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
RLF	6018	broad.mit.edu	37	1	40704122	40704122	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40704122G>A	uc001cfc.3	+	8	3779	c.3748G>A	c.(3748-3750)GAA>AAA	p.E1250K	RLF_uc001cfd.3_Missense_Mutation_p.E941K	NM_012421	NP_036553	Q13129	RLF_HUMAN	rearranged L-myc fusion	1250					chromosome organization|DNA integration|DNA mediated transformation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			ovary(2)|pancreas(1)	3	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			TAAAAAGGATGAATGTAGTTC	0.393													12	20	---	---	---	---	PASS
MUTYH	4595	broad.mit.edu	37	1	45796978	45796978	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45796978A>G	uc001cnm.2	-	14	1559	c.1343T>C	c.(1342-1344)CTG>CCG	p.L448P	MUTYH_uc009vxn.2_Missense_Mutation_p.L273P|MUTYH_uc001cnf.2_Missense_Mutation_p.L423P|MUTYH_uc009vxo.2_Missense_Mutation_p.L423P|MUTYH_uc001cng.2_Missense_Mutation_p.L434P|MUTYH_uc001cnj.2_Missense_Mutation_p.L331P|MUTYH_uc001cni.2_Missense_Mutation_p.L423P|MUTYH_uc001cnh.2_Missense_Mutation_p.L424P|MUTYH_uc001cno.2_Missense_Mutation_p.L331P|MUTYH_uc001cnk.2_Missense_Mutation_p.L308P|MUTYH_uc010oll.1_Missense_Mutation_p.L132P|MUTYH_uc001cnl.2_Missense_Mutation_p.L437P|MUTYH_uc009vxp.2_Missense_Mutation_p.L451P|MUTYH_uc001cnn.2_Missense_Mutation_p.L438P	NM_012222	NP_036354	Q9UIF7	MUTYH_HUMAN	mutY homolog isoform 1	448	Nudix hydrolase.				depurination|mismatch repair	nucleoplasm	4 iron, 4 sulfur cluster binding|DNA N-glycosylase activity|endonuclease activity|metal ion binding|MutSalpha complex binding				0	Acute lymphoblastic leukemia(166;0.155)					TTGATATGTCAGCTTGATGTG	0.537			Mis			colorectal		BER_DNA_glycosylases	MUTYH-associated_polyposis				49	88	---	---	---	---	PASS
CLCA1	1179	broad.mit.edu	37	1	86957042	86957042	+	Silent	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86957042G>A	uc001dlt.2	+	9	1581	c.1452G>A	c.(1450-1452)CAG>CAA	p.Q484Q	CLCA1_uc001dls.1_Silent_p.Q423Q	NM_001285	NP_001276	A8K7I4	CLCA1_HUMAN	chloride channel accessory 1 precursor	484					calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		CTGTCTCTCAGCGCTCCATCC	0.388													81	142	---	---	---	---	PASS
ATP1A1	476	broad.mit.edu	37	1	116941357	116941357	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116941357G>A	uc001ege.2	+	16	2578	c.2239G>A	c.(2239-2241)GAC>AAC	p.D747N	ATP1A1_uc010owv.1_Missense_Mutation_p.D716N|ATP1A1_uc010oww.1_Missense_Mutation_p.D747N|ATP1A1_uc010owx.1_Missense_Mutation_p.D716N|C1orf203_uc009whb.2_Intron|ATP1A1_uc001egh.2_5'Flank	NM_000701	NP_000692	P05023	AT1A1_HUMAN	Na+/K+ -ATPase alpha 1 subunit isoform a	747	Cytoplasmic (Potential).				ATP biosynthetic process	melanosome|sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Captopril(DB01197)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Esomeprazole(DB00736)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Ouabain(DB01092)|Pantoprazole(DB00213)|Trichlormethiazide(DB01021)	GCAAGCTGCTGACATGATTCT	0.463													100	217	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145302695	145302695	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145302695C>T	uc001end.3	+	8	1168	c.1133C>T	c.(1132-1134)ACC>ATC	p.T378I	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_5'UTR|NBPF10_uc001emq.1_Missense_Mutation_p.T107I	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	378											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CGAGAGCTGACCCAGTTAAAG	0.507													4	41	---	---	---	---	PASS
SETDB1	9869	broad.mit.edu	37	1	150923946	150923946	+	Silent	SNP	T	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150923946T>C	uc001evu.2	+	14	2509	c.2319T>C	c.(2317-2319)TGT>TGC	p.C773C	SETDB1_uc001evv.2_Silent_p.C773C|SETDB1_uc009wmg.1_Silent_p.C773C	NM_001145415	NP_001138887	Q15047	SETB1_HUMAN	SET domain, bifurcated 1 isoform 1	773	Pre-SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|Golgi apparatus|nucleus|plasma membrane	DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			TAGAAGAGTGTCTACCCACAG	0.468													5	119	---	---	---	---	PASS
NIT1	4817	broad.mit.edu	37	1	161088477	161088477	+	Intron	SNP	C	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161088477C>G	uc001fxv.1	+						PFDN2_uc001fxu.2_5'Flank|NIT1_uc001fxw.2_Intron|NIT1_uc001fxx.1_5'UTR|NIT1_uc001fxy.1_Intron|NIT1_uc010pka.1_Intron	NM_005600	NP_005591	Q86X76	NIT1_HUMAN	nitrilase 1						nitrogen compound metabolic process	mitochondrion	nitrilase activity				0	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			ACTGGCAGGGCCCTGATTCAG	0.443													7	51	---	---	---	---	PASS
CD247	919	broad.mit.edu	37	1	167404444	167404444	+	Intron	SNP	T	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167404444T>A	uc001gei.3	-						CD247_uc001gej.3_Intron|CD247_uc001gek.2_Silent_p.G176G	NM_198053	NP_932170	P20963	CD3Z_HUMAN	T-cell receptor zeta chain isoform 1 precursor						interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)			ctccagcccttcctccagccc	0.055													4	28	---	---	---	---	PASS
QSOX1	5768	broad.mit.edu	37	1	180165532	180165532	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180165532T>G	uc001gnz.2	+	12	1679	c.1604T>G	c.(1603-1605)TTC>TGC	p.F535C	QSOX1_uc001gny.2_Missense_Mutation_p.F535C|QSOX1_uc001goa.2_Missense_Mutation_p.F535C|QSOX1_uc001goc.2_Missense_Mutation_p.F77C|FLJ23867_uc001god.3_5'Flank	NM_002826	NP_002817	O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1 isoform a	535					cell redox homeostasis|protein thiol-disulfide exchange	extracellular space|integral to Golgi membrane	flavin-linked sulfhydryl oxidase activity			ovary(1)|central_nervous_system(1)	2						AAGGCCCACTTCTCCCCAAGC	0.622													17	67	---	---	---	---	PASS
SMC6	79677	broad.mit.edu	37	2	17876536	17876536	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17876536C>A	uc002rco.2	-	23	2857	c.2561G>T	c.(2560-2562)TGC>TTC	p.C854F	SMC6_uc010exo.2_Missense_Mutation_p.C854F|SMC6_uc002rcn.2_Missense_Mutation_p.C854F	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	854	Potential.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					ACGCTCTGGGCAGATTTGTCT	0.338													9	251	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21242762	21242762	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21242762C>A	uc002red.2	-	19	2960	c.2832G>T	c.(2830-2832)TTG>TTT	p.L944F		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	944	Heparin-binding.				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	TGGTAGAGACCAAATGTAATG	0.448													57	107	---	---	---	---	PASS
