	IGR	DEL	GG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60625017_60625018delGG								C5orf43 (166715 upstream) : ZSWIM6 (3082 downstream)																							cacagcagctgggtggaggatg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	72817203	72817204	+	IGR	INS	-	A	A	rs138385025	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72817203_72817204insA								BTF3 (15755 upstream) : ANKRA2 (30959 downstream)																							AAGAGCTGCTCGGCTTCTTTTG	0.525													5	3	---	---	---	---	
COL4A3BP	10087	broad.mit.edu	37	5	74761458	74761458	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74761458delC	uc011csu.1	-						COL4A3BP_uc003kds.2_Intron|COL4A3BP_uc003kdt.2_Intron|COL4A3BP_uc003kdu.2_Intron	NM_005713	NP_005704	Q9Y5P4	C43BP_HUMAN	alpha 3 type IV collagen binding protein isoform						ER to Golgi ceramide transport|immune response	cytosol|endoplasmic reticulum membrane|Golgi apparatus	ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity			skin(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		gtagactaggcaacaaaaacc	0.000													4	2	---	---	---	---	
SV2C	22987	broad.mit.edu	37	5	75484697	75484698	+	Intron	DEL	GG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75484697_75484698delGG	uc003kei.1	+							NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		GTCTGGCCAAGGGAAGACCACA	0.574													4	2	---	---	---	---	
MEF2C	4208	broad.mit.edu	37	5	88202137	88202137	+	5'Flank	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88202137delT	uc003kjm.2	-						MEF2C_uc003kjl.2_5'Flank|uc003kjn.1_Intron	NM_001131005	NP_001124477	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C isoform 2						apoptosis|B cell proliferation|innate immune response|learning or memory|muscle cell differentiation|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|neuron development|positive regulation of muscle cell differentiation|positive regulation of survival gene product expression|positive regulation of transcription from RNA polymerase II promoter|regulation of germinal center formation|regulation of megakaryocyte differentiation|regulation of synaptic 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	nuclear speck	activating transcription factor binding|protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			lung(3)|breast(2)|ovary(1)|large_intestine(1)	7		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		GCATAAATGGTAGAGATTATC	0.338										HNSCC(66;0.2)			4	2	---	---	---	---	
SLC12A2	6558	broad.mit.edu	37	5	127503766	127503767	+	Intron	DEL	AT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127503766_127503767delAT	uc003kus.2	+						SLC12A2_uc010jdf.2_Intron|SLC12A2_uc010jdg.2_Intron|SLC12A2_uc003kut.1_3'UTR	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12						potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	acatacatgcatatatatatat	0.188													4	2	---	---	---	---	
AFF4	27125	broad.mit.edu	37	5	132294724	132294724	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132294724delC	uc003kyd.2	-						AFF4_uc011cxk.1_Intron|AFF4_uc003kye.1_Intron|AFF4_uc003kyf.3_Intron	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31						transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGCTACGTTTCCTTGCCTAAA	0.343													4	2	---	---	---	---	
PHF15	23338	broad.mit.edu	37	5	133867867	133867868	+	Intron	INS	-	C	C	rs146878532	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133867867_133867868insC	uc003kzo.1	+						PHF15_uc011cxt.1_Intron|PHF15_uc003kzk.2_Intron|PHF15_uc003kzl.2_Intron|PHF15_uc003kzm.2_Intron|PHF15_uc003kzn.2_Intron	NM_015288	NP_056103	Q9NQC1	JADE2_HUMAN	PHD finger protein 15						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			gagtcaccgcaccccgactgat	0.000													2	4	---	---	---	---	
FAM53C	51307	broad.mit.edu	37	5	137680102	137680102	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137680102delC	uc003lcv.2	+						FAM53C_uc003lcw.2_Intron|FAM53C_uc011cyq.1_Intron|FAM53C_uc011cyr.1_Intron	NM_001135647	NP_001129119	Q9NYF3	FA53C_HUMAN	hypothetical protein LOC51307											ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GCATCCAGGGCAAGCGTGGGG	0.522													4	2	---	---	---	---	
KDM3B	51780	broad.mit.edu	37	5	137727992	137727993	+	Intron	DEL	GG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137727992_137727993delGG	uc003lcy.1	+						KDM3B_uc010jew.1_Intron|KDM3B_uc011cys.1_Intron	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11						CTCTGGCACTGGGCTCAAATGC	0.470													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	138596154	138596154	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138596154delC								SIL1 (62089 upstream) : SNHG4 (13624 downstream)																							ggtacctcagccagagttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	141930023	141930023	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141930023delG								SPRY4 (225403 upstream) : FGF1 (41721 downstream)																							GCTTCCCAAAGGATGCCCTCT	0.438													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148196323	148196324	+	Intron	DEL	GT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148196323_148196324delGT	uc003lpp.1	-							NM_024577		Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			gtgtgtgtgagtgtgtgtgtgt	0.257													4	2	---	---	---	---	
NDST1	3340	broad.mit.edu	37	5	149919109	149919109	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149919109delT	uc003lsk.3	+						NDST1_uc011dcj.1_Intron|NDST1_uc003lsl.2_3'UTR	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan						heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)|skin(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCGAGCATGCTTTTTTTTTCC	0.204													5	3	---	---	---	---	
STK10	6793	broad.mit.edu	37	5	171475808	171475809	+	Intron	DEL	AG	-	-	rs150132127		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171475808_171475809delAG	uc003mbo.1	-							NM_005990	NP_005981	O94804	STK10_HUMAN	serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			catctcacacagagtaaaagcc	0.000													3	3	---	---	---	---	
SH3PXD2B	285590	broad.mit.edu	37	5	171812986	171812986	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171812986delA	uc003mbr.2	-						SH3PXD2B_uc003mbs.1_Intron	NM_001017995	NP_001017995	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B						adipose tissue development|bone development|cell communication|cell differentiation|eye development|heart development|podosome assembly	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-5-phosphate binding|SH2 domain binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CAGCTCCAGCAAACTCAGTCC	0.507													4	2	---	---	---	---	
HMP19	51617	broad.mit.edu	37	5	173531010	173531010	+	Intron	DEL	C	-	-	rs77400651	byFrequency	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173531010delC	uc003mcx.2	+						HMP19_uc011dfh.1_Intron	NM_015980	NP_057064	Q9Y328	NSG2_HUMAN	HMP19 protein						dopamine receptor signaling pathway	cytoplasmic vesicle membrane|Golgi cisterna membrane|integral to membrane|multivesicular body membrane	dopamine receptor binding			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00925)|all_lung(126;0.0148)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			acaaaaAAAACCAAAACAAAA	0.109													6	3	---	---	---	---	
MXD3	83463	broad.mit.edu	37	5	176737949	176737949	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176737949delG	uc003mgb.2	-						MXD3_uc010jkk.2_Intron|MXD3_uc003mga.3_Intron|MXD3_uc003mgc.2_Intron	NM_031300	NP_112590	Q9BW11	MAD3_HUMAN	MAX dimerization protein 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			cctgccagctggccagaaagg	0.129													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	177621250	177621250	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177621250delT								GMCL1L (6817 upstream) : HNRNPAB (10258 downstream)																							GCTTCTTGCGTTTCCTGTTCA	0.667													4	2	---	---	---	---	
GRM6	2916	broad.mit.edu	37	5	178418302	178418303	+	Intron	INS	-	G	G	rs141591491	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178418302_178418303insG	uc003mjr.2	-						GRM6_uc010jla.1_5'Flank|GRM6_uc003mjs.1_5'Flank	NM_000843	NP_000834	O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6 precursor						detection of visible light|visual perception	integral to plasma membrane				lung(4)|ovary(2)|breast(1)|pancreas(1)	8	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		GCAGGGAAGGTGGGGGGTGCGG	0.649													13	13	---	---	---	---	
PSORS1C1	170679	broad.mit.edu	37	6	31091930	31091930	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31091930delA	uc003nsl.1	+						PSORS1C1_uc010jsj.1_Intron|PSORS1C1_uc003nsn.1_5'Flank	NM_014068	NP_054787	Q9UIG5	PS1C1_HUMAN	SEEK1 protein											ovary(1)	1						AGTAAATGTGAGAGGGTGCAG	0.363													4	2	---	---	---	---	
CAPN11	11131	broad.mit.edu	37	6	44145230	44145230	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44145230delT	uc003owt.1	+						CAPN11_uc011dvn.1_Intron	NM_007058	NP_008989	Q9UMQ6	CAN11_HUMAN	calpain 11						proteolysis	acrosomal vesicle	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)|breast(1)	2	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			tctttctttcttttttttttt	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	89000595	89000595	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89000595delT								CNR1 (124828 upstream) : RNGTT (319394 downstream)																							CACTATACTCTTTTTCAGCAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	99601712	99601712	+	IGR	DEL	A	-	-	rs113158895		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99601712delA								FBXL4 (205863 upstream) : C6orf168 (119082 downstream)																							acaggaaaggaaagaggaatt	0.010													3	3	---	---	---	---	
LAMA4	3910	broad.mit.edu	37	6	112469188	112469191	+	Intron	DEL	ATAG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112469188_112469191delATAG	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TTAGACAGGTATAGATAGATAGAT	0.289													4	2	---	---	---	---	
MAP3K5	4217	broad.mit.edu	37	6	136901834	136901835	+	Intron	DEL	TC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136901834_136901835delTC	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron|MAP3K5_uc011edk.1_Intron	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		TTTTATAATGTCTGCAGAATGG	0.366													4	2	---	---	---	---	
TIAM2	26230	broad.mit.edu	37	6	155520025	155520025	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155520025delG	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron|TIAM2_uc010kjj.2_Intron|TIAM2_uc003qqf.2_Intron|TIAM2_uc011efl.1_Intron|TIAM2_uc003qqg.2_Intron	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		TGGCTGTGGTGGTGGAGAACC	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156781728	156781728	+	IGR	DEL	T	-	-	rs79612600		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156781728delT								MIR1202 (513715 upstream) : ARID1B (317358 downstream)																							CCCACCCCCCTCCACGCCGCC	0.502													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156978736	156978737	+	IGR	DEL	GG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156978736_156978737delGG								MIR1202 (710723 upstream) : ARID1B (120349 downstream)																							TGTCTCTGCTGGGCCCTCCATA	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	163808016	163808016	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163808016delT								LOC285796 (62522 upstream) : QKI (27659 downstream)																							CAGTTCTGCCTTTGTAGGAGT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	2556156	2556157	+	IGR	INS	-	C	C	rs1982157	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2556156_2556157insC								CHST12 (81942 upstream) : LFNG (3322 downstream)																							CCAGCAGGAGAACCCCCGGGCT	0.649													4	3	---	---	---	---	
RAC1	5879	broad.mit.edu	37	7	6439467	6439468	+	Intron	DEL	AA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6439467_6439468delAA	uc003spx.2	+						RAC1_uc003spw.2_Intron	NM_006908	NP_008839	P63000	RAC1_HUMAN	ras-related C3 botulinum toxin substrate 1						actin filament polymerization|apoptosis|axon guidance|cell motility|cell-matrix adhesion|induction of apoptosis by extracellular signals|inflammatory response|lamellipodium assembly|localization within membrane|negative regulation of interleukin-23 production|negative regulation of receptor-mediated endocytosis|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of lamellipodium assembly|positive regulation of Rho protein signal transduction|regulation of cell migration|regulation of defense response to virus by virus|regulation of hydrogen peroxide metabolic process|regulation of respiratory burst|ruffle organization|small GTPase mediated signal transduction|T cell costimulation|viral reproduction	cytosol|melanosome|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity|thioesterase binding			lung(2)	2		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.104)	Pravastatin(DB00175)|Simvastatin(DB00641)	AGTTAGGCGTAAAGGAAGCCTC	0.401													4	2	---	---	---	---	
HDAC9	9734	broad.mit.edu	37	7	18127524	18127525	+	Intron	DEL	CA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18127524_18127525delCA	uc011jya.1	+							NM_014707	NP_055522	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 3						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)	GTGCTGGTGTCAGGCCTGTGTG	0.609													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	20858115	20858115	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20858115delC								SP8 (31607 upstream) : RPL23P8 (8802 downstream)																							cctcaaaaaacccatactctt	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	30266771	30266771	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30266771delT								C7orf41 (64390 upstream) : ZNRF2 (57152 downstream)																							TCGCTCACTGTTTTTTTTTGT	0.443													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	33682582	33682583	+	IGR	INS	-	T	T	rs145793118	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33682582_33682583insT								BBS9 (36902 upstream) : BMPER (262529 downstream)																							atacttttgactttttttTTCA	0.005													4	2	---	---	---	---	
NPSR1	387129	broad.mit.edu	37	7	34786840	34786840	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34786840delG	uc003teg.1	+						AAA1_uc010kwo.1_Intron|AAA1_uc010kwp.1_Intron|AAA1_uc003tdz.2_Intron|AAA1_uc010kwq.1_Intron|AAA1_uc003teb.1_Intron|AAA1_uc011kaq.1_Intron|NPSR1_uc003teh.1_Intron|NPSR1_uc010kwt.1_Intron|NPSR1_uc010kwu.1_Intron|NPSR1_uc010kwv.1_Intron|NPSR1_uc003tei.1_Intron|NPSR1_uc010kww.1_Intron|NPSR1_uc011kar.1_Intron|AAA1_uc010kwy.2_Intron|AAA1_uc003tek.3_Intron|AAA1_uc010kwx.1_Intron	NM_207172	NP_997055	Q6W5P4	NPSR1_HUMAN	G protein-coupled receptor for asthma							cytoplasm|integral to membrane|plasma membrane	vasopressin receptor activity			skin(3)|pancreas(1)	4					Halothane(DB01159)	GCTGCAGGTTGGAGAACATCA	0.453													4	2	---	---	---	---	
POU6F2	11281	broad.mit.edu	37	7	39415224	39415224	+	Intron	DEL	T	-	-	rs72463292		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39415224delT	uc003thb.1	+							NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1						TCCTCCTTGATTTTTTTTTTT	0.458													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	39876766	39876766	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39876766delT								LOC349114 (42545 upstream) : CDK13 (113193 downstream)																							TGAACATTTATTTTTTTTGCC	0.095													4	2	---	---	---	---	
DDX56	54606	broad.mit.edu	37	7	44607131	44607131	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44607131delC	uc003tlg.2	-						DDX56_uc003tle.2_Intron|DDX56_uc003tlf.2_Intron|DDX56_uc003tlh.2_Intron|DDX56_uc010kyg.2_Intron	NM_019082	NP_061955	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 56						rRNA processing	nucleolus	ATP binding|ATP-dependent RNA helicase activity|identical protein binding|RNA binding			upper_aerodigestive_tract(1)	1						GTATTAATGGCCACATAAAGC	0.517													4	2	---	---	---	---	
DDC	1644	broad.mit.edu	37	7	50599276	50599276	+	Intron	DEL	G	-	-	rs10718396		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50599276delG	uc003tpf.3	-						DDC_uc010kza.2_Intron|DDC_uc003tpg.3_Intron	NM_000790	NP_000781	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid						cellular amino acid metabolic process|hormone biosynthetic process|neurotransmitter secretion	cytosol	aromatic-L-amino-acid decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(2)	2	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Flupenthixol(DB00875)|L-Tryptophan(DB00150)|Levodopa(DB01235)|Pimozide(DB01100)|Pyridoxal Phosphate(DB00114)|Remoxipride(DB00409)	GCTTTTCTCTGGGGGGGGATG	0.348													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54732574	54732574	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54732574delT								VSTM2A (94387 upstream) : SEC61G (87367 downstream)																							catatccaggttaggtcacgg	0.080													4	2	---	---	---	---	
PSPH	5723	broad.mit.edu	37	7	56085251	56085251	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56085251delT	uc003trg.2	-						PSPH_uc003trh.2_Intron|PSPH_uc003tri.2_Intron|PSPH_uc003trj.2_Intron	NM_004577	NP_004568	P78330	SERB_HUMAN	phosphoserine phosphatase						L-serine biosynthetic process	cytoplasm	calcium ion binding|magnesium ion binding|phosphoserine phosphatase activity|protein homodimerization activity			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			tttctttttcttttttttttg	0.154													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56635395	56635396	+	IGR	INS	-	C	C	rs113595102		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56635395_56635396insC								DKFZp434L192 (70418 upstream) : ZNF479 (551932 downstream)																							ACAAACAAACAAAacacacaca	0.272													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	69021587	69021587	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69021587delC								None (None upstream) : AUTS2 (42318 downstream)																							ACATAACAAGCCCCCACTTAC	0.363													4	2	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	70131638	70131639	+	Intron	INS	-	T	T	rs149897558	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70131638_70131639insT	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		TTCCCACCACATTTTTTTTTAT	0.446													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	71942310	71942311	+	IGR	DEL	GG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71942310_71942311delGG								CALN1 (30174 upstream) : TYW1B (81418 downstream)																							TTGAAGGTGAGGGACAGAGAGA	0.455													4	2	---	---	---	---	
WBSCR22	114049	broad.mit.edu	37	7	73111776	73111776	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73111776delA	uc003tyt.2	+						WBSCR22_uc003tyu.2_Intron|WBSCR22_uc003tyv.2_Intron|WBSCR22_uc003tyw.1_Intron	NM_017528	NP_059998	O43709	WBS22_HUMAN	Williams Beuren syndrome chromosome region 22							nucleus	methyltransferase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)				GGGTGTCCAGAGCGGGGAATT	0.582													9	7	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73663895	73663895	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73663895delA	uc003uaj.2	-						RFC2_uc011kfa.1_Intron|RFC2_uc003uak.2_Intron|RFC2_uc010lbp.2_Intron|RFC2_uc003ual.2_Intron	NM_181471	NP_852136	P35250	RFC2_HUMAN	replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2						ataaataaataaaaaaAAATA	0.279													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	77080648	77080658	+	IGR	DEL	TTCCATCATAG	-	-	rs67486350		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77080648_77080658delTTCCATCATAG								PION (34931 upstream) : PTPN12 (86115 downstream)																							CAGCCATTCCTTCCATCATAGTTCCATCATA	0.327													7	4	---	---	---	---	
PTPN12	5782	broad.mit.edu	37	7	77266620	77266620	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77266620delA	uc003ugh.2	+						PTPN12_uc011kgp.1_Intron|PTPN12_uc011kgq.1_Intron|PTPN12_uc010lds.2_Intron	NM_002835	NP_002826	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type							soluble fraction	non-membrane spanning protein tyrosine phosphatase activity|SH3 domain binding			ovary(1)|breast(1)|pancreas(1)	3						GAGATTTTTTAAAAATATTTT	0.284													4	2	---	---	---	---	
MYH16	84176	broad.mit.edu	37	7	98881188	98881188	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98881188delA	uc003upw.2	+	5	631	c.589delA	c.(589-591)AAAfs	p.K197fs		NR_002147				SubName: Full=cDNA: FLJ22037 fis, clone HEP08868; Flags: Fragment;												0						GTCCTTCCAGAAAACCCTGGA	0.547													4	2	---	---	---	---	
SLC12A9	56996	broad.mit.edu	37	7	100448897	100448897	+	5'Flank	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100448897delG	uc003uwp.2	+						SLC12A9_uc003uwo.1_5'Flank|SLC12A9_uc003uwq.2_5'Flank|SLC12A9_uc011kki.1_5'Flank	NM_020246	NP_064631	Q9BXP2	S12A9_HUMAN	solute carrier family 12 (potassium/chloride							integral to membrane|plasma membrane	cation:chloride symporter activity				0	Lung NSC(181;0.041)|all_lung(186;0.0581)					ctgaagaggaggggctgcagt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	102020719	102020719	+	Intron	DEL	A	-	-	rs77963773		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102020719delA	uc003uzd.1	+						uc003uze.1_Intron|PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_Intron	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																		actctgtctcaaaaaaaaaaa	0.164													13	7	---	---	---	---	
ANKRD7	56311	broad.mit.edu	37	7	117875903	117875903	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117875903delT	uc003vji.2	+							NM_019644	NP_062618	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7						male gonad development						0						GGAACTTAAATTTTTTTGTCT	0.303													4	2	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151319421	151319421	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151319421delA	uc003wkk.2	-						PRKAG2_uc003wki.2_Intron|PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.2_Intron|PRKAG2_uc010lqe.1_Intron	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		TTTGCAATATAATGGATCTTT	0.413													4	2	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151548427	151548427	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151548427delA	uc003wkk.2	-						PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		GGCCTCTGGCaaaaaaaaaaa	0.488													6	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157962789	157962790	+	Intron	DEL	CC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157962789_157962790delCC	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		AACTATTCTTCCCTTAagaaag	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	6826000	6826001	+	IGR	DEL	CA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6826000_6826001delCA								DEFA4 (30214 upstream) : DEFA1B (9170 downstream)																							TCTGCCCCATCACACACACACC	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	30190628	30190629	+	IGR	DEL	AC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30190628_30190629delAC								DCTN6 (149569 upstream) : RBPMS (51315 downstream)																							GGAAGGAAAGACATTAGAGGTG	0.322													0	6	---	---	---	---	
HOOK3	84376	broad.mit.edu	37	8	42798750	42798750	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42798750delC	uc003xpr.2	+						HOOK3_uc010lxq.1_Intron	NM_032410	NP_115786	Q86VS8	HOOK3_HUMAN	golgi-associated microtubule-binding protein						cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			TGTTTTTAAGCTTAAATGAAT	0.299			T	RET	papillary thyroid								4	2	---	---	---	---	
SNTG1	54212	broad.mit.edu	37	8	51314601	51314601	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51314601delT	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				ATCATTCTCCTTTTTTTCCCT	0.378													4	2	---	---	---	---	
COPS5	10987	broad.mit.edu	37	8	67967660	67967660	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67967660delG	uc003xxe.2	-						COPS5_uc003xxd.2_Intron|COPS5_uc003xxf.2_Intron|COPS5_uc010lyu.1_Intron|COPS5_uc010lyv.1_Intron	NM_006837	NP_006828	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5						cullin deneddylation|transcription from RNA polymerase II promoter	eukaryotic translation initiation factor 3 complex|signalosome	metal ion binding|metallopeptidase activity|protein binding|transcription coactivator activity|translation initiation factor activity			ovary(1)|skin(1)	2	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)			gtgcttgattggggctccaga	0.050													4	2	---	---	---	---	
ARFGEF1	10565	broad.mit.edu	37	8	68109222	68109223	+	Intron	DEL	AG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68109222_68109223delAG	uc003xxl.1	-							NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			CAACCATGTTAGATGATATTGA	0.371													4	2	---	---	---	---	
ARFGEF1	10565	broad.mit.edu	37	8	68184315	68184315	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68184315delA	uc003xxo.1	-							NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TCTATAACATAAAAAAAGTAC	0.279													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	97231372	97231372	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97231372delT								GDF6 (58352 upstream) : UQCRB (7938 downstream)																							AAGGAATCTATTTTTTTTTTG	0.075													9	4	---	---	---	---	
MATN2	4147	broad.mit.edu	37	8	99045070	99045071	+	Intron	DEL	TG	-	-	rs2444897	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99045070_99045071delTG	uc003yic.2	+						MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron|MATN2_uc010mbi.1_Intron|MATN2_uc010mbj.1_Intron|RPL30_uc010mbk.1_Intron	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			gtttttgttttgttttttgttg	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102035968	102035969	+	IGR	INS	-	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102035968_102035969insA								YWHAZ (70345 upstream) : ZNF706 (173299 downstream)																							tgttccatattaaaaaaaaagt	0.069													4	2	---	---	---	---	
TMEM74	157753	broad.mit.edu	37	8	109739741	109739742	+	Intron	INS	-	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109739741_109739742insT	uc003ymx.2	-									Q96NL1	TMM74_HUMAN	Homo sapiens cDNA FLJ30668 fis, clone FCBBF1000675.						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(57;3.08e-10)			gaaaagatagatttgccatcaa	0.000													4	2	---	---	---	---	
ZHX2	22882	broad.mit.edu	37	8	123815792	123815792	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123815792delC	uc003ypk.1	+							NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2							cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			caactccatgccagcagcacc	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	132654027	132654027	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132654027delA								ADCY8 (601192 upstream) : EFR3A (262332 downstream)																							TGCTGTTATTATTAATATCAC	0.119													4	2	---	---	---	---	
LYNX1	66004	broad.mit.edu	37	8	143852785	143852785	+	3'UTR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143852785delC	uc003yxc.1	-	4					LYNX1_uc003yxa.2_5'Flank|LYNX1_uc003yxb.2_Intron|LYNX1_uc003yxd.1_3'UTR|LYNX1_uc003yxe.1_3'UTR	NM_177476	NP_803429	Q9BZG9	LYNX1_HUMAN	Ly-6 neurotoxin-like protein 1 isoform c							anchored to membrane|plasma membrane					0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GGCACTTATGCCCACGACCAG	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	31434007	31434007	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31434007delA								None (None upstream) : ACO1 (950594 downstream)																							cttgtactataacacgaataa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	38088315	38088315	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38088315delG								SHB (19105 upstream) : ALDH1B1 (304387 downstream)																							CAGCGTGCCTGGACCAAGGTT	0.493											OREG0019199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68420735	68420735	+	IGR	DEL	A	-	-	rs150487532		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68420735delA								FAM27B (626546 upstream) : MIR1299 (581504 downstream)																							CAGGTGTTGCAGAAACTGGGC	0.363													3	3	---	---	---	---	
GDA	9615	broad.mit.edu	37	9	74859655	74859655	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74859655delA	uc004aiq.2	+						GDA_uc011lse.1_Intron|GDA_uc011lsf.1_Intron|GDA_uc004air.2_Intron|GDA_uc010mow.1_Intron|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)		CAGAAAGAACAAAAAAAAGCA	0.318													4	2	---	---	---	---	
HNRNPK	3190	broad.mit.edu	37	9	86584095	86584096	+	3'UTR	INS	-	C	C			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86584095_86584096insC	uc004ang.3	-	17					HNRNPK_uc011lsw.1_3'UTR|HNRNPK_uc004and.3_3'UTR|HNRNPK_uc004ank.3_3'UTR|HNRNPK_uc004anf.3_3'UTR|HNRNPK_uc004anh.3_3'UTR|HNRNPK_uc011lsx.1_3'UTR|HNRNPK_uc004ani.3_3'UTR|HNRNPK_uc004anj.3_3'UTR|HNRNPK_uc004ann.3_3'UTR|HNRNPK_uc004anl.3_3'UTR|HNRNPK_uc004anm.3_3'UTR	NM_031262	NP_112552	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K						interspecies interaction between organisms|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of receptor-mediated endocytosis|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of low-density lipoprotein particle clearance|signal transduction	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nuclear chromatin|nucleoplasm	protein binding|RNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|single-stranded DNA binding			skin(1)	1						TGCACGCCCTTCCCCCCCCCAA	0.401													4	2	---	---	---	---	
NAA35	60560	broad.mit.edu	37	9	88568998	88568998	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88568998delT	uc004aoi.3	+						NAA35_uc004aoj.3_Intron|NAA35_uc004aok.1_Intron	NM_024635	NP_078911	Q5VZE5	NAA35_HUMAN	corneal wound healing-related protein						smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3						ctgtttaaaatttttttttgt	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91428649	91428649	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91428649delG								LOC286238 (161574 upstream) : C9orf47 (177129 downstream)																							CAGGTCCTCAGAGAGCAAAAC	0.498													4	2	---	---	---	---	
SUSD3	203328	broad.mit.edu	37	9	95835527	95835527	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95835527delT	uc004atb.2	+						SUSD3_uc004atc.2_Intron	NM_145006	NP_659443	Q96L08	SUSD3_HUMAN	sushi domain containing 3							integral to membrane				breast(2)|skin(2)|ovary(1)|lung(1)	6						GTCCCTGttcttttttttttt	0.303													9	4	---	---	---	---	
C9orf89	84270	broad.mit.edu	37	9	95871595	95871596	+	Intron	DEL	CA	-	-	rs144966072		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95871595_95871596delCA	uc004atd.2	+						C9orf89_uc004ate.2_Intron|C9orf89_uc004atf.2_Intron	NM_032310	NP_115686	Q96LW7	BINCA_HUMAN	chromosome 9 open reading frame 89						negative regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|nucleus	CARD domain binding				0						GGTTTAACTCCAGTTCCCTGTG	0.535											OREG0019319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	4	---	---	---	---	
HIATL1	84641	broad.mit.edu	37	9	97220946	97220947	+	Intron	INS	-	A	A	rs141945511	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97220946_97220947insA	uc004aur.2	+						HIATL1_uc011luh.1_Intron	NM_032558	NP_115947	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1						transmembrane transport	integral to membrane|plasma membrane	protein binding|transporter activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)				AGATATGTCTTAACTTTGTTCA	0.337													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110196933	110196933	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110196933delT								RAD23B (102464 upstream) : KLF4 (50202 downstream)																							TGACATATGATTTTTTTTTTT	0.269													3	5	---	---	---	---	
RGS3	5998	broad.mit.edu	37	9	116267987	116267987	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116267987delT	uc004bhq.2	+						RGS3_uc004bhr.2_Intron|RGS3_uc004bhs.2_Intron|RGS3_uc004bht.2_Intron|RGS3_uc010muy.2_Intron|RGS3_uc004bhu.2_Intron	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3						ATATGCCCACTTTTTTTTTGT	0.318													4	2	---	---	---	---	
DENND1A	57706	broad.mit.edu	37	9	126213261	126213261	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126213261delT	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						ATGGCACAGATTTTTTTTTTC	0.368													6	3	---	---	---	---	
DENND1A	57706	broad.mit.edu	37	9	126414604	126414604	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126414604delG	uc004bnz.1	-						DENND1A_uc011lzl.1_5'Flank|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						TACAGAGGAAGGAGCCTGAGC	0.388													4	2	---	---	---	---	
ODF2	4957	broad.mit.edu	37	9	131220041	131220041	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131220041delG	uc011mbd.1	+						ODF2_uc011maz.1_Intron|ODF2_uc011mba.1_Intron|ODF2_uc010myb.2_Intron|ODF2_uc011mbb.1_Intron|ODF2_uc011mbc.1_Intron|ODF2_uc004bva.2_Intron|ODF2_uc004bvb.2_Intron|ODF2_uc011mbe.1_Intron|ODF2_uc004bvc.2_Intron|ODF2_uc010myc.2_Intron|ODF2_uc011mbf.1_Intron|ODF2_uc004bvd.3_Intron|ODF2_uc004bve.2_Intron	NM_002540	NP_002531	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2 isoform 1						cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centriole|cilium|cytosol|microtubule|spindle pole	protein binding|structural molecule activity			ovary(1)	1						CGTAGGAGGTGGATGTGGCAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137496491	137496492	+	IGR	DEL	TC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137496491_137496492delTC								RXRA (164060 upstream) : COL5A1 (37160 downstream)																							TCAAATCCAATCTCTCTCTCTC	0.480													4	2	---	---	---	---	
WDR85	92715	broad.mit.edu	37	9	140468517	140468517	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140468517delA	uc004cnk.1	-						WDR85_uc004cnl.1_Intron|WDR85_uc004cnm.1_Intron|WDR85_uc004cnn.1_Intron	NM_138778	NP_620133	Q9BTV6	WDR85_HUMAN	WD repeat domain 85						peptidyl-diphthamide biosynthetic process from peptidyl-histidine						0	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.00029)|Epithelial(140;0.000509)		actcagtttcaaaaaaaaaaG	0.239													4	4	---	---	---	---	