HK2	3099	broad.mit.edu	37	2	75107668	75107668	+	Silent	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75107668C>T	uc002snd.2	+	10	3468	c.1542C>T	c.(1540-1542)ACC>ACT	p.T514T		NM_000189	NP_000180	P52789	HXK2_HUMAN	hexokinase 2	514	Catalytic.				apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2						TGCTGCCCACCTACGTGTGTG	0.597													9	87	---	---	---	---	PASS
TMEM182	130827	broad.mit.edu	37	2	103431419	103431419	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103431419C>T	uc010fjb.2	+	5	869	c.682C>T	c.(682-684)CAT>TAT	p.H228Y	TMEM182_uc002tcc.3_Missense_Mutation_p.H185Y|TMEM182_uc002tcd.3_Missense_Mutation_p.H132Y|TMEM182_uc010ywe.1_RNA	NM_144632	NP_653233	Q6ZP80	TM182_HUMAN	transmembrane protein 182 precursor	228	Cytoplasmic (Potential).					integral to membrane					0						TATTCAGATACATCACTAAAT	0.358													16	261	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152436113	152436113	+	Intron	SNP	A	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152436113A>C	uc010fnx.2	-						NEB_uc002txr.2_Missense_Mutation_p.C203W	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3						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)		TGGCGCTGCGACAGCCAATGT	0.428													15	44	---	---	---	---	PASS
DPP4	1803	broad.mit.edu	37	2	162894910	162894910	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162894910A>C	uc002ubz.2	-	8	1076	c.515T>G	c.(514-516)ATT>AGT	p.I172S	DPP4_uc010fpb.2_5'UTR|DPP4_uc002uca.1_RNA|DPP4_uc002ucb.1_RNA	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV	172	Extracellular (Potential).				cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	TTTAACATAAATGTCATTGTT	0.303													23	59	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179596909	179596909	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179596909T>G	uc010zfg.1	-	54	13279	c.13055A>C	c.(13054-13056)GAG>GCG	p.E4352A	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.E1013A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	5279							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCAGTAGACTCCACAAAAGA	0.438													13	191	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188218	10188218	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188218G>T	uc003bvc.2	+	2	574	c.361G>T	c.(361-363)GAT>TAT	p.D121Y	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	121	Involved in binding to CCT complex.				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.D121Y(2)|p.D121E(2)|p.D121G(2)|p.R120fs*38(1)|p.?(1)|p.D121_A122del(1)|p.R120fs*34(1)|p.D121*(1)|p.A122fs*7(1)|p.D121D(1)|p.D121fs*11(1)|p.D121fs*10(1)|p.D121fs*12(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)		GCTCTTCAGAGATGCAGGGAC	0.378		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				94	80	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52443574	52443574	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52443574G>A	uc003ddx.2	-	3	233	c.118C>T	c.(118-120)CAG>TAG	p.Q40*	PHF7_uc003ddy.2_5'Flank|PHF7_uc003ddz.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	40					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	p.Q40*(1)		pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		ACTCACCCCTGACATTTGCTC	0.582			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								65	60	---	---	---	---	PASS
LRIG1	26018	broad.mit.edu	37	3	66436782	66436782	+	Intron	SNP	G	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66436782G>T	uc003dmx.2	-						SLC25A26_uc011bft.1_RNA|LRIG1_uc011bfu.1_Intron|LRIG1_uc003dmw.2_Intron|LRIG1_uc010hnz.2_Intron|LRIG1_uc010hoa.2_Intron	NM_015541	NP_056356	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like							integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		AGAGGAACCAGCTGCTGTTCA	0.537													10	69	---	---	---	---	PASS
CD86	942	broad.mit.edu	37	3	121825286	121825286	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121825286G>C	uc003eet.2	+	4	758	c.642G>C	c.(640-642)ATG>ATC	p.M214I	CD86_uc011bjo.1_Missense_Mutation_p.M132I|CD86_uc011bjp.1_Missense_Mutation_p.M102I|CD86_uc003eeu.2_Missense_Mutation_p.M208I	NM_175862	NP_787058	P42081	CD86_HUMAN	CD86 antigen isoform 1	214	Ig-like C2-type.|Extracellular (Potential).				interspecies interaction between organisms|positive regulation of cell proliferation|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of lymphotoxin A biosynthetic process|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation		coreceptor activity|protein binding			pancreas(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)	CGAGCAATATGACCATCTTCT	0.393													52	92	---	---	---	---	PASS
PAK2	5062	broad.mit.edu	37	3	196539709	196539709	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196539709A>G	uc003fwy.3	+	10	1244	c.922A>G	c.(922-924)AAC>GAC	p.N308D		NM_002577	NP_002568	Q13177	PAK2_HUMAN	p21-activated kinase 2	308	Protein kinase.				axon guidance|cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of apoptosis|regulation of defense response to virus by virus|regulation of growth|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|nucleus|perinuclear region of cytoplasm|plasma membrane	ATP binding|identical protein binding|protein kinase binding|protein serine/threonine kinase activity|protein tyrosine kinase activator activity			ovary(1)|lung(1)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		CAACATCGTTAACTTTTTGGA	0.383													8	156	---	---	---	---	PASS
ANKRD17	26057	broad.mit.edu	37	4	73956463	73956463	+	Silent	SNP	T	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73956463T>A	uc003hgp.2	-	29	6999	c.6882A>T	c.(6880-6882)TCA>TCT	p.S2294S	ANKRD17_uc003hgo.2_Silent_p.S2181S|ANKRD17_uc003hgq.2_Silent_p.S2043S|ANKRD17_uc003hgr.2_Silent_p.S2293S	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	2294					interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTAAAGGATCTGAATTTGGCA	0.433													97	167	---	---	---	---	PASS