CACNA1B	774	broad.mit.edu	37	9	140968697	140968697	+	Intron	DEL	T	-	-	rs78547363		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140968697delT	uc004cog.2	+						CACNA1B_uc004coi.2_Intron|CACNA1B_uc004cok.1_5'Flank|CACNA1B_uc010ncp.1_5'Flank	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,						membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)	tttcttactcttttttttttt	0.020													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2875131	2875131	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2875131delA								None (None upstream) : PFKP (234621 downstream)																							gctcagatccaaaccttggag	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	27949376	27949376	+	IGR	DEL	A	-	-	rs10714662		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27949376delA								RAB18 (120279 upstream) : MKX (12428 downstream)																							gtctctaaagaaaaaaaaaaa	0.249													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31996717	31996717	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31996717delT								ZEB1 (178590 upstream) : ARHGAP12 (98508 downstream)																							CCTGAGTTTCTTTTTTTTTTC	0.443													3	3	---	---	---	---	
ARHGAP12	94134	broad.mit.edu	37	10	32185908	32185909	+	Intron	INS	-	T	T	rs144036334	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32185908_32185909insT	uc001ivz.1	-						ARHGAP12_uc001ivy.1_Intron|ARHGAP12_uc009xls.2_Intron|ARHGAP12_uc001iwb.1_Intron|ARHGAP12_uc001iwc.1_Intron|ARHGAP12_uc009xlq.1_Intron|ARHGAP12_uc001iwd.1_Intron|ARHGAP12_uc009xlr.1_Intron	NM_018287	NP_060757	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)				gaacatttaaaggtcatttcaa	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	36498557	36498558	+	IGR	DEL	TG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36498557_36498558delTG								FZD8 (568195 upstream) : ANKRD30A (916227 downstream)																							AGACCAGATATGTGTGTGTGTG	0.455													4	2	---	---	---	---	
SLC29A3	55315	broad.mit.edu	37	10	73109464	73109464	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73109464delC	uc001jrr.3	+						SLC29A3_uc001jrs.3_Intron|SLC29A3_uc010qjq.1_Intron|SLC29A3_uc001jrt.3_Intron|SLC29A3_uc001jru.3_Intron	NM_018344	NP_060814	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (nucleoside						nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|late endosome membrane|lysosomal membrane	nucleoside transmembrane transporter activity				0						CCACGCCTCTCCCCAGCATCA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	77258340	77258341	+	IGR	INS	-	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77258340_77258341insG								C10orf41 (89601 upstream) : MIR606 (53875 downstream)																							atcagagacttggggaaactgg	0.129													4	2	---	---	---	---	
LIPK	643414	broad.mit.edu	37	10	90491172	90491173	+	Intron	DEL	GT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90491172_90491173delGT	uc010qmv.1	+							NM_001080518	NP_001073987	Q5VXJ0	LIPK_HUMAN	lipase, family member K precursor						lipid catabolic process	extracellular region	hydrolase activity			ovary(2)	2		Colorectal(252;0.0381)		Colorectal(12;7.03e-05)|COAD - Colon adenocarcinoma(12;8.33e-05)		gtgtgagtgagtgtgtgtgtgt	0.401													4	2	---	---	---	---	
HECTD2	143279	broad.mit.edu	37	10	93252438	93252438	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93252438delG	uc001khl.2	+						LOC100188947_uc010qnl.1_Intron|HECTD2_uc010qnm.1_Intron|HECTD2_uc001khm.2_Intron|HECTD2_uc009xty.1_Intron|HECTD2_uc001khn.1_Intron	NM_182765	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing 2 isoform a						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			skin(1)	1						TTCTCTTACTGGGAATCCTAC	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113897981	113897981	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113897981delG								None (None upstream) : GPAM (11641 downstream)																							GTGCTCCCAAGACAGCAGGTG	0.577											OREG0020537	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
TCF7L2	6934	broad.mit.edu	37	10	114710870	114710870	+	Intron	DEL	C	-	-	rs72101402		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114710870delC	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_5'Flank|TCF7L2_uc010qrs.1_5'Flank|TCF7L2_uc010qrt.1_5'Flank	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		TTTTTTTCTACCCCCCCCTCG	0.502													3	3	---	---	---	---	
NRAP	4892	broad.mit.edu	37	10	115396142	115396144	+	Intron	DEL	CTG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115396142_115396144delCTG	uc001laj.2	-						NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Intron	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TTCCTCCTATCTGCTGCTAACTC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	116189815	116189815	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116189815delT								AFAP1L2 (25300 upstream) : ABLIM1 (1055 downstream)																							AAGAAATACCTTTGATAAAGC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	118908222	118908225	+	IGR	DEL	TTTG	-	-	rs72405745		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118908222_118908225delTTTG								VAX1 (10410 upstream) : KCNK18 (48775 downstream)																							AAGGtgtttttttgtttgtttgtt	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	120630075	120630076	+	IGR	DEL	GG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120630075_120630076delGG								C10orf46 (115317 upstream) : NANOS1 (159152 downstream)																							TGAGCTCCCAGGAAATAGTAAT	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	121749505	121749505	+	IGR	DEL	G	-	-	rs76411657		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121749505delG								SEC23IP (48260 upstream) : PPAPDC1A (466961 downstream)																							CTGTGGGGATGGGGGGGTGGT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125993922	125993922	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125993922delG								CHST15 (140716 upstream) : OAT (91950 downstream)																							cagatcacatgggtagttaag	0.000													4	2	---	---	---	---	
EBF3	253738	broad.mit.edu	37	10	131687144	131687144	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131687144delA	uc001lki.1	-							NM_001005463	NP_001005463	Q9H4W6	COE3_HUMAN	early B-cell factor 3						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		CTGCAATTACAAAAAAAAAGG	0.413											OREG0020630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	4994909	4994909	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4994909delG								OR51A2 (17966 upstream) : MMP26 (14515 downstream)																							GTCAGAGAGAGCCAACATGGA	0.438													4	2	---	---	---	---	
GALNTL4	374378	broad.mit.edu	37	11	11410784	11410784	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11410784delT	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		gacttggctcttttcCAGTCT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15928585	15928586	+	IGR	DEL	CA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15928585_15928586delCA								INSC (659833 upstream) : SOX6 (59410 downstream)																							acacacacaccacacacacacc	0.059													4	2	---	---	---	---	
PLEKHA7	144100	broad.mit.edu	37	11	16883586	16883586	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16883586delC	uc001mmo.2	-						PLEKHA7_uc010rcu.1_Intron	NM_175058	NP_778228	Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3						CACAGACAGACCGCCAACGCT	0.493													4	2	---	---	---	---	
NAV2	89797	broad.mit.edu	37	11	20058424	20058424	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20058424delG	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron|NAV2_uc001mpt.2_Intron|NAV2_uc009yhx.2_Intron|NAV2_uc009yhy.1_Intron	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						ccaaggcactggagttttcca	0.174													4	2	---	---	---	---	
TNKS1BP1	85456	broad.mit.edu	37	11	57078042	57078042	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57078042delA	uc001njr.2	-						TNKS1BP1_uc001njs.2_Intron|TNKS1BP1_uc009ymd.1_Intron	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1						nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				TGGGAATAAGAAAAAAAAACA	0.383													6	3	---	---	---	---	
ZP1	22917	broad.mit.edu	37	11	60640377	60640377	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60640377delC	uc001nqd.2	+						ZP1_uc001nqe.2_Intron	NM_207341	NP_997224	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 precursor						single fertilization	integral to membrane|plasma membrane|proteinaceous extracellular matrix					0						CTCTATCCTGCTGTATTCTCC	0.637													4	2	---	---	---	---	
NXF1	10482	broad.mit.edu	37	11	62565741	62565743	+	Intron	DEL	AAT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62565741_62565743delAAT	uc001nvf.1	-						NXF1_uc001nvg.1_Intron|NXF1_uc009yog.1_Intron	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1 isoform 1						gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(3)	3						ctctactaaaaatacaaaaatta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	68935489	68935490	+	IGR	DEL	TG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68935489_68935490delTG								TPCN2 (5582 upstream) : MYEOV (126132 downstream)																							GATCCAGCGATGTGTGTGTGTG	0.579													4	2	---	---	---	---	
ANO1	55107	broad.mit.edu	37	11	69952922	69952922	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69952922delG	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_5'Flank	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						CATTCAATCTGTCCTGGCATT	0.542													4	2	---	---	---	---	
GDPD5	81544	broad.mit.edu	37	11	75186552	75186552	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75186552delC	uc001owo.3	-						GDPD5_uc001owp.3_Intron|GDPD5_uc009yuc.2_Intron|GDPD5_uc009yud.2_Intron	NM_030792	NP_110419	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1						GAGAGTCCAGCCCCACCGCTG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	82209939	82209940	+	IGR	INS	-	T	T	rs143437184	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82209939_82209940insT								None (None upstream) : FAM181B (233113 downstream)																							GTGTTGGATGCTTTTTTTTTAA	0.391													0	6	---	---	---	---	
FAT3	120114	broad.mit.edu	37	11	92616884	92616885	+	Intron	INS	-	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92616884_92616885insA	uc001pdj.3	+						FAT3_uc001pdi.3_Intron	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGTCAAAGTGCAAAAGAAAAGA	0.233										TCGA Ovarian(4;0.039)			4	2	---	---	---	---	
FAM76B	143684	broad.mit.edu	37	11	95521938	95521938	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95521938delG	uc001pfn.2	-						CEP57_uc001pfo.1_5'Flank|CEP57_uc010ruh.1_5'Flank|CEP57_uc010rui.1_5'Flank|CEP57_uc009ywn.1_5'Flank|CEP57_uc001pfp.1_5'Flank|CEP57_uc001pfq.1_5'Flank|CEP57_uc001pfr.1_5'Flank|FAM76B_uc001pfm.2_Intron	NM_144664	NP_653265	Q5HYJ3	FA76B_HUMAN	hypothetical protein LOC143684												0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TAGTAGACGTGGGGGTATATT	0.403													4	2	---	---	---	---	
ATM	472	broad.mit.edu	37	11	108206006	108206006	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108206006delT	uc001pkb.1	+						ATM_uc009yxr.1_Intron|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_RNA|ATM_uc001pke.1_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		CTTTTCTCCATTTTTTTTGTG	0.303			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			4	2	---	---	---	---	
ZC3H12C	85463	broad.mit.edu	37	11	110036661	110036661	+	3'UTR	DEL	T	-	-	rs35138658		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110036661delT	uc009yxw.2	+	6					ZC3H12C_uc010rwc.1_3'UTR|ZC3H12C_uc010rwd.1_3'UTR|ZC3H12C_uc001pkr.3_3'UTR	NM_033390	NP_203748	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C								endonuclease activity|nucleic acid binding|zinc ion binding				0		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		ACATTTAAACTTTTTTTTTTT	0.303													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	111337261	111337261	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111337261delT								POU2AF1 (87104 upstream) : BTG4 (997 downstream)																							CTGAAAATCATTTTTTCCATA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116529602	116529603	+	IGR	INS	-	G	G	rs139852443	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116529602_116529603insG								None (None upstream) : BUD13 (89285 downstream)																							CAAGGACCACAGTCGCCAGAAA	0.490													9	4	---	---	---	---	
PRDM10	56980	broad.mit.edu	37	11	129780674	129780674	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129780674delT	uc001qfm.2	-						PRDM10_uc001qfj.2_Intron|PRDM10_uc001qfk.2_Intron|PRDM10_uc001qfl.2_Intron|PRDM10_uc010sbx.1_Intron|PRDM10_uc001qfn.2_Intron	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		ATCGTTGCTAttttttttttc	0.174													6	3	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	5845931	5845932	+	Intron	DEL	GA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5845931_5845932delGA	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						ACTGCATACTGAGCCCTGTCCC	0.525													4	2	---	---	---	---	
LOC642846	642846	broad.mit.edu	37	12	9465398	9465399	+	Intron	INS	-	GT	GT			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9465398_9465399insGT	uc010sgp.1	+							NR_024374				Homo sapiens cDNA FLJ60280 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX11 (EC 3.6.1.-).												0						GAGGAAGGGGAGGGGGTCGCCA	0.599													9	5	---	---	---	---	
DUSP16	80824	broad.mit.edu	37	12	12636596	12636597	+	Intron	DEL	GA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12636596_12636597delGA	uc001rao.1	-						DUSP16_uc001ran.1_Intron	NM_030640	NP_085143	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16						inactivation of MAPK activity|MAPK export from nucleus|MAPK phosphatase export from nucleus, leptomycin B sensitive	cytoplasmic membrane-bounded vesicle|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		AAGAGCCCAGGAGACAGTGAAG	0.406													4	2	---	---	---	---	
DDX23	9416	broad.mit.edu	37	12	49227553	49227553	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49227553delT	uc001rsm.2	-							NM_004818	NP_004809	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent RNA helicase activity|nucleic acid binding|protein binding			kidney(3)|ovary(1)|lung(1)|skin(1)	6						CAGTAGAAACTTTTTTTTTTT	0.388													4	2	---	---	---	---	
RACGAP1	29127	broad.mit.edu	37	12	50395167	50395168	+	Intron	DEL	TC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50395167_50395168delTC	uc001rvt.2	-						RACGAP1_uc009zlm.1_Intron|RACGAP1_uc001rvs.2_Intron|RACGAP1_uc001rvu.2_Intron	NM_013277	NP_037409	Q9H0H5	RGAP1_HUMAN	Rac GTPase activating protein 1						blood coagulation|cytokinesis, actomyosin contractile ring assembly|cytokinesis, initiation of separation|embryo development|microtubule-based movement|neuroblast proliferation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|spermatogenesis|sulfate transport	acrosomal vesicle|cytosol|microtubule|midbody|nucleus|spindle	alpha-tubulin binding|beta-tubulin binding|gamma-tubulin binding|GTPase activator activity|metal ion binding			kidney(1)	1						AACAATGTGTTCTCTCTCTCTC	0.376													6	3	---	---	---	---	
KRT86	3892	broad.mit.edu	37	12	52690919	52690919	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52690919delC	uc010snq.1	+						KRT86_uc009zmg.2_Intron|KRT81_uc001sac.2_Intron	NM_002284	NP_002275	O43790	KRT86_HUMAN	keratin 86						cytoskeleton organization	keratin filament	structural molecule activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(357;0.189)		CACTGTCCTGCCCGCCTTTTG	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55223615	55223615	+	IGR	DEL	A	-	-	rs137923525		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55223615delA								DCD (181466 upstream) : MUCL1 (24684 downstream)																							caagtgccataaatattttct	0.139													0	6	---	---	---	---	
ZC3H10	84872	broad.mit.edu	37	12	56510338	56510338	+	5'Flank	DEL	G	-	-	rs34778558		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56510338delG	uc001sjp.1	+						RPL41_uc001sjn.2_5'Flank|RPL41_uc001sjo.2_5'Flank	NM_032786	NP_116175	Q96K80	ZC3HA_HUMAN	zinc finger CCCH-type containing 10								nucleic acid binding|zinc ion binding				0			OV - Ovarian serous cystadenocarcinoma(18;0.12)			CCCCGCCCTTGGGGGGGGCAA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	57981894	57981894	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57981894delC								KIF5A (3340 upstream) : PIP4K2C (3048 downstream)																							aaactcaactccccttggctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68811504	68811504	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68811504delC								MDM1 (85343 upstream) : RAP1B (193148 downstream)																							aactcaaatgcccaccagaat	0.199													4	2	---	---	---	---	
LGR5	8549	broad.mit.edu	37	12	71906537	71906537	+	Intron	DEL	G	-	-	rs35894607		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71906537delG	uc001swl.2	+						LGR5_uc001swm.2_Intron|LGR5_uc001swn.1_Intron	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9						gggaagaactgattttggagg	0.199													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80690470	80690471	+	IGR	DEL	AC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80690470_80690471delAC								PPP1R12A (361235 upstream) : PTPRQ (147655 downstream)																							GTTAAAAATGACTTTTTATTTT	0.213													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80706601	80706601	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80706601delT								PPP1R12A (377366 upstream) : PTPRQ (131525 downstream)																							cttcttcttctttttttttat	0.139													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	85333633	85333636	+	IGR	DEL	AGAC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85333633_85333636delAGAC								SLC6A15 (27027 upstream) : TSPAN19 (74459 downstream)																							cctaaagtagagacagagaaagag	0.000													4	2	---	---	---	---	
ATP2B1	490	broad.mit.edu	37	12	90015178	90015178	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90015178delT	uc001tbh.2	-						ATP2B1_uc001tbg.2_Intron|ATP2B1_uc001tbf.2_Intron	NM_001682	NP_001673	P20020	AT2B1_HUMAN	plasma membrane calcium ATPase 1 isoform 1b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						ATAACACAAATTTAAAAACCA	0.303													4	2	---	---	---	---	
NTN4	59277	broad.mit.edu	37	12	96156083	96156083	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96156083delC	uc001tei.2	-						NTN4_uc009ztf.2_Intron|NTN4_uc009ztg.2_Intron	NM_021229	NP_067052	Q9HB63	NET4_HUMAN	netrin 4 precursor						axon guidance	basement membrane|plasma membrane				upper_aerodigestive_tract(1)|ovary(1)	2						TTCAAAGGCACCTCCAACTTG	0.438													4	2	---	---	---	---	
USP30	84749	broad.mit.edu	37	12	109519429	109519432	+	Intron	DEL	CACA	-	-	rs61164773	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109519429_109519432delCACA	uc010sxi.1	+						USP30_uc001tnu.3_Intron|USP30_uc001tnw.3_5'Flank	NM_032663	NP_116052	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30						ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial outer membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(1)	1						cgcatgcgcgcacacacacacaca	0.260													4	2	---	---	---	---	
C12orf51	283450	broad.mit.edu	37	12	112600573	112600573	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112600573delT	uc009zwc.2	-							NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						AAATTGTTTCTTTTTTTTTtt	0.269													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116030327	116030327	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116030327delT								TBX3 (908358 upstream) : MED13L (366056 downstream)																							ctccattttcTTTTTTTTTTT	0.229													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116797200	116797201	+	IGR	INS	-	G	G	rs144047511	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116797200_116797201insG								MED13L (82209 upstream) : NCRNA00173 (174026 downstream)																							TCCTGTGTTACGGGGGGGGAAA	0.396													4	2	---	---	---	---	
FBXO21	23014	broad.mit.edu	37	12	117600075	117600077	+	Intron	DEL	AGA	-	-	rs149885656		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117600075_117600077delAGA	uc001twk.2	-						FBXO21_uc001twj.2_Intron|FBXO21_uc009zwq.2_Intron|FBXO21_uc001twl.1_Intron	NM_033624	NP_296373	O94952	FBX21_HUMAN	F-box only protein 21 isoform 1						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			kidney(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)		AGCAGGAAGGAGAAGGTGCCTGT	0.463													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	117851627	117851627	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117851627delA								NOS1 (52045 upstream) : KSR2 (39190 downstream)																							tagtccagccaaacctagctg	0.000													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	117965108	117965109	+	Intron	DEL	AC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117965108_117965109delAC	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					acacacacagacacacacacac	0.218													4	2	---	---	---	---	
SFRS9	8683	broad.mit.edu	37	12	120899703	120899703	+	3'UTR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120899703delA	uc001tyi.2	-	4						NM_003769	NP_003760	Q13242	SRSF9_HUMAN	splicing factor, arginine/serine-rich 9						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|RNA binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TTTCTTCtttaaaaaaaaaaa	0.289													2	4	---	---	---	---	
HPD	3242	broad.mit.edu	37	12	122281970	122281970	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122281970delT	uc001ubj.2	-						HPD_uc001ubk.2_Intron	NM_002150	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase						L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	4-hydroxyphenylpyruvate dioxygenase activity|metal ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	tctttttttctttttttttga	0.100													4	3	---	---	---	---	
AACS	65985	broad.mit.edu	37	12	125626402	125626402	+	Intron	DEL	A	-	-	rs35836097		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125626402delA	uc001uhc.2	+						AACS_uc001uhd.2_Intron|AACS_uc009zyh.2_Intron|AACS_uc009zyi.2_Intron	NM_023928	NP_076417	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase						fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		CCAGTCCTTGAAAGTGCCTTT	0.537													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126545797	126545797	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126545797delT								TMEM132B (402208 upstream) : LOC100128554 (381230 downstream)																							GCTGAACTCCTGGCTCATGTA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128345360	128345361	+	IGR	DEL	CA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128345360_128345361delCA								None (None upstream) : TMEM132C (553930 downstream)																							TTGAGTTGGTCACTGATGGAGT	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	20813994	20813995	+	IGR	DEL	TG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20813994_20813995delTG								GJB6 (7460 upstream) : CRYL1 (163814 downstream)																							ACCCAGAGGATGTGTGTGTGTG	0.391													6	3	---	---	---	---	
ATP8A2	51761	broad.mit.edu	37	13	26153293	26153293	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26153293delA	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc010aaj.1_Intron	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		CCTTTCTCAGAAAACTCATAT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27500269	27500269	+	IGR	DEL	T	-	-	rs35385122		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27500269delT								GPR12 (165347 upstream) : USP12 (142169 downstream)																							CACATGTACCTTTGTACTCAA	0.458													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30511280	30511280	+	5'Flank	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30511280delC	uc010aav.2	+											Homo sapiens similar to bA90M5.1 (novel protein), mRNA (cDNA clone IMAGE:40146832).																		GTTTTTCTTTCTTTTTTCTAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31383925	31383934	+	IGR	DEL	GCTTGAGATA	-	-	rs150932569		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31383925_31383934delGCTTGAGATA								ALOX5AP (45369 upstream) : C13orf33 (96378 downstream)																							tcagactaaggcttgagatagcacaaccaa	0.000													5	3	---	---	---	---	
SUGT1L1	283507	broad.mit.edu	37	13	41481681	41481681	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41481681delA	uc001uxp.1	-							NR_003365				Homo sapiens cDNA FLJ35913 fis, clone TESTI2010239.												0						TATGATTTTTATTGCACAAAC	0.333													4	2	---	---	---	---	
C13orf31	144811	broad.mit.edu	37	13	44464090	44464090	+	Intron	DEL	C	-	-	rs7989857	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44464090delC	uc010acg.2	+						C13orf31_uc001uzf.3_Intron	NM_001128303	NP_001121775	Q8IV20	CM031_HUMAN	hypothetical protein LOC144811												0		Lung NSC(96;0.000163)|all_hematologic(4;0.0127)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Breast(139;0.0364)|Lung SC(185;0.0367)|Acute lymphoblastic leukemia(4;0.138)		GBM - Glioblastoma multiforme(144;0.000573)|BRCA - Breast invasive adenocarcinoma(63;0.121)		GCATTTTTTTCCCTGACTAGT	0.323													4	2	---	---	---	---	
SERP2	387923	broad.mit.edu	37	13	44954139	44954139	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44954139delA	uc001uzj.2	+						SERP2_uc001uzk.2_Intron	NM_001010897	NP_001010897	Q8N6R1	SERP2_HUMAN	stress-associated endoplasmic reticulum protein						protein transport|transmembrane transport	endoplasmic reticulum membrane|integral to membrane					0		all_hematologic(4;1.49e-06)|Acute lymphoblastic leukemia(4;1.5e-06)|Lung NSC(96;0.00043)|Breast(139;0.0044)|Prostate(109;0.0137)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;0.00026)|BRCA - Breast invasive adenocarcinoma(63;0.123)		ACATAGCCTTAAAAGGGCATT	0.393													4	2	---	---	---	---	
FAM194B	220081	broad.mit.edu	37	13	46148741	46148741	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46148741delG	uc001val.2	-						FAM194B_uc001vam.1_Intron	NM_182542	NP_872348	Q5W0A0	F194B_HUMAN	hypothetical protein LOC220081											central_nervous_system(1)	1						tttctgtcttgccaggttgcc	0.124													4	2	---	---	---	---	
DLEU2	8847	broad.mit.edu	37	13	50655194	50655194	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50655194delA	uc001vdn.1	-						DLEU2_uc001vdo.1_Intron|DLEU1_uc010adl.1_5'Flank|DLEU1_uc001vee.1_5'Flank|DLEU1_uc010adm.1_5'Flank|DLEU1_uc010adn.1_5'Flank|DLEU1_uc001vef.1_5'Flank|DLEU1_uc001veg.1_5'Flank|DLEU1_uc010tgn.1_5'Flank|DLEU1_uc001vei.1_5'Flank|DLEU1_uc010ado.1_5'Flank|DLEU1_uc010adp.1_5'Flank|DLEU2_uc001vdx.2_Intron|DLEU2_uc001vdy.2_Intron|DLEU2_uc001vdz.2_Intron|DLEU2_uc001veb.1_Intron|DLEU1_uc001vec.2_5'Flank|DLEU1_uc001ved.2_5'Flank	NR_002612				Homo sapiens BCMS-upstream neighbor (BCMSUN) mRNA, partial sequence.												0						AGCAAATGACAAAAATCCCCA	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	72917957	72917957	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72917957delT								DACH1 (476627 upstream) : C13orf37 (364538 downstream)																							TCATGACAGGTTTTTTTTTCC	0.428													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	93973095	93973095	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93973095delG	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				AAATCTTCATGGCGGAGTACA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	109152580	109152580	+	IGR	DEL	G	-	-	rs28474804		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109152580delG								TNFSF13B (193216 upstream) : MYO16 (95920 downstream)																							ttttttttttgttttttttgt	0.174													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112857086	112857087	+	IGR	DEL	GA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112857086_112857087delGA								SOX1 (131066 upstream) : C13orf28 (173582 downstream)																							TCCCACATCTGAGTCCTGGGCA	0.604													4	2	---	---	---	---	
UPF3A	65110	broad.mit.edu	37	13	115062698	115062698	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115062698delT	uc001vup.2	+						UPF3A_uc001vuq.2_Intron|UPF3A_uc001vus.2_Intron|UPF3A_uc001vur.2_Intron|UPF3A_uc001vut.2_Intron|UPF3A_uc001vuu.2_Intron	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A						mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		GGTGCTTCCGTTTTTTTTTTT	0.413													4	2	---	---	---	---	
C14orf93	60686	broad.mit.edu	37	14	23466822	23466823	+	Intron	DEL	CT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23466822_23466823delCT	uc001wib.1	-						C14orf93_uc001wic.1_Intron|C14orf93_uc001wid.1_Intron|C14orf93_uc001wig.2_Intron|C14orf93_uc001wih.2_Intron|C14orf93_uc001wie.2_Intron|C14orf93_uc001wia.3_Intron|C14orf93_uc001wif.2_Intron	NM_021944	NP_068763	Q9H972	CN093_HUMAN	hypothetical protein LOC60686 precursor							extracellular region				ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		GATTTTCCTGCTCATATGGCCC	0.391													4	2	---	---	---	---	
STXBP6	29091	broad.mit.edu	37	14	25461454	25461454	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25461454delC	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpx.1_Intron	NM_014178	NP_054897	Q8NFX7	STXB6_HUMAN	amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)		ACTACTTAGTCCCATAGTCAC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35855218	35855218	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35855218delT								KIAA0391 (68545 upstream) : NFKBIA (15499 downstream)																							CCGACTGGCCTTTTTCCTCTG	0.478													4	2	---	---	---	---	
C14orf135	64430	broad.mit.edu	37	14	60591443	60591443	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60591443delT	uc001xer.3	+	8	2374	c.1852delT	c.(1852-1854)TTTfs	p.F618fs	C14orf135_uc001xeq.2_Frame_Shift_Del_p.F618fs|C14orf135_uc010apm.2_RNA	NM_022495	NP_071940	Q63HM2	CN135_HUMAN	hepatitis C virus F protein-binding protein 2	852						integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)		TACAAATTTGTTTATTCCAGG	0.358													4	2	---	---	---	---	
PLEKHH1	57475	broad.mit.edu	37	14	68042292	68042293	+	Intron	INS	-	AT	AT			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68042292_68042293insAT	uc001xjl.1	+						PLEKHH1_uc010tsw.1_Intron|PLEKHH1_uc001xjm.1_3'UTR|PLEKHH1_uc001xjn.1_Intron|PLEKHH1_uc010tsx.1_5'Flank	NM_020715	NP_065766	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H							cytoskeleton	binding				0				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		GTAACCCCACAATAAATACAAA	0.525													34	16	---	---	---	---	
ACTN1	87	broad.mit.edu	37	14	69375373	69375374	+	Intron	DEL	GT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69375373_69375374delGT	uc001xkl.2	-						ACTN1_uc010ttb.1_Intron|ACTN1_uc001xkm.2_Intron|ACTN1_uc001xkn.2_Intron|ACTN1_uc001xko.1_Intron|ACTN1_uc010ttd.1_Intron	NM_001102	NP_001093	P12814	ACTN1_HUMAN	actinin, alpha 1 isoform b						focal adhesion assembly|negative regulation of cellular component movement|platelet activation|platelet degranulation|regulation of apoptosis	actin cytoskeleton|cytosol|extracellular region|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|sarcomere	actin binding|calcium ion binding|integrin binding|vinculin binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		AACCTGGAGAGTGTGGTCAGAG	0.574													4	2	---	---	---	---	
PCNX	22990	broad.mit.edu	37	14	71517112	71517113	+	Intron	INS	-	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71517112_71517113insT	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		AAGGCATAGAATTTTTTTTAAA	0.282													4	2	---	---	---	---	
RGS6	9628	broad.mit.edu	37	14	73017003	73017003	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73017003delG	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron|RGS6_uc010ttp.1_Intron|RGS6_uc001xmz.1_Intron	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		TCTATCAGGTGCAGTTGGTGC	0.473													4	2	---	---	---	---	
DNAL1	83544	broad.mit.edu	37	14	74133664	74133665	+	Intron	DEL	TT	-	-	rs76510526		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74133664_74133665delTT	uc001xoq.3	+						DNAL1_uc010aru.2_Intron|DNAL1_uc010arv.2_Intron	NM_031427	NP_113615	Q4LDG9	DNAL1_HUMAN	axonemal dynein light chain 1												0				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)		atcccttctctttttttttttt	0.000													3	3	---	---	---	---	
LOC646214	646214	broad.mit.edu	37	15	21941542	21941545	+	5'Flank	DEL	ACTT	-	-	rs138766428		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21941542_21941545delACTT	uc010tzj.1	-							NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						GGGCAATCTGACTTACACCTTAAT	0.446													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22516781	22516782	+	IGR	INS	-	TTCA	TTCA	rs113720943		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22516781_22516782insTTCA								MIR1268 (3501 upstream) : GOLGA8DP (185503 downstream)																							ttccaaaggctgtgtcctttcA	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22516782	22516783	+	IGR	INS	-	ATT	ATT	rs75610703		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22516782_22516783insATT								MIR1268 (3502 upstream) : GOLGA8DP (185502 downstream)																							tccaaaggctgtgtcctttcAC	0.104													4	2	---	---	---	---	
SNORD116-4	100033416	broad.mit.edu	37	15	25296907	25296907	+	5'Flank	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25296907delC	uc001yxh.1	+						SNORD116-2_uc001yxi.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0						GGCGTGGTGGCCGTGGAAGCA	0.572													4	2	---	---	---	---	
FAM189A1	23359	broad.mit.edu	37	15	29456236	29456236	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29456236delT	uc010azk.1	-						FAM189A1_uc001zcn.2_Intron	NM_015307	NP_056122	O60320	F1891_HUMAN	hypothetical protein LOC23359							integral to membrane					0						aacaaaacgattatcagctaa	0.000													4	2	---	---	---	---	