ANK2	287	broad.mit.edu	37	4	114290829	114290829	+	Silent	SNP	A	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114290829A>T	uc003ibe.3	+	43	11578	c.11478A>T	c.(11476-11478)ATA>ATT	p.I3826I	ANK2_uc003ibd.3_Silent_p.I1732I|ANK2_uc003ibf.3_Silent_p.I1741I|ANK2_uc011cgc.1_Silent_p.I917I|ANK2_uc003ibg.3_Silent_p.I725I|ANK2_uc003ibh.3_Silent_p.I415I|ANK2_uc011cgd.1_Silent_p.I1128I	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	3793					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CTCCCATCATACAAGAACCCG	0.582													10	83	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	4	165980637	165980637	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165980637T>G	uc011cjl.1	+	1	338	c.338T>G	c.(337-339)ATG>AGG	p.M113R		NM_001105575	NP_001099045			tripartite motif-containing 75																		GAGGACCTGATGGTGTTGTGT	0.522													14	82	---	---	---	---	PASS
NEIL3	55247	broad.mit.edu	37	4	178283613	178283613	+	Silent	SNP	T	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178283613T>A	uc003iut.2	+	10	1923	c.1806T>A	c.(1804-1806)ATT>ATA	p.I602I		NM_018248	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3	602					base-excision repair|nucleotide-excision repair	nucleus	bubble DNA binding|damaged DNA binding|DNA N-glycosylase activity|DNA-(apurinic or apyrimidinic site) lyase activity|double-stranded DNA binding|single-stranded DNA binding|zinc ion binding			lung(2)|ovary(1)|central_nervous_system(1)	4		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		TAAAAATTATTCCTGGATGCT	0.358								BER_DNA_glycosylases					55	81	---	---	---	---	PASS
SORBS2	8470	broad.mit.edu	37	4	186508841	186508841	+	Silent	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186508841C>T	uc003iyl.2	-	21	4101	c.3243G>A	c.(3241-3243)GGG>GGA	p.G1081G	SORBS2_uc003iyh.2_Silent_p.G805G|SORBS2_uc011ckw.1_Silent_p.G642G|SORBS2_uc003iyi.2_Silent_p.G712G|SORBS2_uc011ckx.1_Silent_p.G647G|SORBS2_uc003iyk.2_Silent_p.G625G|SORBS2_uc003iym.2_Silent_p.G1181G|SORBS2_uc011cku.1_Silent_p.G473G|SORBS2_uc011ckv.1_Silent_p.G985G|SORBS2_uc003iyd.2_Silent_p.G780G|SORBS2_uc003iye.2_Silent_p.G654G|SORBS2_uc003iya.2_Silent_p.G601G|SORBS2_uc003iyb.2_Silent_p.G554G|SORBS2_uc003iyc.2_Silent_p.G534G|SORBS2_uc003iyg.2_Silent_p.G1195G|SORBS2_uc003iyf.2_Silent_p.G617G	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2	1081	SH3 3.					actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TTCTTGAGGTCCCTGAAAATA	0.493													11	111	---	---	---	---	PASS
FAM173B	134145	broad.mit.edu	37	5	10250009	10250009	+	5'UTR	SNP	T	A	A	rs35316698		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10250009T>A	uc003jeo.2	-	1					FAM173B_uc003jep.2_RNA|FAM173B_uc010itr.2_5'UTR|CCT5_uc011cmq.1_5'Flank|CCT5_uc003jeq.2_5'Flank|CCT5_uc003jer.2_5'Flank|CCT5_uc010its.2_5'Flank|CCT5_uc011cmr.1_5'Flank|CCT5_uc011cms.1_5'Flank|CCT5_uc011cmt.1_5'Flank	NM_199133	NP_954584	Q6P4H8	F173B_HUMAN	hypothetical protein LOC134145							integral to membrane				kidney(1)|central_nervous_system(1)	2						ACAGCGTTTTTaaaaaaaaaa	0.483													3	18	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	89989763	89989763	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89989763T>A	uc003kju.2	+	33	7286	c.7190T>A	c.(7189-7191)GTG>GAG	p.V2397E	GPR98_uc003kjt.2_Missense_Mutation_p.V103E|GPR98_uc003kjv.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	2397	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)		ATTGATGTAGTGGCTCTGGCA	0.448													27	119	---	---	---	---	PASS
PCDHAC2	56134	broad.mit.edu	37	5	140389673	140389673	+	3'UTR	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140389673C>A	uc003lii.2	+	4					PCDHA1_uc003lha.2_3'UTR|PCDHA1_uc003lhb.2_3'UTR|PCDHA2_uc003lhd.2_3'UTR|PCDHA3_uc003lhf.2_3'UTR|PCDHA4_uc003lhi.2_3'UTR|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_3'UTR|PCDHA6_uc003lhn.2_3'UTR|PCDHA6_uc003lho.2_3'UTR|PCDHA7_uc003lhq.2_3'UTR|PCDHA8_uc003lhs.2_3'UTR|PCDHA9_uc003lhu.2_3'UTR|PCDHA10_uc003lhw.2_3'UTR|PCDHA10_uc003lhx.2_3'UTR|PCDHA11_uc003lia.2_3'UTR|PCDHA12_uc003lic.2_3'UTR|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_3'UTR|PCDHAC1_uc003lih.2_3'UTR	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGTCTAGAACGCATTTAACA	0.423													11	274	---	---	---	---	PASS
PCDHGA7	56108	broad.mit.edu	37	5	140762766	140762766	+	Silent	SNP	G	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140762766G>C	uc003lka.1	+	1	300	c.300G>C	c.(298-300)GCG>GCC	p.A100A	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.A100A	NM_018920	NP_061743	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7 isoform 1	100	Cadherin 1.|Extracellular (Potential).				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)			CTCAGAGTGCGCGGTGTCTGG	0.483													4	61	---	---	---	---	PASS
HMGXB3	22993	broad.mit.edu	37	5	149431465	149431465	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149431465T>A	uc003lrk.3	+	20	4165	c.3589T>A	c.(3589-3591)TTG>ATG	p.L1197M		NM_014983	NP_055798	Q12766	HMGX3_HUMAN	HMG box domain containing 3	1443						nucleus	DNA binding|kinase activity			kidney(1)|central_nervous_system(1)	2						GTGCCCTGAATTGGCACCTTA	0.602													29	124	---	---	---	---	PASS
ADAMTS2	9509	broad.mit.edu	37	5	178566983	178566983	+	Silent	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178566983G>A	uc003mjw.2	-	11	1683	c.1683C>T	c.(1681-1683)GAC>GAT	p.D561D		NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	561	TSP type-1 1.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		CCCAGCTGCCGTCCCGTTTGA	0.592													7	147	---	---	---	---	PASS
BTNL9	153579	broad.mit.edu	37	5	180475150	180475150	+	Silent	SNP	C	T	T	rs112433732		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180475150C>T	uc003mmt.2	+	3	564	c.333C>T	c.(331-333)ATC>ATT	p.I111I	BTNL9_uc011dhi.1_Silent_p.I42I	NM_152547	NP_689760	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9 precursor	111	Extracellular (Potential).|Ig-like V-type.					integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGACGACATCGCCTATGGCA	0.587													7	48	---	---	---	---	PASS