FRMD5	84978	broad.mit.edu	37	15	44214354	44214355	+	Intron	DEL	TC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44214354_44214355delTC	uc001ztl.2	-						FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		TCAGAGGCTATCAGTTATACAT	0.267													4	2	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	47933446	47933448	+	Intron	DEL	ATC	-	-	rs138785711		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47933446_47933448delATC	uc001zvw.2	+							NM_020858	NP_065909	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		GTCTAGAAATATCATGGCTTTAA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	51425425	51425425	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51425425delT								TNFAIP8L3 (27952 upstream) : CYP19A1 (74830 downstream)																							AAACTGTTGCTTTTTTTTTAA	0.229											OREG0023120	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
RAB8B	51762	broad.mit.edu	37	15	63481198	63481198	+	5'Flank	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63481198delA	uc002alz.2	+						RAB8B_uc010uih.1_5'Flank	NM_016530	NP_057614	Q92930	RAB8B_HUMAN	RAB8B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(1)|kidney(1)	2						TTAGCATGGTAACCATTCTTT	0.537													4	2	---	---	---	---	
MEGF11	84465	broad.mit.edu	37	15	66306437	66306437	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66306437delC	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821	A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1						aggcgatggtccaggcacaag	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	67127789	67127790	+	IGR	INS	-	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67127789_67127790insT								SMAD6 (53454 upstream) : SMAD3 (230405 downstream)																							ccttcagtgtgggctgggccta	0.045													4	2	---	---	---	---	
EFTUD1	79631	broad.mit.edu	37	15	82533098	82533098	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82533098delA	uc002bgt.1	-						EFTUD1_uc002bgu.1_Intron	NM_024580	NP_078856	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain						mature ribosome assembly		GTP binding|GTPase activity|ribosome binding|translation elongation factor activity			ovary(1)	1						GACAGTTAAGAAGGATAAATA	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88153839	88153839	+	IGR	DEL	T	-	-	rs11325967		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88153839delT								NCRNA00052 (30922 upstream) : NTRK3 (266149 downstream)																							GCTCCAACGATTTTTTTTCCT	0.438													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98560725	98560725	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98560725delT								ARRDC4 (43658 upstream) : FAM169B (419666 downstream)																							cagcagtgcctttgcacctgc	0.000													4	2	---	---	---	---	
PGPEP1L	145814	broad.mit.edu	37	15	99514432	99514440	+	Intron	DEL	GGGGGGGGT	-	-	rs72362970		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99514432_99514440delGGGGGGGGT	uc002bum.2	-						PGPEP1L_uc010bop.2_Intron|PGPEP1L_uc002bun.2_Intron	NM_001102612	NP_001096082	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase 1-like protein						proteolysis		cysteine-type peptidase activity				0						ATGGGGGGGGGGGGGGGGTGGGCACCAAG	0.612													15	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	101277971	101277972	+	IGR	DEL	AC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101277971_101277972delAC								ASB7 (86069 upstream) : ALDH1A3 (142037 downstream)																							TGTCCCCACTACACACACACAC	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	3238787	3238788	+	IGR	DEL	GT	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3238787_3238788delGT								ZNF213 (45983 upstream) : OR1F1 (15459 downstream)																							GAAGGGCAGAGTGACAGTAAAG	0.609													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5880381	5880381	+	IGR	DEL	T	-	-	rs112765671		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5880381delT								FAM86A (732592 upstream) : A2BP1 (188751 downstream)																							TTGCTTTTTGTTTTTTTTTTT	0.388													2	4	---	---	---	---	
USP31	57478	broad.mit.edu	37	16	23161922	23161923	+	5'Flank	INS	-	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23161922_23161923insA	uc002dll.2	-							NM_020718	NP_065769	Q70CQ4	UBP31_HUMAN	ubiquitin specific peptidase 31						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(3)|lung(3)|breast(2)|pancreas(1)|skin(1)	10				GBM - Glioblastoma multiforme(48;0.0187)		TTGGTTCCATTAAAAAAAAAAT	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33542155	33542155	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33542155delA								SLC6A10P (645692 upstream) : MIR1826 (423353 downstream)																							tttgagagccaggcaggatga	0.179													4	2	---	---	---	---	
VPS53	55275	broad.mit.edu	37	17	514696	514697	+	Intron	INS	-	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:514696_514697insG	uc002frn.2	-						VPS53_uc002frk.2_Intron|VPS53_uc010cjo.1_Intron|VPS53_uc002frl.2_Intron|VPS53_uc002frm.2_Intron|VPS53_uc002fro.2_Intron|VPS53_uc010cjp.1_Intron	NM_018289	NP_060759	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 2						protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		agcaaggatatggggaaactgg	0.000													4	2	---	---	---	---	
SMG6	23293	broad.mit.edu	37	17	2078141	2078141	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2078141delG	uc002fub.1	-						SMG6_uc010vqv.1_Intron	NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4						GTGATGTAATGGGAAACGCGG	0.428													4	2	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2791808	2791809	+	Intron	INS	-	GT	GT			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2791808_2791809insGT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						gagaacccacagtgtgtgtgtt	0.000													4	2	---	---	---	---	
ZZEF1	23140	broad.mit.edu	37	17	3924778	3924779	+	Intron	DEL	TG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3924778_3924779delTG	uc002fxe.2	-							NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4						AATTACACTTTGTGACCGAAGA	0.332													4	2	---	---	---	---	
TP53	7157	broad.mit.edu	37	17	7573819	7573820	+	Intron	INS	-	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7573819_7573820insG	uc002gim.2	-						TP53_uc002gig.1_Intron|TP53_uc002gih.2_Intron|TP53_uc010cne.1_Intron|TP53_uc010cnf.1_Intron|TP53_uc010cng.1_Intron|TP53_uc002gii.1_Intron|TP53_uc010cnh.1_Intron|TP53_uc010cni.1_Intron|TP53_uc002gij.2_Intron	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a						activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.0?(7)|p.?(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CCCAATGAGATGGGGTCAGCTG	0.510		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			4	2	---	---	---	---	
EPN2	22905	broad.mit.edu	37	17	19174483	19174483	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19174483delG	uc002gvd.3	+						EPN2_uc002gvc.2_Intron|EPN2_uc010vyn.1_Intron|EPN2_uc010cql.1_Intron|EPN2_uc002gve.3_Intron|EPN2_uc002gvf.3_Intron|EPN2_uc010vyo.1_Intron	NM_014964	NP_055779	O95208	EPN2_HUMAN	epsin 2 isoform b						endocytosis		lipid binding			skin(1)	1	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)					ggggtggtgtgggggcaggag	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20416848	20416849	+	IGR	INS	-	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20416848_20416849insA								LGALS9B (46000 upstream) : CCDC144NL (349861 downstream)																							CAGGCTGAAAGAAAAAAAAAAA	0.554													5	3	---	---	---	---	
CCDC144NL	339184	broad.mit.edu	37	17	20768999	20769000	+	Intron	INS	-	AACAC	AACAC			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20768999_20769000insAACAC	uc002gyf.2	-						uc002gyg.1_5'Flank|uc002gyh.1_5'Flank	NM_001004306	NP_001004306	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family,												0						ATTCCTTGAATAACACATTAGT	0.193													4	3	---	---	---	---	
CCDC144NL	339184	broad.mit.edu	37	17	20801228	20801228	+	5'Flank	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20801228delT	uc002gyf.2	-						uc002gyg.1_Intron|uc002gyh.1_Intron	NM_001004306	NP_001004306	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family,												0						TAGTCACACATTGCACATATC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21234377	21234378	+	IGR	INS	-	CG	CG	rs138103866		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21234377_21234378insCG								MAP2K3 (15828 upstream) : KCNJ12 (45321 downstream)																							TGTGGAAGTCATATTgagagga	0.282													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21329284	21329284	+	IGR	DEL	C	-	-	rs67728666		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21329284delC								KCNJ12 (6105 upstream) : C17orf51 (102288 downstream)																							GGAGAGGGCACGGGGGTGGAA	0.358													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25419260	25419260	+	IGR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25419260delT								None (None upstream) : WSB1 (201846 downstream)																							CTCTCTCACATATTTTTTCTG	0.318													3	3	---	---	---	---	
SSH2	85464	broad.mit.edu	37	17	28174683	28174684	+	Intron	DEL	CA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28174683_28174684delCA	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_Intron|SSH2_uc002her.2_Intron|SSH2_uc010csc.1_Intron	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						gttttctggtcacaacactgct	0.134													4	2	---	---	---	---	
CCDC55	84081	broad.mit.edu	37	17	28499865	28499865	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28499865delA	uc002heu.2	+						CCDC55_uc002hev.2_Intron|CCDC55_uc010wbl.1_Intron|CCDC55_uc010wbm.1_Intron|CCDC55_uc002hex.2_Intron	NM_032141	NP_115517	Q9H0G5	NSRP1_HUMAN	coiled-coil domain containing 55 isoform 1						developmental process|nucleocytoplasmic transport|regulation of alternative nuclear mRNA splicing, via spliceosome	nuclear speck|ribonucleoprotein complex	mRNA binding|protein binding				0						ACTTGCAGGGAAAAAAAAAAC	0.313													4	2	---	---	---	---	
SYNRG	11276	broad.mit.edu	37	17	35921850	35921850	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35921850delA	uc002hoa.2	-						SYNRG_uc010wde.1_Intron|SYNRG_uc010wdf.1_Intron|SYNRG_uc002hoc.2_Intron|SYNRG_uc002hoe.2_Intron|SYNRG_uc002hod.2_Intron|SYNRG_uc010wdg.1_Intron|SYNRG_uc002hob.2_Intron|SYNRG_uc002hof.2_Intron|SYNRG_uc010cvd.1_Intron	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1						endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2						TACCACAAATAAAAAAAAAAC	0.274													5	5	---	---	---	---	
ACLY	47	broad.mit.edu	37	17	40048933	40048933	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40048933delT	uc002hyg.2	-						ACLY_uc002hyh.2_Intron|ACLY_uc002hyi.2_Intron|ACLY_uc010wfx.1_Intron|ACLY_uc010wfy.1_Intron	NM_001096	NP_001087	P53396	ACLY_HUMAN	ATP citrate lyase isoform 1						ATP catabolic process|cellular carbohydrate metabolic process|citrate metabolic process|coenzyme A metabolic process|energy reserve metabolic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	citrate lyase complex|cytosol|nucleus	ATP binding|ATP citrate synthase activity|citrate (pro-3S)-lyase activity|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			ovary(2)|central_nervous_system(1)	3		Breast(137;0.000143)				AAGCCTTGCCttttttttttc	0.264													8	7	---	---	---	---	
SKAP1	8631	broad.mit.edu	37	17	46267040	46267040	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46267040delT	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						ttgctttttcttttttttttt	0.124													7	4	---	---	---	---	
SKAP1	8631	broad.mit.edu	37	17	46408187	46408187	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46408187delA	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						CAGGGGGCGGAAAAAAAAAAA	0.428													2	5	---	---	---	---	
CA10	56934	broad.mit.edu	37	17	49734516	49734516	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49734516delG	uc002itw.3	-						CA10_uc002itu.3_Intron|CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			GTGCTGAAGAGGCACCAGGAG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	55883632	55883632	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55883632delA								MSI2 (126333 upstream) : MRPS23 (33212 downstream)																							actgcctctgaaaagccttct	0.050													4	2	---	---	---	---	
CUEDC1	404093	broad.mit.edu	37	17	55959548	55959548	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55959548delT	uc002ivd.1	-						CUEDC1_uc002ive.1_Intron	NM_017949	NP_060419	Q9NWM3	CUED1_HUMAN	CUE domain-containing 1											skin(2)	2						CCAGAAAGGGTTTTTTTTTCC	0.547													4	2	---	---	---	---	
CSH2	1443	broad.mit.edu	37	17	61959727	61959728	+	Intron	INS	-	CTC	CTC	rs138744925	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61959727_61959728insCTC	uc002jck.2	-						GH2_uc002jcj.2_5'Flank|GH2_uc002jcl.1_5'Flank|GH2_uc002jcm.1_5'Flank|GH2_uc002jcn.1_5'Flank|GH2_uc002jco.1_5'Flank	NM_001317	NP_001308	P01243	CSH_HUMAN	chorionic somatomammotropin hormone 1 isoform 1						female pregnancy|signal transduction	extracellular region	hormone activity|metal ion binding				0						ACTTTTGCTGACTCCTGGGCTC	0.535													9	8	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	63794086	63794086	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63794086delG	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron|CCDC46_uc002jfk.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			TGATGCTACTGGCTAAAGTGG	0.527													4	2	---	---	---	---	
NOL11	25926	broad.mit.edu	37	17	65735158	65735158	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65735158delA	uc002jgd.1	+						NOL11_uc010wql.1_Intron|NOL11_uc010deu.1_Intron|SNORA38B_uc010dev.2_5'Flank	NM_015462	NP_056277	Q9H8H0	NOL11_HUMAN	nucleolar protein 11							nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			ATAGAATTTTACTTCTGGTTT	0.363													180	86	---	---	---	---	
HEXDC	284004	broad.mit.edu	37	17	80397737	80397738	+	Intron	DEL	CA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80397737_80397738delCA	uc002kew.2	+						HEXDC_uc002kev.3_Intron|HEXDC_uc010diq.2_Intron|HEXDC_uc010wvm.1_RNA|HEXDC_uc010wvn.1_Frame_Shift_Del_p.P140fs			Q8WVB3	HEXDC_HUMAN	SubName: Full=Hexosaminidase (Glycosyl hydrolase family 20, catalytic domain) containing, isoform CRA_c; SubName: Full=Hexosaminidase D;						carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)|skin(1)	2	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			CCAGCTCAGCCACCCACCTGCC	0.668													6	3	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3701617	3701617	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3701617delC	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				GAGAATATGGCCAAGGAGTCC	0.448													4	2	---	---	---	---	
PTPRM	5797	broad.mit.edu	37	18	8009135	8009135	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8009135delT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)				acaaaggAGCTTCTCCGATAT	0.239													4	2	---	---	---	---	
FAM59A	64762	broad.mit.edu	37	18	29922594	29922595	+	Intron	INS	-	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29922594_29922595insA	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A											ovary(1)|skin(1)	2						ACTGCTCCAGCAAAATTGTCTG	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	44249448	44249448	+	RNA	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44249448delC	uc002lch.1	-	1		c.805delG								Homo sapiens cDNA FLJ30193 fis, clone BRACE2001340.																		GTGTCACTTTCCCCCAGAAAT	0.308													4	2	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50303091	50303092	+	Intron	INS	-	A	A	rs148870306	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50303091_50303092insA	uc002lfe.1	+						DCC_uc010xdr.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		cacatacataccaaaacatact	0.000													1	6	---	---	---	---	
ALPK2	115701	broad.mit.edu	37	18	56153196	56153199	+	Intron	DEL	TAAC	-	-	rs151318932		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56153196_56153199delTAAC	uc002lhj.3	-							NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase								ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						CAGAGAAAAATAACTAATTCACAC	0.480													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	72846361	72846362	+	IGR	DEL	TG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72846361_72846362delTG								ZNF407 (68733 upstream) : ZADH2 (62917 downstream)																							tgtgtatgtctgtgtgtgtgtg	0.312													4	2	---	---	---	---	
CFD	1675	broad.mit.edu	37	19	859068	859068	+	5'Flank	DEL	A	-	-	rs3834645		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:859068delA	uc002lqc.2	+						CFD_uc010drv.2_5'Flank	NM_001928	NP_001919	P00746	CFAD_HUMAN	complement factor D preproprotein						complement activation, alternative pathway|platelet activation|platelet degranulation|proteolysis	platelet alpha granule lumen	serine-type endopeptidase activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ctgaaggcggacatccctgaa	0.070													2	5	---	---	---	---	