VARS	7407	broad.mit.edu	37	6	31745339	31745339	+	3'UTR	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31745339G>A	uc003nxe.2	-	30					C6orf27_uc011dog.1_5'Flank|C6orf27_uc003nxd.2_5'Flank|C6orf27_uc011doh.1_5'Flank	NM_006295	NP_006286	P26640	SYVC_HUMAN	valyl-tRNA synthetase						translational elongation|valyl-tRNA aminoacylation	cytosol	ATP binding|protein binding|valine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3					L-Valine(DB00161)	ATGGTGAGCCGCTGGGGGTGA	0.572													51	97	---	---	---	---	PASS
ENPP1	5167	broad.mit.edu	37	6	132181589	132181589	+	Silent	SNP	T	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132181589T>C	uc011ecf.1	+	8	878	c.858T>C	c.(856-858)GCT>GCC	p.A286A	ENPP1_uc003qcy.2_5'Flank	NM_006208	NP_006199	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	286	Phosphodiesterase.|Extracellular (Potential).				3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	AAATGAATGCTTCCTTTTCAC	0.299													6	164	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152647465	152647465	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152647465G>A	uc010kiw.2	-	79	15861	c.15259C>T	c.(15259-15261)CGG>TGG	p.R5087W	SYNE1_uc003qot.3_Missense_Mutation_p.R5016W|SYNE1_uc003qou.3_Missense_Mutation_p.R5087W|SYNE1_uc010kiz.2_Missense_Mutation_p.R842W	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5087	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CCAGAGTCCCGGCTCATCCTC	0.478										HNSCC(10;0.0054)			16	127	---	---	---	---	PASS
SCRN1	9805	broad.mit.edu	37	7	29963599	29963599	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29963599C>A	uc010kvp.2	-	7	1423	c.1219G>T	c.(1219-1221)GAC>TAC	p.D407Y	SCRN1_uc011jzy.1_Missense_Mutation_p.D339Y|SCRN1_uc003tak.2_Missense_Mutation_p.D407Y|SCRN1_uc011jzz.1_Missense_Mutation_p.D407Y|SCRN1_uc011kaa.1_Missense_Mutation_p.D427Y|SCRN1_uc011jzw.1_Missense_Mutation_p.D274Y|SCRN1_uc011jzx.1_Missense_Mutation_p.D230Y	NM_001145515	NP_001138987	Q12765	SCRN1_HUMAN	secernin 1 isoform c	407					exocytosis|proteolysis	cytoplasm|nuclear membrane	dipeptidase activity			ovary(2)	2						ATCTCCGTGTCAACACAGTCA	0.483													55	105	---	---	---	---	PASS
LRRC17	10234	broad.mit.edu	37	7	102579923	102579923	+	Silent	SNP	T	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102579923T>G	uc003vau.2	+	3	1208	c.819T>G	c.(817-819)CTT>CTG	p.L273L	FBXL13_uc010liq.1_Intron|FBXL13_uc003vaq.2_Intron|FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Intron|LRRC17_uc003vat.2_Silent_p.L273L	NM_001031692	NP_001026862	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17 isoform 1	273	LRR 4.				bone marrow development|negative regulation of osteoclast differentiation|ossification	extracellular space				ovary(1)	1						TTGTTAAACTTGACTTGTCAT	0.348													12	188	---	---	---	---	PASS
AASS	10157	broad.mit.edu	37	7	121766489	121766489	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121766489T>A	uc003vka.2	-	3	508	c.412A>T	c.(412-414)AAA>TAA	p.K138*	AASS_uc011knu.1_RNA|AASS_uc011knv.1_RNA|AASS_uc003vkb.2_Nonsense_Mutation_p.K138*|AASS_uc011knw.1_Intron	NM_005763	NP_005754	Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase precursor	138	Lysine-ketoglutarate reductase.				protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)	TCCACCATTTTCTCATAATCA	0.398													106	202	---	---	---	---	PASS
EPHB6	2051	broad.mit.edu	37	7	142563846	142563846	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142563846G>T	uc011kst.1	+	9	2021	c.1234G>T	c.(1234-1236)GGC>TGC	p.G412C	EPHB6_uc011ksu.1_Missense_Mutation_p.G412C|EPHB6_uc003wbs.2_Missense_Mutation_p.G120C|EPHB6_uc003wbt.2_Translation_Start_Site|EPHB6_uc003wbu.2_Missense_Mutation_p.G120C|EPHB6_uc003wbv.2_5'Flank	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	412	Extracellular (Potential).|Fibronectin type-III 1.					extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19	Melanoma(164;0.059)					GGAGTGTGAAGGCCGCCAGGA	0.642													11	34	---	---	---	---	PASS
XKR6	286046	broad.mit.edu	37	8	10782282	10782282	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10782282G>A	uc003wtk.1	-	2	850	c.823C>T	c.(823-825)CGC>TGC	p.R275C		NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related	275						integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		CAGTAGAAGCGTCGCTGGTGT	0.572													29	62	---	---	---	---	PASS
FAM86B2	653333	broad.mit.edu	37	8	12285132	12285132	+	Intron	SNP	C	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12285132C>G	uc003wvt.3	-						FAM66D_uc011kxp.1_Intron|uc003wvm.1_Intron|uc011kxs.1_5'Flank|uc003wvp.1_5'Flank|FAM86B2_uc003wvq.3_Intron|FAM86B2_uc003wvr.3_Intron|FAM86B2_uc003wvs.3_Intron|FAM86B2_uc010lsn.2_Intron|FAM86B2_uc003wvu.3_Intron|FAM86B2_uc010lso.2_Intron|FAM86B2_uc011kxt.1_Missense_Mutation_p.C81S|FAM86B2_uc011kxu.1_RNA|FAM86B2_uc010lsl.2_Intron	NM_001137610	NP_001131082	P0C5J1	F86B2_HUMAN	hypothetical protein LOC653333												0						ACAGCTCGGGCACCATGTAGG	0.622													4	13	---	---	---	---	PASS
MATN2	4147	broad.mit.edu	37	8	99028778	99028778	+	Silent	SNP	T	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99028778T>C	uc003yic.2	+	11	1815	c.1584T>C	c.(1582-1584)TCT>TCC	p.S528S	MATN2_uc010mbh.1_Silent_p.S487S|MATN2_uc003yid.2_Silent_p.S528S|MATN2_uc003yie.1_Silent_p.S528S|MATN2_uc010mbi.1_Silent_p.S361S|MATN2_uc010mbj.1_Silent_p.S27S	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor	528	EGF-like 8.					proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			AATTGGACTCTTGTGCTCTGG	0.393													81	196	---	---	---	---	PASS
KCNV2	169522	broad.mit.edu	37	9	2729659	2729659	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2729659G>A	uc003zho.1	+	2	1784	c.1570G>A	c.(1570-1572)GCC>ACC	p.A524T		NM_133497	NP_598004	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	524	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(50;0.0257)		CATGCAGAGAGCCAGAAAGAA	0.453													42	34	---	---	---	---	PASS