ZNF555	148254	broad.mit.edu	37	19	2851298	2851299	+	Intron	DEL	AT	-	-	rs74739029		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2851298_2851299delAT	uc002lwo.2	+						ZNF555_uc002lwn.3_Intron	NM_152791	NP_690004	Q8NEP9	ZN555_HUMAN	zinc finger protein 555						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ctggccGTGaattttttttttt	0.144													6	3	---	---	---	---	
TLE6	79816	broad.mit.edu	37	19	2981970	2981970	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2981970delA	uc002lwu.2	+						TLE6_uc002lwt.2_Intron|TLE6_uc010dtg.2_Intron	NM_024760	NP_079036	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6 isoform 2						regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ctctctgaggaaaaaaaaGGT	0.104													4	2	---	---	---	---	
CHAF1A	10036	broad.mit.edu	37	19	4409831	4409831	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4409831delC	uc002mal.2	+							NM_005483	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)						cell cycle|DNA repair|DNA replication|DNA replication-dependent nucleosome assembly|protein complex assembly|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|WINAC complex	chromatin binding|chromo shadow domain binding|unfolded protein binding			ovary(1)|skin(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CACTGGGTCACCCAGGTGTTT	0.592								Chromatin_Structure					4	2	---	---	---	---	
SAFB	6294	broad.mit.edu	37	19	5668381	5668381	+	3'UTR	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5668381delT	uc002mcf.2	+	21					SAFB_uc002mcg.2_3'UTR|SAFB_uc002mce.3_3'UTR|SAFB_uc010xir.1_3'UTR|SAFB_uc010xis.1_3'UTR|SAFB_uc010xit.1_3'UTR|SAFB_uc010xiu.1_3'UTR	NM_002967	NP_002958	Q15424	SAFB1_HUMAN	scaffold attachment factor B						chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		TGTAAAAATATTTTTTTTTAA	0.368													9	4	---	---	---	---	
FBN3	84467	broad.mit.edu	37	19	8183498	8183499	+	Intron	INS	-	AC	AC	rs141431028	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8183498_8183499insAC	uc002mjf.2	-							NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						cccttgtacagacacacagtca	0.119													9	5	---	---	---	---	
PRAM1	84106	broad.mit.edu	37	19	8562948	8562948	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8562948delT	uc002mkd.2	-						PRAM1_uc002mkc.2_Intron	NM_032152	NP_115528	Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1								lipid binding|protein binding				0						gtatttttagtagacggggtt	0.050													4	2	---	---	---	---	
RGL3	57139	broad.mit.edu	37	19	11527833	11527833	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11527833delT	uc002mrp.2	-						RGL3_uc002mrn.2_Intron|RGL3_uc002mrm.2_Intron|RGL3_uc002mro.2_Intron|RGL3_uc002mrq.2_Intron	NM_001035223	NP_001030300	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1						tttttttttgttttttttttt	0.249													5	3	---	---	---	---	
NDUFB7	4713	broad.mit.edu	37	19	14678219	14678220	+	Intron	INS	-	CT	CT	rs138677274	by1000genomes	TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14678219_14678220insCT	uc002mzg.2	-							NM_004146	NP_004137	P17568	NDUB7_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			ovary(1)	1					NADH(DB00157)	GGCGGCGTGGCCTCTCTCTCAG	0.609													5	5	---	---	---	---	
CYP4F22	126410	broad.mit.edu	37	19	15661808	15661808	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15661808delT	uc002nbh.3	+							NM_173483	NP_775754	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F,							endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen			ovary(1)|pancreas(1)	2						tcccattggctctatgatgcc	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	16407044	16407044	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16407044delC								AP1M1 (60888 upstream) : KLF2 (28607 downstream)																							AAGGCTCTGTCCTGGTCTCAA	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30603166	30603167	+	IGR	DEL	GA	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30603166_30603167delGA								C19orf2 (96555 upstream) : ZNF536 (260161 downstream)																							atggcttcctgagagactttca	0.208													4	2	---	---	---	---	
UPK1A	11045	broad.mit.edu	37	19	36157489	36157490	+	5'Flank	INS	-	A	A			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36157489_36157490insA	uc002oaw.2	+						UPK1A_uc010eeh.2_5'Flank	NM_007000	NP_008931	O00322	UPK1A_HUMAN	uroplakin 1A						epithelial cell differentiation|protein oligomerization	endoplasmic reticulum|integral to membrane	monosaccharide binding|protein homodimerization activity				0	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGGTCTGAGGCTCAGGGAGGGG	0.644													4	2	---	---	---	---	
ZNF83	55769	broad.mit.edu	37	19	53164471	53164472	+	Intron	INS	-	GT	GT			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53164471_53164472insGT	uc010epz.2	-						ZNF83_uc010eqb.1_Intron	NM_001105554	NP_001099024	P51522	ZNF83_HUMAN	zinc finger protein 83 isoform b							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		CATACACAGGGGAGACCTTACC	0.347													6	7	---	---	---	---	
ZNF264	9422	broad.mit.edu	37	19	57724481	57724481	+	3'UTR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57724481delG	uc002qob.2	+	4						NM_003417	NP_003408	O43296	ZN264_HUMAN	zinc finger protein 264						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		GCACATAGGAGAACCTTCAGC	0.373													4	2	---	---	---	---	
ZNF264	9422	broad.mit.edu	37	19	57724484	57724485	+	3'UTR	INS	-	AT	AT			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57724484_57724485insAT	uc002qob.2	+	4						NM_003417	NP_003408	O43296	ZN264_HUMAN	zinc finger protein 264						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		CATAGGAGAACCTTCAGCTGCA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	720663	720664	+	IGR	DEL	TC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:720663_720664delTC								SRXN1 (63840 upstream) : C20orf54 (20061 downstream)																							CATTCTCCCTTCTCTCTCTCTT	0.371													4	2	---	---	---	---	
EBF4	57593	broad.mit.edu	37	20	2709830	2709830	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2709830delA	uc002wgt.3	+						EBF4_uc002wgs.3_Intron	NM_001110514	NP_001103984	Q9BQW3	COE4_HUMAN	early B-cell factor 4						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding				0						ccatggcaccaaaaaaaaaag	0.194													3	3	---	---	---	---	
CDS2	8760	broad.mit.edu	37	20	5157978	5157978	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5157978delT	uc002wls.2	+						CDS2_uc002wlr.1_Intron|CDS2_uc010zqt.1_Intron|CDS2_uc002wlu.2_Intron|CDS2_uc010zqu.1_Intron|CDS2_uc002wlv.2_Intron|CDS2_uc010zqv.1_5'Flank	NM_003818	NP_003809	O95674	CDS2_HUMAN	phosphatidate cytidylyltransferase 2						phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphatidate cytidylyltransferase activity				0						GACTTACTGGTTTCCAGACTG	0.498													4	2	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19360962	19360963	+	Intron	INS	-	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19360962_19360963insT	uc002wrl.2	+							NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						gaaaaggagagtgcggtgtgag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26080035	26080036	+	IGR	DEL	AA	-	-	rs113138903		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26080035_26080036delAA								FAM182A (12483 upstream) : C20orf191 (4017 downstream)																							AGCCTAATCTAAGAAGATGCCT	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26080038	26080038	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26080038delA								FAM182A (12486 upstream) : C20orf191 (4015 downstream)																							CTAATCTAAGAAGATGCCTTC	0.413													4	2	---	---	---	---	
DUSP15	128853	broad.mit.edu	37	20	30453099	30453099	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30453099delA	uc002wwu.1	-						DUSP15_uc002wwv.1_Intron|DUSP15_uc002www.1_Intron|DUSP15_uc002wwx.1_Intron			Q9H1R2	DUS15_HUMAN	RecName: Full=Dual specificity protein phosphatase 15;          EC=3.1.3.48;          EC=3.1.3.16; AltName: Full=Vaccinia virus VH1-related dual-specific protein phosphatase Y; AltName: Full=VH1-related member Y;							cytoplasm|plasma membrane	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			AGTAGCTAGGAAAGGGCTACT	0.438													4	2	---	---	---	---	
PIGU	128869	broad.mit.edu	37	20	33150222	33150222	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33150222delG	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron	NM_080476	NP_536724	Q9H490	PIGU_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0						accctgtcctgggcagcttct	0.234													4	2	---	---	---	---	
BLCAP	10904	broad.mit.edu	37	20	36150308	36150308	+	5'Flank	DEL	A	-	-	rs76972566		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36150308delA	uc002xha.2	-						BLCAP_uc002xhb.2_Intron|BLCAP_uc002xhc.2_Intron|NNAT_uc002xhd.2_Intron|NNAT_uc002xhe.2_Intron	NM_006698	NP_006689	P62952	BLCAP_HUMAN	bladder cancer associated protein						apoptosis|cell cycle	integral to membrane					0		Myeloproliferative disorder(115;0.00878)				ATTACTTCGCAAAAAAAAAAA	0.333													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50196608	50196608	+	IGR	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50196608delC								NFATC2 (17440 upstream) : ATP9A (16706 downstream)																							TGACCCTTCACCCCACCTCTG	0.473													4	2	---	---	---	---	
ZFP64	55734	broad.mit.edu	37	20	50799388	50799388	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50799388delC	uc002xwl.2	-						ZFP64_uc002xwk.2_Intron|ZFP64_uc002xwm.2_Intron|ZFP64_uc002xwn.2_Intron	NM_018197	NP_060667	Q9NPA5	ZF64A_HUMAN	zinc finger protein 64 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						ATAATAAGTGCCTTGGTGCTG	0.438													4	2	---	---	---	---	
PHACTR3	116154	broad.mit.edu	37	20	58367200	58367200	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58367200delG	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron|PHACTR3_uc002yaw.2_Intron|PHACTR3_uc002yax.2_Intron	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			TGCCATGTGTGGTCTTCTTGG	0.448													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11096053	11096053	+	Intron	DEL	T	-	-	rs75995777		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11096053delT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CAAAAAAAAATGTGACAAATA	0.189													1	5	---	---	---	---	
TIAM1	7074	broad.mit.edu	37	21	32791100	32791100	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32791100delC	uc002yow.1	-						TIAM1_uc002yox.1_Intron	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10						ATACCAGCGACACTGGACTTT	0.502													4	2	---	---	---	---	
SYNJ1	8867	broad.mit.edu	37	21	34017073	34017073	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34017073delC	uc002yqh.2	-						SYNJ1_uc011ads.1_Intron|SYNJ1_uc002yqf.2_Intron|SYNJ1_uc002yqg.2_Intron|SYNJ1_uc002yqi.2_Intron|SYNJ1_uc002yqe.3_5'Flank	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a								inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5						AATGAATCGACCACATTTATT	0.294													4	2	---	---	---	---	
DOPEY2	9980	broad.mit.edu	37	21	37541192	37541193	+	Intron	INS	-	T	T			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37541192_37541193insT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						ctccctgtgggtttTTTTTTTT	0.045													4	2	---	---	---	---	
CBS	875	broad.mit.edu	37	21	44479212	44479213	+	Intron	INS	-	G	G			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44479212_44479213insG	uc002zcu.2	-						CBS_uc002zcs.1_Intron|CBS_uc002zct.2_Intron|CBS_uc002zcw.3_Intron|CBS_uc002zcv.2_Intron|CBS_uc002zcx.2_Intron	NM_000071	NP_000062	P35520	CBS_HUMAN	cystathionine-beta-synthase						cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process	cytosol|nucleolus	cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding				0					L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118)	GCACAGGCCACGGGGACCGCTC	0.698													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17402529	17402530	+	IGR	DEL	TC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17402529_17402530delTC								HSFYL1 (92304 upstream) : GAB4 (40299 downstream)																							ATAGGTTTATTCCCCCCTGTAT	0.530													13	6	---	---	---	---	
GGT3P	2679	broad.mit.edu	37	22	18769967	18769968	+	5'Flank	INS	-	AT	AT	rs111331306		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18769967_18769968insAT	uc010gri.1	-						GGT3P_uc011ago.1_Intron|GGT3P_uc011agp.1_Intron|GGT3P_uc002zob.1_Intron					Homo sapiens cDNA clone IMAGE:5761295, **** WARNING: chimeric clone ****.												0						TAGGAGGAAAGAtttttttttc	0.292													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25717830	25717833	+	IGR	DEL	TCTC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25717830_25717833delTCTC								IGLL3 (1639 upstream) : LRP5L (29553 downstream)																							ctcccactcttctctctctctctc	0.000													6	4	---	---	---	---	
TTC28	23331	broad.mit.edu	37	22	29029307	29029308	+	Intron	INS	-	T	T	rs112876654		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29029307_29029308insT	uc003adp.3	-							NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28								binding				0						aagaaaaaAAATTTTTTTTTCA	0.030													4	2	---	---	---	---	
OSBP2	23762	broad.mit.edu	37	22	31222087	31222087	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31222087delG	uc003aiy.1	+						OSBP2_uc011ala.1_Intron|OSBP2_uc010gwc.1_Intron|OSBP2_uc003aix.1_Intron|OSBP2_uc011alb.1_Intron|OSBP2_uc003aiz.1_Intron|OSBP2_uc003aja.1_Intron|OSBP2_uc011alc.1_Intron	NM_030758	NP_110385	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2						TATTGTTTTTGATGATGTGTT	0.498													4	2	---	---	---	---	
PLA2G6	8398	broad.mit.edu	37	22	38523229	38523230	+	Intron	DEL	CC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38523229_38523230delCC	uc003auy.1	-						PLA2G6_uc003auz.1_Intron|PLA2G6_uc003ava.1_Intron|PLA2G6_uc003avb.2_Intron|PLA2G6_uc010gxk.1_Intron|PLA2G6_uc011ano.1_3'UTR	NM_003560	NP_003551	O60733	PA2G6_HUMAN	phospholipase A2, group VI isoform a						cardiolipin biosynthetic process|cell death|lipid catabolic process	centrosome|membrane				ovary(1)	1	Melanoma(58;0.045)				Quinacrine(DB01103)	GTCTCCCCCTCCCCAGGGCACA	0.658													4	2	---	---	---	---	
WBP2NL	164684	broad.mit.edu	37	22	42335850	42335851	+	Intron	INS	-	G	G	rs66832914		TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42335850_42335851insG	uc011ape.1	+						LOC339674_uc003bba.1_Intron|CENPM_uc003bbm.2_Intron|CENPM_uc003bbn.2_Intron|CENPM_uc003bbo.2_Intron|CENPM_uc010gyq.2_Intron	NM_152613	NP_689826	Q6ICG8	WBP2L_HUMAN	WBP2 N-terminal like						egg activation|male pronucleus assembly|meiosis	perinuclear theca	WW domain binding			ovary(2)	2						aagaaaaagaaagaaagaaaga	0.079													4	2	---	---	---	---	
FAM118A	55007	broad.mit.edu	37	22	45733235	45733236	+	Intron	DEL	CC	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45733235_45733236delCC	uc003bfz.3	+						FAM118A_uc003bga.3_Intron|FAM118A_uc011aqr.1_Intron	NM_001104595	NP_001098065	Q9NWS6	F118A_HUMAN	hypothetical protein LOC55007							integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TGTCTGTGGGCCCAGTGCCACG	0.455													4	2	---	---	---	---	
SMC1B	27127	broad.mit.edu	37	22	45790203	45790203	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45790203delA	uc003bgc.2	-						SMC1B_uc003bgd.2_Intron|SMC1B_uc003bge.1_Intron	NM_148674	NP_683515	Q8NDV3	SMC1B_HUMAN	SMC1 structural maintenance of chromosomes						chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		accctgtctcaaaaaaaaagg	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48702074	48702074	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48702074delA								None (None upstream) : FAM19A5 (183214 downstream)																							TTGGTGGAGCAAAGGGGCAAG	0.562													4	2	---	---	---	---	
C22orf34	348645	broad.mit.edu	37	22	49981971	49981971	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49981971delC	uc003biq.2	-											Homo sapiens cDNA FLJ42972 fis, clone BRSTN2019129.												0						GTCGCCCTGGCCTTCCTCGCC	0.607													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	110892469	110892469	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110892469delG								DCX (237063 upstream) : ALG13 (31944 downstream)																							gcgtagcactgggtgggcctg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	112110608	112110608	+	IGR	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112110608delG								AMOT (26565 upstream) : None (None downstream)																							TTCAGGAACAGGAAAAGAGAA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	139551653	139551653	+	IGR	DEL	A	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139551653delA								CXorf66 (503976 upstream) : SOX3 (33499 downstream)																							CACCCGGCTCAAAAAAAAAAG	0.284													9	4	---	---	---	---	
MECP2	4204	broad.mit.edu	37	X	153323771	153323771	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153323771delG	uc004fjv.2	-						MECP2_uc004fjw.2_Intron	NM_004992	NP_004983	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCTGTTCATCGTTCTCTTTCA	0.537													4	2	---	---	---	---	