IL33	90865	broad.mit.edu	37	9	6251225	6251225	+	Silent	SNP	C	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6251225C>G	uc003zjt.2	+	4	360	c.303C>G	c.(301-303)GTC>GTG	p.V101V	IL33_uc011lmg.1_Silent_p.V101V|IL33_uc011lmh.1_Intron|IL33_uc003zju.1_Silent_p.V101V	NM_033439	NP_254274	O95760	IL33_HUMAN	interleukin 33 precursor	101					positive regulation of chemokine secretion|positive regulation of inflammatory response|positive regulation of macrophage activation|positive regulation of transcription from RNA polymerase II promoter	extracellular space	cytokine activity				0		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		TATCAGGGGTCCAGAAATATA	0.502													17	205	---	---	---	---	PASS
GBA2	57704	broad.mit.edu	37	9	35740973	35740973	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35740973C>A	uc003zxw.2	-	5	1399	c.875G>T	c.(874-876)CGG>CTG	p.R292L	GBA2_uc003zxx.1_5'Flank|GBA2_uc011lpb.1_Missense_Mutation_p.R292L|GBA2_uc011lpc.1_Missense_Mutation_p.R292L|GBA2_uc011lpd.1_Missense_Mutation_p.R298L|GBA2_uc003zxy.1_Missense_Mutation_p.R5L	NM_020944	NP_065995	Q9HCG7	GBA2_HUMAN	bile acid beta-glucosidase	292	Extracellular (Potential).				bile acid metabolic process|glucosylceramide catabolic process|O-glycoside catabolic process	integral to membrane|microsome|plasma membrane|smooth endoplasmic reticulum	beta-glucosidase activity|glucosylceramidase activity			ovary(3)|skin(1)	4	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGTCCATTCCGCATGGAGAA	0.577													6	91	---	---	---	---	PASS
MSMP	692094	broad.mit.edu	37	9	35753713	35753713	+	Silent	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35753713G>A	uc003zyb.1	-	2	329	c.183C>T	c.(181-183)CGC>CGT	p.R61R		NM_001044264	NP_001037729	Q1L6U9	MSMP_HUMAN	PC3-secreted microprotein precursor	61						extracellular region					0						AACAGTCCTTGCGGAGCCAAG	0.512													22	38	---	---	---	---	PASS
SPTAN1	6709	broad.mit.edu	37	9	131371420	131371420	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131371420C>T	uc004bvl.3	+	36	4728	c.4615C>T	c.(4615-4617)CAG>TAG	p.Q1539*	SPTAN1_uc004bvm.3_Nonsense_Mutation_p.Q1539*|SPTAN1_uc004bvn.3_Nonsense_Mutation_p.Q1519*	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	1539	Spectrin 16.				actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						TCTGAAAGCCCAGATGATTGA	0.488													16	108	---	---	---	---	PASS
KCNT1	57582	broad.mit.edu	37	9	138679959	138679959	+	Intron	SNP	T	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138679959T>A	uc011mdq.1	+						KCNT1_uc011mdr.1_Missense_Mutation_p.N999K|KCNT1_uc010nbf.2_Missense_Mutation_p.N1127K	NM_020822	NP_065873	Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1							membrane	binding|calcium-activated potassium channel activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		ACGTAGCAAATTTAACAGCCA	0.552													13	117	---	---	---	---	PASS
SEC24C	9632	broad.mit.edu	37	10	75520019	75520019	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75520019G>A	uc001juw.2	+	6	904	c.725G>A	c.(724-726)AGC>AAC	p.S242N	SEC24C_uc010qkn.1_RNA|SEC24C_uc009xrj.1_Missense_Mutation_p.S100N|SEC24C_uc001jux.2_Missense_Mutation_p.S242N|SEC24C_uc010qko.1_Missense_Mutation_p.S100N|SEC24C_uc010qkp.1_Intron|SEC24C_uc010qkq.1_Intron	NM_004922	NP_004913	P53992	SC24C_HUMAN	SEC24-related protein C	242					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|zinc ion binding			skin(2)|central_nervous_system(1)	3	Prostate(51;0.0112)					CCCTCAGTGAGCCAGCCCAAC	0.642													27	52	---	---	---	---	PASS
PTPMT1	114971	broad.mit.edu	37	11	47593082	47593082	+	Silent	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47593082C>A	uc001nfs.3	+	4	700	c.507C>A	c.(505-507)ATC>ATA	p.I169I	PTPMT1_uc001nfv.3_Missense_Mutation_p.P142T|PTPMT1_uc009ylt.2_Silent_p.I105I|PTPMT1_uc001nfu.3_3'UTR|NDUFS3_uc001nft.3_5'UTR	NM_175732	NP_783859	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	169	Tyrosine-protein phosphatase.				inositol phosphate dephosphorylation	mitochondrial inner membrane	phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(1)	1						GGTCATACATCCACATCAGGC	0.478													56	97	---	---	---	---	PASS
OR4C12	283093	broad.mit.edu	37	11	50003858	50003858	+	Silent	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50003858G>A	uc010ria.1	-	1	180	c.180C>T	c.(178-180)TTC>TTT	p.F60F		NM_001005270	NP_001005270	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C,	60	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3						GGTGGGTCAGGAAGAAGTACA	0.408													14	83	---	---	---	---	PASS
TMEM132A	54972	broad.mit.edu	37	11	60703295	60703295	+	Intron	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60703295G>A	uc001nqj.2	+						TMEM132A_uc001nqi.2_Intron|TMEM132A_uc001nqm.2_Translation_Start_Site	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1						GCATGCGTGCGTGCCCTCGCA	0.572													6	122	---	---	---	---	PASS
ACER3	55331	broad.mit.edu	37	11	76731470	76731470	+	3'UTR	SNP	C	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76731470C>G	uc009yum.1	+	11					ACER3_uc001oxu.2_RNA|ACER3_uc009yun.1_3'UTR|ACER3_uc009yuo.1_3'UTR|ACER3_uc010rsh.1_3'UTR|ACER3_uc010rsi.1_3'UTR|ACER3_uc010rsj.1_3'UTR	NM_018367	NP_060837	Q9NUN7	ACER3_HUMAN	phytoceramidase, alkaline						ceramide metabolic process|phytosphingosine biosynthetic process|positive regulation of cell proliferation|sphingosine biosynthetic process	integral to endoplasmic reticulum membrane|integral to Golgi membrane	phytoceramidase activity				0						TATGTCATGACCATCACAGCA	0.413													4	49	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2778099	2778099	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2778099C>T	uc009zdu.1	+	40	5081	c.4768C>T	c.(4768-4770)CGC>TGC	p.R1590C	CACNA1C_uc009zdv.1_Missense_Mutation_p.R1539C|CACNA1C_uc001qkb.2_Missense_Mutation_p.R1542C|CACNA1C_uc001qkc.2_Missense_Mutation_p.R1542C|CACNA1C_uc001qke.2_Missense_Mutation_p.R1531C|CACNA1C_uc001qkf.2_Missense_Mutation_p.R1531C|CACNA1C_uc001qjz.2_Missense_Mutation_p.R1542C|CACNA1C_uc001qkd.2_Missense_Mutation_p.R1542C|CACNA1C_uc001qkg.2_Missense_Mutation_p.R1529C|CACNA1C_uc009zdw.1_Missense_Mutation_p.R1564C|CACNA1C_uc001qkh.2_Missense_Mutation_p.R1531C|CACNA1C_uc001qkl.2_Missense_Mutation_p.R1590C|CACNA1C_uc001qkn.2_Missense_Mutation_p.R1542C|CACNA1C_uc001qko.2_Missense_Mutation_p.R1562C|CACNA1C_uc001qkp.2_Missense_Mutation_p.R1542C|CACNA1C_uc001qkr.2_Missense_Mutation_p.R1559C|CACNA1C_uc001qku.2_Missense_Mutation_p.R1542C|CACNA1C_uc001qkq.2_Missense_Mutation_p.R1570C|CACNA1C_uc001qks.2_Missense_Mutation_p.R1542C|CACNA1C_uc001qkt.2_Missense_Mutation_p.R1542C|CACNA1C_uc001qki.1_Missense_Mutation_p.R1278C|CACNA1C_uc001qkj.1_Missense_Mutation_p.R1278C|CACNA1C_uc001qkk.1_Missense_Mutation_p.R1278C|CACNA1C_uc001qkm.1_Missense_Mutation_p.R1267C|CACNA1C_uc010sea.1_Missense_Mutation_p.R233C	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	1590	Cytoplasmic (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	TCGCCTGCAGCGCCTGGTCTC	0.507													16	58	---	---	---	---	PASS
ANO2	57101	broad.mit.edu	37	12	5672713	5672713	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5672713C>T	uc001qnm.2	-	26	2821	c.2749G>A	c.(2749-2751)GTC>ATC	p.V917I		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	922	Helical; (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						TCCACGAGGACGCTCAGGAAC	0.488													20	75	---	---	---	---	PASS
ETV6	2120	broad.mit.edu	37	12	11905414	11905414	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11905414A>T	uc001qzz.2	+	2	338	c.64A>T	c.(64-66)AGC>TGC	p.S22C		NM_001987	NP_001978	P41212	ETV6_HUMAN	ets variant 6	22				S->A: No effect.		cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				ACCTCCAGAGAGCCCAGTGCC	0.547			T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								42	64	---	---	---	---	PASS
KLHDC5	57542	broad.mit.edu	37	12	27933951	27933951	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27933951T>C	uc001rij.2	+	1	765	c.688T>C	c.(688-690)TTC>CTC	p.F230L	KLHDC5_uc009zjj.2_RNA	NM_020782	NP_065833	Q9P2K6	KLDC5_HUMAN	kelch domain containing 5	230	Kelch 1.									ovary(1)|central_nervous_system(1)	2	Lung SC(9;0.0873)					TGAGCGTTGGTTCCCGCTGGC	0.637													22	63	---	---	---	---	PASS
ABCD2	225	broad.mit.edu	37	12	39980001	39980001	+	Missense_Mutation	SNP	C	G	G	rs151149571	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39980001C>G	uc001rmb.2	-	7	2171	c.1745G>C	c.(1744-1746)CGT>CCT	p.R582P		NM_005164	NP_005155	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D, member 2	582	ABC transporter.				fatty acid metabolic process|transport	ATP-binding cassette (ABC) transporter complex|integral to plasma membrane|peroxisomal membrane	ATP binding|ATPase activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)|skin(1)	6						GTGTAGGATACGTTCCAGATC	0.363													10	76	---	---	---	---	PASS
GOLGA2B	55592	broad.mit.edu	37	12	100562907	100562907	+	Intron	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100562907C>A	uc001tgu.2	-						GOLGA2B_uc001tgy.3_5'Flank|GOLGA2B_uc001tgz.3_RNA	NM_017600	NP_060070			golgi autoantigen, golgin subfamily a, 2-like 1												0						TTTCCAAGCCCATGGTCTCAT	0.244													14	25	---	---	---	---	PASS
HMGB1	3146	broad.mit.edu	37	13	31035409	31035409	+	3'UTR	SNP	A	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31035409A>G	uc001usw.2	-	5					HMGB1_uc001usz.2_3'UTR|HMGB1_uc001usv.2_3'UTR|HMGB1_uc001usx.2_3'UTR|HMGB1_uc001usy.2_3'UTR|HMGB1_uc001uta.1_3'UTR	NM_002128	NP_002119	P09429	HMGB1_HUMAN	high-mobility group box 1						base-excision repair, DNA ligation|dendritic cell chemotaxis|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|inflammatory response to antigenic stimulus|innate immune response|myeloid dendritic cell activation|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|neuron projection development|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	cell surface|condensed chromosome|extracellular space|nucleolus|nucleoplasm	chemoattractant activity|cytokine activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|repressing transcription factor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		TTACATTTCAATTTTTTTCTT	0.333													3	14	---	---	---	---	PASS
KL	9365	broad.mit.edu	37	13	33634984	33634984	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33634984G>A	uc001uus.2	+	4	1776	c.1768G>A	c.(1768-1770)GTT>ATT	p.V590I	KL_uc001uur.1_3'UTR	NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho precursor	590	Glycosyl hydrolase-1 2.|Extracellular (Potential).				aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		GGAAATGCACGTTACACATTT	0.517													52	117	---	---	---	---	PASS
DAD1	1603	broad.mit.edu	37	14	23058134	23058134	+	5'UTR	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23058134G>A	uc001wgl.2	-	1						NM_001344	NP_001335	P61803	DAD1_HUMAN	defender against cell death 1						anti-apoptosis|apoptosis|post-translational protein modification	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity			ovary(1)	1	all_cancers(95;5.49e-05)			GBM - Glioblastoma multiforme(265;0.0156)		CGGATGTGCTGTTTGCGCATG	0.622													8	8	---	---	---	---	PASS
HECTD1	25831	broad.mit.edu	37	14	31613394	31613394	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31613394T>G	uc001wrc.1	-	17	3190	c.2701A>C	c.(2701-2703)AAG>CAG	p.K901Q	HECTD1_uc001wrd.1_Missense_Mutation_p.K416Q	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	901					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTTTCATCCTTCAAAAGTACA	0.313													33	18	---	---	---	---	PASS
KIAA0586	9786	broad.mit.edu	37	14	58949396	58949396	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58949396C>T	uc001xdv.3	+	20	3155	c.2882C>T	c.(2881-2883)TCT>TTT	p.S961F	KIAA0586_uc010trr.1_Missense_Mutation_p.S1078F|KIAA0586_uc001xdt.3_Missense_Mutation_p.S993F|KIAA0586_uc001xdu.3_Missense_Mutation_p.S1022F|KIAA0586_uc010trs.1_Missense_Mutation_p.S952F|KIAA0586_uc010trt.1_Missense_Mutation_p.S897F|KIAA0586_uc010tru.1_Missense_Mutation_p.S897F	NM_014749	NP_055564	E9PGW8	E9PGW8_HUMAN	talpid3 protein	961										ovary(1)	1						ACAGGTGTTTCTGGGGATGCT	0.388													25	129	---	---	---	---	PASS
YLPM1	56252	broad.mit.edu	37	14	75279329	75279329	+	Splice_Site	SNP	A	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75279329A>G	uc001xqj.3	+	11	5472	c.5348_splice	c.e11-2	p.G1783_splice	YLPM1_uc001xql.3_Splice_Site|YLPM1_uc001xqm.1_Splice_Site_p.G266_splice	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CTGGAATCCTAGGAGAACGAA	0.448													43	29	---	---	---	---	PASS