FAM197Y2	252946	broad.mit.edu	37	Y	9198247	9198248	+	Intron	DEL	TG	-	-			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9198247_9198248delTG	uc004frp.1	-							NR_001553				Homo sapiens CYorf16 protein (CYorf16) mRNA, partial cds.												0						tctttgtgtttgtgtgtgtgtg	0.218													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28587130	28587131	+	IGR	INS	-	AA	AA			TCGA-B2-3924-01A-02D-1386-10	TCGA-B2-3924-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28587130_28587131insAA								None (None upstream) : None (None downstream)																							ttttcactaattaggcaactct	0.005													5	5	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	57498845	57498846	+	Intron	DEL	AC	-	-	rs66580844		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57498845_57498846delAC	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						ACTTTTGTTTacacacacacac	0.252													4	3	---	---	---	---	
MCOLN3	55283	broad.mit.edu	37	1	85506997	85506997	+	Intron	DEL	G	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85506997delG	uc001dkp.2	-						MCOLN3_uc001dkq.2_Intron|MCOLN3_uc001dkr.2_Intron|MCOLN3_uc001dks.3_Intron	NM_018298	NP_060768	Q8TDD5	MCLN3_HUMAN	mucolipin 3							integral to membrane	ion channel activity			skin(1)	1				all cancers(265;0.00957)|Epithelial(280;0.0254)		TTTTGCAGCAGGTGGATAATA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	100288483	100288488	+	IGR	DEL	CCTCTA	-	-	rs115122615		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100288483_100288488delCCTCTA								FRRS1 (57134 upstream) : AGL (27152 downstream)																							acctcctcttcctctacctctacctc	0.029													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244932512	244932513	+	IGR	DEL	GT	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244932512_244932513delGT								PPPDE1 (60180 upstream) : FAM36A (66126 downstream)																							ttatgaaggggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
IFT172	26160	broad.mit.edu	37	2	27694905	27694906	+	Intron	INS	-	A	A	rs112509425		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27694905_27694906insA	uc002rku.2	-						IFT172_uc002rkw.2_Intron|IFT172_uc010yls.1_3'UTR|IFT172_uc010ezc.2_3'UTR|IFT172_uc002rkv.2_3'UTR	NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog						cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)					acactgtctccaaaaaaaaaaa	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114552156	114552159	+	IGR	DEL	GAAG	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114552156_114552159delGAAG								SLC35F5 (37756 upstream) : ACTR3 (95378 downstream)																							ggaagggaaagaaggaaggaagga	0.000													4	2	---	---	---	---	
ANKMY1	51281	broad.mit.edu	37	2	241419258	241419259	+	Intron	INS	-	C	C			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241419258_241419259insC	uc002vyz.1	-						ANKMY1_uc002vza.1_Intron|ANKMY1_uc010fzd.1_Intron|ANKMY1_uc002vzb.1_Intron|ANKMY1_uc002vzc.1_Intron|ANKMY1_uc002vzd.1_Intron	NM_016552	NP_057636	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1								zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		TCAAAGAGGGGCCTGCCACACC	0.545													4	2	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52623187	52623187	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52623187delT	uc003des.2	-	18	2876	c.2864delA	c.(2863-2865)AACfs	p.N955fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.N955fs|PBRM1_uc003der.2_Frame_Shift_Del_p.N923fs|PBRM1_uc003det.2_Frame_Shift_Del_p.N970fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.N970fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.N955fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.N955fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.N955fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.N954fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.N867fs|PBRM1_uc003dfa.1_Frame_Shift_Del_p.N301fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	955					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GTACATGCTGTTTTTAAAGCT	0.448			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								196	100	---	---	---	---	
PTPRG	5793	broad.mit.edu	37	3	62268432	62268432	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62268432delC	uc003dlb.2	+	28	4662	c.3943delC	c.(3943-3945)CAGfs	p.Q1315fs	PTPRG_uc003dlc.2_Frame_Shift_Del_p.Q1286fs|PTPRG_uc011bfi.1_Frame_Shift_Del_p.Q561fs|uc010hno.2_Intron|uc003dld.3_Intron|uc010hnp.2_Intron|uc003dle.3_Intron	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	1315	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TCGGCACTTTCAGTGTCCCAA	0.423													176	99	---	---	---	---	
EIF4E3	317649	broad.mit.edu	37	3	71739005	71739006	+	Intron	INS	-	A	A	rs5005116		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71739005_71739006insA	uc003dov.3	-						EIF4E3_uc011bgc.1_Intron|EIF4E3_uc003dox.2_Intron|EIF4E3_uc011bgd.1_Intron|EIF4E3_uc010hoc.2_Intron	NM_001134651	NP_001128123	Q8N5X7	IF4E3_HUMAN	eukaryotic translation initiation factor 4E						regulation of translation	cytoplasm|mRNA cap binding complex	translation initiation factor activity				0		Prostate(10;0.0166)		BRCA - Breast invasive adenocarcinoma(55;2.56e-05)|Epithelial(33;2.9e-05)|Lung(16;9.28e-05)|LUSC - Lung squamous cell carcinoma(21;0.00227)		TTGttttttttaaaaaaaaaaa	0.248													4	2	---	---	---	---	
NPHP3	27031	broad.mit.edu	37	3	132438748	132438749	+	Intron	DEL	AT	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132438748_132438749delAT	uc003epe.1	-						NCRNA00119_uc003epg.1_5'Flank|NPHP3_uc003epf.1_Intron|NCRNA00119_uc010htu.1_5'Flank	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3						maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1						atatatatacatatatatatat	0.248													4	2	---	---	---	---	
FAM194A	131831	broad.mit.edu	37	3	150421899	150421900	+	5'Flank	INS	-	C	C	rs148177227	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150421899_150421900insC	uc003eyg.2	-						FAM194A_uc003eyh.2_5'Flank	NM_152394	NP_689607	Q7L0X2	F194A_HUMAN	hypothetical protein LOC131831											skin(2)|ovary(1)	3						TTCTGTCCCTGCTCTTCAGCGT	0.545													7	4	---	---	---	---	
LIMCH1	22998	broad.mit.edu	37	4	41699388	41699388	+	3'UTR	DEL	T	-	-	rs113753743		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41699388delT	uc003gvu.3	+	27					LIMCH1_uc003gvv.3_3'UTR|LIMCH1_uc003gvw.3_3'UTR|LIMCH1_uc003gvx.3_3'UTR|LIMCH1_uc003gwe.3_3'UTR|LIMCH1_uc003gvy.3_3'UTR|LIMCH1_uc003gwa.3_3'UTR|LIMCH1_uc003gvz.3_3'UTR|LIMCH1_uc011byu.1_3'UTR|LIMCH1_uc003gwc.3_3'UTR|LIMCH1_uc003gwd.3_3'UTR|LIMCH1_uc011byv.1_3'UTR|LIMCH1_uc011byw.1_3'UTR|LIMCH1_uc010ifv.2_RNA	NM_014988	NP_055803	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						attgttttggttttttttttt	0.294													8	5	---	---	---	---	
SCARB2	950	broad.mit.edu	37	4	77087661	77087661	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77087661delA	uc003hju.1	-						SCARB2_uc011cbu.1_Intron	NM_005506	NP_005497	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2						cell adhesion|protein targeting to lysosome	integral to plasma membrane|lysosomal lumen|lysosomal membrane|membrane fraction	enzyme binding|receptor activity				0			Lung(101;0.196)			TACGTTTATCAAAACACAAGA	0.398													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	110475293	110475294	+	IGR	INS	-	CTTCAGGAAG	CTTCAGGAAG	rs148787567	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110475293_110475294insCTTCAGGAAG								SEC24B (13679 upstream) : CCDC109B (6061 downstream)																							GTCTCCTTGCTCAGGCAGAAAA	0.460													4	2	---	---	---	---	
FHDC1	85462	broad.mit.edu	37	4	153889445	153889446	+	Intron	INS	-	T	T	rs75046217		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153889445_153889446insT	uc003inf.2	+							NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1						actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)					AGCCTGATATATTTTTTTTTTT	0.223													3	6	---	---	---	---	
C5orf44	80006	broad.mit.edu	37	5	64948167	64948167	+	Intron	DEL	T	-	-	rs72456938		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64948167delT	uc003jtz.3	+						C5orf44_uc003jua.3_Intron|C5orf44_uc003juc.3_Intron|C5orf44_uc010iwv.2_Intron	NM_024941	NP_079217	A5PLN9	CE044_HUMAN	hypothetical protein LOC80006 isoform 2											ovary(1)	1						ttttcttttcttttttttttt	0.159													6	3	---	---	---	---	
DMXL1	1657	broad.mit.edu	37	5	118507261	118507261	+	Intron	DEL	T	-	-	rs140718009		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118507261delT	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1											ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		TATTGTCTTATTTTTTTTTTC	0.353													4	2	---	---	---	---	
KDM3B	51780	broad.mit.edu	37	5	137727992	137727993	+	Intron	DEL	GG	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137727992_137727993delGG	uc003lcy.1	+						KDM3B_uc010jew.1_Intron|KDM3B_uc011cys.1_Intron	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11						CTCTGGCACTGGGCTCAAATGC	0.470													56	38	---	---	---	---	
PCDHB11	56125	broad.mit.edu	37	5	140581875	140581875	+	3'UTR	DEL	T	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140581875delT	uc003liy.2	+	1						NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor						calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCTCCCCCAAttttttttttt	0.119													6	5	---	---	---	---	
PCDHGA2	56113	broad.mit.edu	37	5	140790416	140790417	+	Intron	INS	-	TT	TT	rs67450739		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140790416_140790417insTT	uc003ljk.1	+						PCDHGA1_uc003lji.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc011day.1_5'Flank|PCDHGA10_uc003lkl.1_5'Flank	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGTCtttgtcttttttttttt	0.124													4	2	---	---	---	---	
IL17F	112744	broad.mit.edu	37	6	52109409	52109409	+	5'Flank	DEL	T	-	-	rs3215541		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52109409delT	uc003pam.1	-							NM_052872	NP_443104	Q96PD4	IL17F_HUMAN	interleukin 17F precursor						cartilage development|inflammatory response|lymphotoxin A biosynthetic process|negative regulation of angiogenesis|proteoglycan metabolic process|regulation of granulocyte macrophage colony-stimulating factor biosynthetic process|regulation of interleukin-2 biosynthetic process|regulation of interleukin-6 biosynthetic process|regulation of interleukin-8 biosynthetic process|regulation of transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|cytokine binding|protein homodimerization activity			ovary(1)	1	Lung NSC(77;0.116)					AATGCAGGGGTTTTTTTTTTT	0.418													6	6	---	---	---	---	
MTO1	25821	broad.mit.edu	37	6	74192512	74192512	+	Intron	DEL	C	-	-	rs35121302		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74192512delC	uc003pgy.3	+						MTO1_uc010kav.2_Intron|MTO1_uc003pgz.3_Intron|MTO1_uc003pha.3_Intron|MTO1_uc003phb.3_Intron	NM_133645	NP_598400	Q9Y2Z2	MTO1_HUMAN	mitochondrial translation optimization 1 homolog						tRNA processing	mitochondrion	flavin adenine dinucleotide binding			ovary(3)|skin(2)|pancreas(1)	6						TTTtttctttctttttttttt	0.159													7	7	---	---	---	---	
HS3ST5	222537	broad.mit.edu	37	6	114405250	114405250	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114405250delT	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840	Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		ttttcttttcttttttttttt	0.154													4	2	---	---	---	---	
GET4	51608	broad.mit.edu	37	7	932269	932292	+	Intron	DEL	TGGGTGTATGTGCAAGTGTAGACA	-	-	rs66553046	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:932269_932292delTGGGTGTATGTGCAAGTGTAGACA	uc003sjl.1	+						GET4_uc003sjj.1_Intron	NM_015949	NP_057033	Q7L5D6	GET4_HUMAN	hypothetical protein LOC51608						tail-anchored membrane protein insertion into ER membrane|transport	BAT3 complex	protein binding				0						ggtagctgtgtgggtgtatgtgCAAGTGTAGACATGGCGTGGGG	0.272													4	3	---	---	---	---	
FOXK1	221937	broad.mit.edu	37	7	4720599	4720600	+	5'Flank	INS	-	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4720599_4720600insA	uc003snc.1	+						FOXK1_uc003sna.1_Intron|FOXK1_uc003snb.1_5'Flank	NM_001037165	NP_001032242	P85037	FOXK1_HUMAN	forkhead box K1						cell differentiation|embryo development|muscle organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			upper_aerodigestive_tract(1)|skin(1)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		aactccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
DLX5	1749	broad.mit.edu	37	7	96649884	96649885	+	3'UTR	INS	-	G	G	rs138874462	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96649884_96649885insG	uc003uon.2	-	3						NM_005221	NP_005212	P56178	DLX5_HUMAN	distal-less homeobox 5						cell proliferation|endochondral ossification|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					CTGTAAAAAAAGGGGGGGTCTT	0.337													4	4	---	---	---	---	
DPY19L2P2	349152	broad.mit.edu	37	7	102878163	102878164	+	Intron	INS	-	TAAAATAAAA	TAAAATAAAA			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102878163_102878164insTAAAATAAAA	uc003vbh.3	-						DPY19L2P2_uc003vbg.3_Intron|DPY19L2P2_uc010lit.2_Intron	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						accccagaacttaaaataaaaa	0.129													6	3	---	---	---	---	
ATP6V0A4	50617	broad.mit.edu	37	7	138391635	138391636	+	Intron	DEL	TT	-	-	rs35405334		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138391635_138391636delTT	uc003vuf.2	-						ATP6V0A4_uc003vug.2_Intron|ATP6V0A4_uc003vuh.2_Intron	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit						cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1						ATCCTGAGGAtttttttttttt	0.277													4	2	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139701401	139701402	+	Intron	INS	-	G	G	rs149093007	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139701401_139701402insG	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GCTGCTCTCCCGGGGGGGGGGC	0.545										HNSCC(7;0.00092)			5	5	---	---	---	---	
KIAA0020	9933	broad.mit.edu	37	9	2823904	2823908	+	Intron	DEL	TAATA	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2823904_2823908delTAATA	uc003zhp.1	-						KIAA0020_uc010mhc.1_Intron|KIAA0020_uc003zhq.1_Intron	NM_014878	NP_055693	Q15397	K0020_HUMAN	KIAA0020 protein							endoplasmic reticulum|nucleolus	RNA binding			ovary(1)	1				GBM - Glioblastoma multiforme(50;0.0319)		TTAAACattttaatataatatttat	0.254													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68419546	68419547	+	IGR	INS	-	CA	CA			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68419546_68419547insCA								FAM27B (625357 upstream) : MIR1299 (582692 downstream)																							acaatacactccacacacacat	0.010													6	3	---	---	---	---	
CCBL1	883	broad.mit.edu	37	9	131597417	131597418	+	Intron	INS	-	A	A			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131597417_131597418insA	uc004bwh.2	-						CCBL1_uc004bwf.2_Intron|CCBL1_uc004bwg.2_Intron|CCBL1_uc010myn.2_Intron|CCBL1_uc004bwj.2_Intron|CCBL1_uc011mbl.1_Intron|CCBL1_uc004bwi.2_Intron|CCBL1_uc010myo.2_Intron	NM_004059	NP_004050	Q16773	KAT1_HUMAN	kynurenine aminotransferase I isoform a						kynurenine metabolic process|L-phenylalanine catabolic process|tryptophan catabolic process	cytosol|nucleus	1-aminocyclopropane-1-carboxylate synthase activity|cysteine-S-conjugate beta-lyase activity|glutamine-phenylpyruvate transaminase activity|kynurenine-oxoglutarate transaminase activity|L-glutamine:pyruvate aminotransferase activity|L-phenylalanine:pyruvate aminotransferase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)	1					L-Glutamine(DB00130)|Pyridoxal Phosphate(DB00114)	ccatctcaaccaaaaaaaaaaa	0.000													8	4	---	---	---	---	
CSTF2T	23283	broad.mit.edu	37	10	53457289	53457289	+	3'UTR	DEL	A	-	-	rs143102624		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53457289delA	uc001jjp.2	-	1					PRKG1_uc001jjm.2_Intron|PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_015235	NP_056050	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit						mRNA processing	nucleus	nucleotide binding|RNA binding			ovary(1)	1				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		ACCCTCAATTaaaaaaaaaag	0.313													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	94969501	94969501	+	IGR	DEL	A	-	-	rs55900322	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94969501delA								CYP26A1 (131860 upstream) : MYOF (96686 downstream)																							CCCCCCCcccaaaaaaaaaac	0.219													4	2	---	---	---	---	
PAX2	5076	broad.mit.edu	37	10	102540769	102540769	+	Intron	DEL	A	-	-	rs67321764		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102540769delA	uc001krk.3	+						PAX2_uc001krl.3_Intron|PAX2_uc001krm.3_Intron|PAX2_uc001kro.3_Intron|PAX2_uc001krn.3_Intron|PAX2_uc010qps.1_Intron|PAX2_uc001krp.1_Intron	NM_003990	NP_003981	Q02962	PAX2_HUMAN	paired box protein 2 isoform e						anti-apoptosis|axonogenesis|brain morphogenesis|branching involved in ureteric bud morphogenesis|cell fate determination|cellular response to glucose stimulus|cellular response to hydrogen peroxide|cellular response to retinoic acid|cochlea development|glial cell differentiation|inner ear morphogenesis|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesodermal cell fate specification|mesonephros development|metanephric collecting duct development|metanephric distal convoluted tubule development|metanephric mesenchymal cell differentiation|metanephric nephron tubule formation|negative regulation of caspase activity|negative regulation of cytolysis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|negative regulation of reactive oxygen species metabolic process|negative regulation of transcription, DNA-dependent|nephric duct formation|neural tube closure|optic chiasma development|optic cup morphogenesis involved in camera-type eye development|optic nerve structural organization|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of metanephric glomerulus development|positive regulation of optic nerve formation|positive regulation of transcription from RNA polymerase II promoter|pronephric field specification|protein kinase B signaling cascade|reactive oxygen species metabolic process|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of metanephros size|retinal pigment epithelium development|stem cell differentiation|transcription from RNA polymerase II promoter|ureter maturation|vestibulocochlear nerve formation|visual perception	centriolar satellite|nucleus|protein complex|protein-DNA complex	core promoter proximal region sequence-specific DNA binding|superoxide-generating NADPH oxidase activity				0		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		GCCTGGGGTTAAACTGGGCAC	0.502													5	5	---	---	---	---	
INPP5F	22876	broad.mit.edu	37	10	121556161	121556161	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121556161delT	uc001leo.2	+							NM_014937	NP_055752	Q9Y2H2	SAC2_HUMAN	inositol polyphosphate-5-phosphatase F								phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		CTGACTACTGTTTGGGTTTAA	0.368													74	39	---	---	---	---	
FCHSD2	9873	broad.mit.edu	37	11	72552386	72552387	+	Intron	DEL	AA	-	-	rs139745956		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72552386_72552387delAA	uc009ytl.2	-						FCHSD2_uc010rrg.1_Intron|FCHSD2_uc001oth.3_Intron|ATG16L2_uc009ytj.1_Intron	NM_014824	NP_055639	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			ctctgtctccaaaaaaaaaaaa	0.153													4	2	---	---	---	---	
SYTL2	54843	broad.mit.edu	37	11	85411365	85411365	+	Intron	DEL	T	-	-	rs72171133		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85411365delT	uc010rth.1	-						SYTL2_uc010rtg.1_Intron|SYTL2_uc010rti.1_Intron|SYTL2_uc010rtj.1_Intron|SYTL2_uc001pav.2_Intron|SYTL2_uc010rte.1_Intron|SYTL2_uc001pax.2_Intron|SYTL2_uc001paz.2_Intron|SYTL2_uc001pba.2_Intron|SYTL2_uc001pay.2_Intron|SYTL2_uc001paw.2_Intron|SYTL2_uc009yvj.2_Intron|SYTL2_uc001pbd.2_Intron|SYTL2_uc001pbb.2_Intron|SYTL2_uc001pbc.2_Intron|SYTL2_uc010rtf.1_Intron	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g						intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		ttatgttttcttttttttttt	0.095													4	3	---	---	---	---	
OASL	8638	broad.mit.edu	37	12	121465109	121465109	+	Intron	DEL	A	-	-	rs35811089		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121465109delA	uc001tzj.1	-						OASL_uc001tzk.1_Intron	NM_003733	NP_003724	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like isoform a						interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoplasm|nucleolus	ATP binding|DNA binding|double-stranded RNA binding|thyroid hormone receptor binding|transferase activity			skin(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CAAAGCACTGAAATGGTCTTC	0.299													5	3	---	---	---	---	
HOMEZ	57594	broad.mit.edu	37	14	23764733	23764733	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23764733delA	uc001wjb.2	-							NM_020834	NP_065885	Q8IX15	HOMEZ_HUMAN	homeodomain leucine zipper protein							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		CTTCATTCTTAAAAAAAAAAA	0.403													6	3	---	---	---	---	
SCG3	29106	broad.mit.edu	37	15	51980761	51980763	+	Intron	DEL	AGG	-	-	rs138925498		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51980761_51980763delAGG	uc002abh.2	+						SCG3_uc010ufz.1_Intron	NM_013243	NP_037375	Q8WXD2	SCG3_HUMAN	secretogranin III isoform 1 precursor						platelet activation|platelet degranulation	extracellular region|stored secretory granule				ovary(1)	1				all cancers(107;0.00488)		ttttttttctaggagtttatcat	0.054													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	72091403	72091406	+	IGR	DEL	TCTC	-	-	rs113139413		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72091403_72091406delTCTC								THSD4 (15681 upstream) : NR2E3 (11488 downstream)																							cttccttccttctctccttccttc	0.167													4	2	---	---	---	---	
WDR61	80349	broad.mit.edu	37	15	78585308	78585309	+	Intron	INS	-	T	T	rs71947790		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78585308_78585309insT	uc002bdn.2	-						WDR61_uc002bdo.2_Intron|WDR61_uc010umz.1_Intron|WDR61_uc010una.1_Intron	NM_025234	NP_079510	Q9GZS3	WDR61_HUMAN	WD repeat domain 61								protein binding			ovary(1)|skin(1)	2						GGACTTTAAGATTTTTTTTTTT	0.337													5	3	---	---	---	---	
TTLL13	440307	broad.mit.edu	37	15	90795056	90795057	+	Intron	INS	-	A	A	rs12438066		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90795056_90795057insA	uc002bpd.1	+						TTLL13_uc002bpe.1_Intron	NM_001029964	NP_001025135	A6NNM8	TTL13_HUMAN	tubulin tyrosine ligase-like family, member 13						protein modification process		ATP binding|tubulin-tyrosine ligase activity				0	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)			CAGTAAACAAGAAAAAAAAAAA	0.356													4	3	---	---	---	---	
BOLA2	552900	broad.mit.edu	37	16	30027022	30027023	+	Intron	INS	-	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30027022_30027023insT	uc010bzb.1	-						uc002dtf.2_Intron|DOC2A_uc002dvq.2_5'Flank			Q9H3K6	BOLA2_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0						cttcctttttcttttttttttt	0.025													4	2	---	---	---	---	
C16orf70	80262	broad.mit.edu	37	16	67165083	67165084	+	Intron	INS	-	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67165083_67165084insT	uc002erc.2	+						C16orf70_uc002erd.2_Intron|C16orf70_uc002ere.1_Intron	NM_025187	NP_079463	Q9BSU1	CP070_HUMAN	lin-10											ovary(2)	2		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		ATTGGTAATAGttttttttttt	0.173													5	3	---	---	---	---	
LOC283922	283922	broad.mit.edu	37	16	74378976	74378976	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74378976delT	uc002fcr.2	-						LOC283922_uc010vms.1_Intron					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						ACCTCTTGAAttttttttttt	0.179													4	2	---	---	---	---	
FBXO39	162517	broad.mit.edu	37	17	6690865	6690866	+	3'UTR	INS	-	TC	TC	rs4606762		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6690865_6690866insTC	uc010vtg.1	+	4					FBXO39_uc010cls.1_Intron	NM_153230	NP_694962	Q8N4B4	FBX39_HUMAN	F-box protein 39											ovary(1)|skin(1)	2						CCACTTTTTTTTTTTGTCAGCT	0.470													15	8	---	---	---	---	
KRT27	342574	broad.mit.edu	37	17	38937676	38937677	+	Intron	INS	-	TC	TC	rs143946934	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38937676_38937677insTC	uc002hvg.2	-							NM_181537	NP_853515	Q7Z3Y8	K1C27_HUMAN	keratin 27							cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.000812)				TTTAAGTATGGTCTCTCTCTCT	0.183													1	5	---	---	---	---	
ATP6V0A1	535	broad.mit.edu	37	17	40634913	40634914	+	Intron	INS	-	AAA	AAA			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40634913_40634914insAAA	uc002hzr.2	+						ATP6V0A1_uc002hzq.2_Intron|ATP6V0A1_uc002hzs.2_Intron|ATP6V0A1_uc010wgj.1_Intron|ATP6V0A1_uc010wgk.1_Intron|ATP6V0A1_uc010cyg.2_Intron|ATP6V0A1_uc010wgl.1_Intron	NM_001130021	NP_001123493	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytoplasmic vesicle membrane|endosome membrane|Golgi apparatus|integral to membrane|melanosome|nucleus|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		aactctgtctcaaaaaaaaaaa	0.144													3	3	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	63898116	63898125	+	Intron	DEL	GTGGGGGGGA	-	-	rs56378454		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63898116_63898125delGTGGGGGGGA	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			GGGGGGGGGGGTGGGGGGGAGAAAAACAAA	0.414													4	2	---	---	---	---	
NOL11	25926	broad.mit.edu	37	17	65735158	65735158	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65735158delA	uc002jgd.1	+						NOL11_uc010wql.1_Intron|NOL11_uc010deu.1_Intron|SNORA38B_uc010dev.2_5'Flank	NM_015462	NP_056277	Q9H8H0	NOL11_HUMAN	nucleolar protein 11							nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			ATAGAATTTTACTTCTGGTTT	0.363													112	50	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76490463	76490463	+	5'Flank	DEL	C	-	-	rs34910684		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76490463delC	uc002jvt.1	+											Homo sapiens cDNA FLJ45552 fis, clone BRTHA2038279.																		TTGCCTGAAGCCCCCCCAGCC	0.627													4	4	---	---	---	---	
ANKRD12	23253	broad.mit.edu	37	18	9196187	9196188	+	Intron	INS	-	ACAC	ACAC	rs144984243		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9196187_9196188insACAC	uc002knv.2	+						ANKRD12_uc010wzn.1_Intron|ANKRD12_uc002knw.2_Intron|ANKRD12_uc002knx.2_Intron	NM_015208	NP_056023	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12 isoform 1							nucleus				ovary(2)|central_nervous_system(1)	3						ATAGAATTTTTacacacacaca	0.208													6	3	---	---	---	---	
C3	718	broad.mit.edu	37	19	6707059	6707059	+	Intron	DEL	C	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6707059delC	uc002mfm.2	-							NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor						complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)		ACGGCCCCCTCCCCCTGTCCC	0.706													35	16	---	---	---	---	
KANK3	256949	broad.mit.edu	37	19	8398950	8398961	+	In_Frame_Del	DEL	TCGCTGTCGCCA	-	-	rs111751275		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8398950_8398961delTCGCTGTCGCCA	uc010dwa.2	-	5	1533_1544	c.1467_1478delTGGCGACAGCGA	c.(1465-1479)GATGGCGACAGCGAG>GAG	p.DGDS489del	KANK3_uc002mjp.1_In_Frame_Del_p.MATA1del	NM_198471	NP_940873	Q6NY19	KANK3_HUMAN	ankyrin repeat domain 47	489_492											0						GCCACCGTTCTCGCTGTCGCCATCGCTGTCGC	0.693													7	4	---	---	---	---	
KANK2	25959	broad.mit.edu	37	19	11288976	11288977	+	Intron	INS	-	G	G	rs139114831	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11288976_11288977insG	uc010dxv.2	-						KANK2_uc002mqm.2_Intron|KANK2_uc002mqo.3_Intron|KANK2_uc002mqp.1_Intron	NM_015493	NP_056308	Q63ZY3	KANK2_HUMAN	ankyrin repeat domain 25 isoform 1												0						TGAATGGAGGAGGGGCGGGAAG	0.505													7	4	---	---	---	---	
AP1M1	8907	broad.mit.edu	37	19	16338125	16338125	+	Intron	DEL	G	-	-	rs113011132		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16338125delG	uc002ndu.2	+						AP1M1_uc002ndv.2_Intron|AP1M1_uc010xpd.1_Intron	NM_032493	NP_115882	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit						cellular membrane organization|endosome to melanosome transport|interspecies interaction between organisms|intracellular protein transport|melanosome organization|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding			ovary(3)|breast(1)	4						gatggccgctggggactcagc	0.299													2	6	---	---	---	---	
CAPN12	147968	broad.mit.edu	37	19	39232227	39232227	+	Intron	DEL	A	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39232227delA	uc002ojd.1	-							NM_144691	NP_653292	Q6ZSI9	CAN12_HUMAN	calpain 12						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			aaaaaaaaagaaaaaaaaaaa	0.209													4	2	---	---	---	---	
EML2	24139	broad.mit.edu	37	19	46130218	46130219	+	Intron	INS	-	T	T	rs5828242		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46130218_46130219insT	uc002pcn.2	-						EML2_uc002pco.2_Intron|EML2_uc002pcp.2_Intron|EML2_uc010xxl.1_Intron|EML2_uc010xxm.1_Intron|EML2_uc010xxn.1_Intron|EML2_uc010xxo.1_Intron|EML2_uc010ekj.2_Intron|EML2_uc010ekk.1_Intron	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like						sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CTGAACttttcttttttttttt	0.252													5	4	---	---	---	---	
STRN4	29888	broad.mit.edu	37	19	47225790	47225791	+	Intron	INS	-	T	T	rs142007362	by1000genomes	TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47225790_47225791insT	uc002pfl.2	-						STRN4_uc002pfm.2_Intron|STRN4_uc010xyf.1_Intron	NM_013403	NP_037535	Q9NRL3	STRN4_HUMAN	zinedin isoform 1							cytoplasm|membrane	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding				0		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		TGTTTTGGGGCGGGGGAAGAGG	0.678													3	3	---	---	---	---	
PRR12	57479	broad.mit.edu	37	19	50100809	50100810	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50100809_50100810delCT	uc002poo.3	+	4	3217_3218	c.3217_3218delCT	c.(3217-3219)CTCfs	p.L1073fs		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	252	Pro-rich.						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)		AAAGAAGCTGCTCAAGACATCC	0.520													7	4	---	---	---	---	
MIR1283-1	100302265	broad.mit.edu	37	19	54191516	54191536	+	5'Flank	DEL	GTTTGAGAACAAAACTCGGGA	-	-	rs11274495		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54191516_54191536delGTTTGAGAACAAAACTCGGGA	hsa-mir-1283-1|MI0003832	+						MIR520A_hsa-mir-520a|MI0003149_5'Flank																	0						TGCTTTTTCTGTTTGAGAACAAAACTCGGGAGGATTGTCCC	0.416													4	3	---	---	---	---	
LILRB3	11025	broad.mit.edu	37	19	54725530	54725531	+	Intron	INS	-	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54725530_54725531insT	uc002qef.1	-						LILRB3_uc002qee.1_Intron|LILRB3_uc002qeh.1_Intron|LILRB3_uc002qeg.1_Intron|LILRB3_uc002qei.1_Intron|LILRA6_uc002qek.1_Intron|LILRB3_uc010erh.1_Intron|LILRB3_uc002qej.1_RNA|LILRA6_uc002qel.1_Intron|LILRA6_uc002qem.1_Intron|LILRB3_uc002qen.1_Intron|LILRB3_uc002qeo.1_Intron|LILRB3_uc002qep.1_Intron|LILRB3_uc002qeq.1_Intron|LILRB3_uc002qer.1_Intron|LILRB3_uc002qes.1_Intron|LILRA6_uc010yep.1_Intron|LILRA6_uc010yeq.1_Intron	NM_006864	NP_006855	O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor,						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	transmembrane receptor activity			skin(2)|ovary(1)	3	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGAACGTGGTCGAGGGCTCCTC	0.589													6	5	---	---	---	---	
NLRP7	199713	broad.mit.edu	37	19	55452576	55452576	+	Intron	DEL	A	-	-	rs111382825		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55452576delA	uc002qih.3	-						NLRP7_uc002qig.3_Intron|NLRP7_uc002qii.3_Intron|NLRP7_uc010esk.2_Intron|NLRP7_uc010esl.2_Intron	NM_206828	NP_996611	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7								ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)		ctaaaaatacaaaaaaaaaaa	0.000													3	4	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26271971	26271972	+	Intron	DEL	GT	-	-	rs71753108		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26271971_26271972delGT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						AAGGAAGCCCgtgtgtgtgtgt	0.327													3	3	---	---	---	---	
TCN2	6948	broad.mit.edu	37	22	31012013	31012016	+	Intron	DEL	TGGA	-	-	rs145631512		TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31012013_31012016delTGGA	uc003aip.1	+						TCN2_uc003aiq.1_Intron|TCN2_uc003air.1_Intron	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor						cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAGAAATGTTtggatggatggatg	0.333													6	3	---	---	---	---	
GCAT	23464	broad.mit.edu	37	22	38209775	38209775	+	Intron	DEL	T	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38209775delT	uc003atz.2	+						GCAT_uc003aua.1_Intron	NM_014291	NP_055106	O75600	KBL_HUMAN	glycine C-acetyltransferase precursor						biosynthetic process|cellular amino acid metabolic process		glycine C-acetyltransferase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups				0	Melanoma(58;0.045)				Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	agcattattcttttttttttt	0.000													5	3	---	---	---	---	
FAM133A	286499	broad.mit.edu	37	X	92965209	92965210	+	3'UTR	INS	-	T	T			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:92965209_92965210insT	uc004efr.1	+	4						NM_173698	NP_775969	Q8N9E0	F133A_HUMAN	hypothetical protein LOC286499												0						GTTCCCCTGTGTTAGTAGAATT	0.347													39	39	---	---	---	---	
TMEM164	84187	broad.mit.edu	37	X	109416313	109416324	+	Intron	DEL	CAGAAAACCGAG	-	-			TCGA-B2-3924-01A-01D-1458-08	TCGA-B2-3924-10A-01D-1458-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109416313_109416324delCAGAAAACCGAG	uc004eom.2	+						TMEM164_uc004eol.2_Intron|TMEM164_uc010npq.2_Intron|TMEM164_uc004eon.1_5'Flank	NM_032227	NP_115603	Q5U3C3	TM164_HUMAN	transmembrane protein 164 isoform b							integral to membrane				large_intestine(1)|lung(1)|skin(1)	3						TTGACTCACTCAGAAAACCGAGGGGAGAGAAG	0.524													3	5	---	---	---	---	