C14orf2	9556	broad.mit.edu	37	14	104387524	104387524	+	Intron	SNP	T	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104387524T>C	uc001yoi.3	-						C14orf2_uc001yoj.3_5'UTR|C14orf2_uc010aww.1_Intron|C14orf2_uc001yok.2_Intron	NM_004894	NP_004885	P56378	68MP_HUMAN	6.8 kDa mitochondrial proteolipid isoform 1							mitochondrion					0				Epithelial(152;0.223)		cagctgaacctctcaaggcca	0.224													3	12	---	---	---	---	PASS
TMEM87A	25963	broad.mit.edu	37	15	42529668	42529668	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42529668T>A	uc010udd.1	-	9	989	c.830A>T	c.(829-831)TAT>TTT	p.Y277F	TMEM87A_uc001zpf.3_Missense_Mutation_p.Y216F|TMEM87A_uc010bcu.1_Missense_Mutation_p.Y216F	NM_015497	NP_056312	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A isoform 1	277	Helical; (Potential).					integral to membrane				ovary(1)	1		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		AAATTCCGCATAGAAGACAGC	0.433													15	158	---	---	---	---	PASS
COMMD4	54939	broad.mit.edu	37	15	75631620	75631620	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75631620T>C	uc002azy.2	+	6	374	c.317T>C	c.(316-318)CTG>CCG	p.L106P	COMMD4_uc010umf.1_3'UTR|COMMD4_uc002azz.2_Missense_Mutation_p.C89R|COMMD4_uc002baa.2_Missense_Mutation_p.L106P|COMMD4_uc010umg.1_3'UTR|COMMD4_uc010umh.1_RNA	NM_017828	NP_060298	Q9H0A8	COMD4_HUMAN	COMM domain containing 4	106						cytoplasm	protein binding				0						GCGGCCAGCCTGTGCCGCTGT	0.622													4	56	---	---	---	---	PASS
COMMD4	54939	broad.mit.edu	37	15	75631625	75631625	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75631625C>T	uc002azy.2	+	6	379	c.322C>T	c.(322-324)CGC>TGC	p.R108C	COMMD4_uc010umf.1_3'UTR|COMMD4_uc002azz.2_Silent_p.A90A|COMMD4_uc002baa.2_Missense_Mutation_p.R108C|COMMD4_uc010umg.1_3'UTR|COMMD4_uc010umh.1_RNA	NM_017828	NP_060298	Q9H0A8	COMD4_HUMAN	COMM domain containing 4	108						cytoplasm	protein binding				0						CAGCCTGTGCCGCTGTTATGA	0.612													4	58	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	76074470	76074470	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76074470A>G	uc010umm.1	+	8	649	c.572A>G	c.(571-573)CAG>CGG	p.Q191R	uc002bba.1_5'Flank					SubName: Full=cDNA FLJ59077, highly similar to Golgin subfamily A member 6;																		CGGTTACAGCAGACCATAAAG	0.577													6	23	---	---	---	---	PASS
LOC595101	595101	broad.mit.edu	37	16	30316412	30316412	+	RNA	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30316412G>A	uc002dxp.1	-	3		c.684C>T				NR_002453				Homo sapiens cDNA FLJ39663 fis, clone SMINT2007187.												0						GCTAAAGCACGACTGCCATGC	0.483													6	89	---	---	---	---	PASS
NKD1	85407	broad.mit.edu	37	16	50664121	50664121	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50664121A>G	uc002egg.1	+	7	711	c.487A>G	c.(487-489)ATC>GTC	p.I163V		NM_033119	NP_149110	Q969G9	NKD1_HUMAN	naked cuticle homolog 1	163	EF-hand.|Interaction with DVL1, DVL2 and DVL3 (By similarity).				Wnt receptor signaling pathway	cytoplasm|plasma membrane	calcium ion binding|protein binding				0		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		GCTGCACACCATCTATGAGGT	0.572													17	41	---	---	---	---	PASS
PER1	5187	broad.mit.edu	37	17	8047092	8047092	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8047092T>C	uc002gkd.2	-	19	2802	c.2564A>G	c.(2563-2565)TAT>TGT	p.Y855C	PER1_uc010cns.2_5'Flank|PER1_uc010vuq.1_Intron	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	855	Pro-rich.				circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9						GTGTGAGACATAGCAGGGCGC	0.692			T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					14	51	---	---	---	---	PASS
RNF135	84282	broad.mit.edu	37	17	29302666	29302666	+	Intron	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29302666C>T	uc002hfz.2	+						RNF135_uc002hga.2_Intron|RNF135_uc010csm.2_Intron|RNF135_uc002hgb.2_Intron|DPRXP4_uc002hgc.2_RNA	NM_032322	NP_115698	Q8IUD6	RN135_HUMAN	ring finger protein 135 isoform 1						innate immune response|negative regulation of type I interferon production|positive regulation of interferon-beta production|regulation of innate immune response	cytosol	protein binding|ribonucleoprotein binding|ubiquitin-protein ligase activity|zinc ion binding	p.?(1)		skin(2)	2		all_cancers(10;8.65e-08)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Myeloproliferative disorder(56;0.0255)				ACTCCACAACCGCCAATACCG	0.483													32	44	---	---	---	---	PASS
SLFN11	91607	broad.mit.edu	37	17	33690266	33690266	+	Silent	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33690266C>T	uc010ctp.2	-	4	1003	c.561G>A	c.(559-561)TCG>TCA	p.S187S	SLFN11_uc010ctq.2_Silent_p.S187S|SLFN11_uc002hjh.3_Silent_p.S187S|SLFN11_uc002hjg.3_Silent_p.S187S|SLFN11_uc010ctr.2_Silent_p.S187S	NM_001104588	NP_001098058	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	187						nucleus	ATP binding			large_intestine(1)|ovary(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CAGCAGGATCCGAGTTTGGGT	0.413													32	56	---	---	---	---	PASS
HOXB2	3212	broad.mit.edu	37	17	46620386	46620386	+	3'UTR	SNP	G	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46620386G>T	uc002inm.2	-	2						NM_002145	NP_002136	P14652	HXB2_HUMAN	homeobox B2						blood circulation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CCAGTAGACGGCCAAGGAGCG	0.502													12	15	---	---	---	---	PASS
ANKFN1	162282	broad.mit.edu	37	17	54543856	54543856	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54543856A>G	uc002iun.1	+	14	1741	c.1706A>G	c.(1705-1707)AAG>AGG	p.K569R		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	569										large_intestine(1)|ovary(1)	2						CAGATCTCAAAGCTGCAAAGC	0.403													5	125	---	---	---	---	PASS
BCAS3	54828	broad.mit.edu	37	17	58786584	58786584	+	Silent	SNP	A	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58786584A>T	uc002iyv.3	+	5	328	c.219A>T	c.(217-219)ACA>ACT	p.T73T	BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Silent_p.T73T|BCAS3_uc002iyw.3_Silent_p.T69T	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1	73	WD 1.					nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			ATGCAGATACATCAAGAAATC	0.343													80	141	---	---	---	---	PASS
JMJD6	23210	broad.mit.edu	37	17	74720100	74720100	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74720100G>T	uc002jso.2	-	3	883	c.559C>A	c.(559-561)CAC>AAC	p.H187N	JMJD6_uc002jsn.1_Missense_Mutation_p.H187N|JMJD6_uc010dgz.2_Missense_Mutation_p.H187N|C17orf95_uc002jsp.2_5'Flank|C17orf95_uc002jsq.2_5'Flank|C17orf95_uc002jsr.2_5'Flank|C17orf95_uc002jss.2_5'Flank|C17orf95_uc002jst.2_5'Flank|C17orf95_uc002jsu.2_5'Flank	NM_015167	NP_055982	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6 isoform 2	187	JmjC.	Iron; catalytic.		H->A: Loss of catalytic activity; when associated with A-189 and A-273.	mRNA processing|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine|regulation of nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|RNA splicing|sprouting angiogenesis|transcription, DNA-dependent	nucleolus|nucleoplasm	histone demethylase activity (H3-R2 specific)|histone demethylase activity (H4-R3 specific)|identical protein binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptidyl-lysine 5-dioxygenase activity|single-stranded RNA binding			skin(2)|ovary(1)	3						GGGTCGATGTGAATCCCAGTT	0.507													45	102	---	---	---	---	PASS
PSMA8	143471	broad.mit.edu	37	18	23714010	23714010	+	Silent	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23714010G>A	uc002kvq.2	+	1	195	c.81G>A	c.(79-81)GCG>GCA	p.A27A	PSMA8_uc002kvo.2_Silent_p.A27A|PSMA8_uc002kvp.2_Silent_p.A27A|PSMA8_uc002kvr.2_5'UTR	NM_144662	NP_653263	Q8TAA3	PSA7L_HUMAN	proteasome alpha 8 subunit isoform 1	27					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|M/G1 transition of mitotic cell cycle|mRNA metabolic process|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	threonine-type endopeptidase activity			skin(1)	1	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)			CCCAGGAAGCGGTGAAGAAAG	0.557													11	82	---	---	---	---	PASS
FAM59A	64762	broad.mit.edu	37	18	29867878	29867878	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29867878G>C	uc002kxl.2	-	4	738	c.682C>G	c.(682-684)CAG>GAG	p.Q228E	FAM59A_uc002kxk.1_Missense_Mutation_p.Q228E	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A	228	CABIT.									ovary(1)|skin(1)	2						TCTTGCATCTGAAGTTCCAGG	0.517													77	138	---	---	---	---	PASS
SMAD2	4087	broad.mit.edu	37	18	45374902	45374902	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45374902C>G	uc002lcy.2	-	8	1189	c.941G>C	c.(940-942)GGT>GCT	p.G314A	SMAD2_uc002lcz.2_Missense_Mutation_p.G314A|SMAD2_uc010xdc.1_Missense_Mutation_p.G284A|SMAD2_uc010xdd.1_Missense_Mutation_p.G284A	NM_005901	NP_005892	Q15796	SMAD2_HUMAN	Sma- and Mad-related protein 2 isoform 1	314	MH2.				anterior/posterior pattern formation|cell fate commitment|common-partner SMAD protein phosphorylation|intracellular signal transduction|mesoderm formation|negative regulation of transcription, DNA-dependent|palate development|paraxial mesoderm morphogenesis|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|regulation of binding|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis	activin responsive factor complex|cytosol	activating transcription factor binding|co-SMAD binding|double-stranded DNA binding|I-SMAD binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding			large_intestine(3)|lung(1)|central_nervous_system(1)	5						GGAGAGTAAACCTAAGCAGAA	0.393													8	104	---	---	---	---	PASS
DENND1C	79958	broad.mit.edu	37	19	6467951	6467951	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6467951G>C	uc002mfe.2	-	23	2062	c.1970C>G	c.(1969-1971)TCC>TGC	p.S657C	DENND1C_uc002mfb.2_Missense_Mutation_p.S207C|DENND1C_uc002mfc.2_Missense_Mutation_p.S207C|DENND1C_uc002mfd.2_Missense_Mutation_p.S207C|DENND1C_uc010xje.1_Missense_Mutation_p.S613C	NM_024898	NP_079174	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	657						clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity			large_intestine(1)	1						AGCTGTTGAGGACTGGGATGG	0.557													69	139	---	---	---	---	PASS
ZNF844	284391	broad.mit.edu	37	19	12186656	12186656	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12186656C>A	uc002mtb.2	+	4	864	c.721C>A	c.(721-723)CAA>AAA	p.Q241K	ZNF844_uc010dym.1_Missense_Mutation_p.Q84K	NM_001136501	NP_001129973	Q08AG5	ZN844_HUMAN	zinc finger protein 844	241	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AACTTCCCTTCAAATACATGA	0.368													10	20	---	---	---	---	PASS
HOOK2	29911	broad.mit.edu	37	19	12883813	12883813	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12883813G>C	uc002muy.2	-	4	421	c.250C>G	c.(250-252)CAG>GAG	p.Q84E	HOOK2_uc002muz.2_Missense_Mutation_p.Q84E	NM_013312	NP_037444	Q96ED9	HOOK2_HUMAN	hook homolog 2 isoform 1	84	Sufficient for interaction with microtubules.|Required for localization to the centrosome and induction of aggresome formation.				early endosome to late endosome transport|endocytosis|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|protein transport	centrosome|FHF complex|microtubule	identical protein binding|microtubule binding			ovary(1)|breast(1)|skin(1)	3						CTCACATCCTGGGAGTACTCT	0.557													6	48	---	---	---	---	PASS
OR10H5	284433	broad.mit.edu	37	19	15904911	15904911	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15904911C>G	uc010xos.1	+	1	53	c.53C>G	c.(52-54)TCT>TGT	p.S18C		NM_001004466	NP_001004466	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H,	18	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						GTTGGCTTCTCTGCCTTCCCC	0.572													88	177	---	---	---	---	PASS
SCN1B	6324	broad.mit.edu	37	19	35524563	35524563	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35524563T>C	uc002nxp.2	+	3	559	c.368T>C	c.(367-369)GTC>GCC	p.V123A	SCN1B_uc002nxo.1_Missense_Mutation_p.V123A|SCN1B_uc010xsg.1_Intron	NM_001037	NP_001028	Q07699	SCN1B_HUMAN	sodium channel, voltage-gated, type I, beta	123	Extracellular (Potential).|Ig-like C2-type.				axon guidance|synaptic transmission	integral to membrane	voltage-gated sodium channel activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GAGTGCCACGTCTACCGCCTG	0.552													5	100	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	38990554	38990554	+	Silent	SNP	T	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38990554T>C	uc002oit.2	+	45	7351	c.7221T>C	c.(7219-7221)GGT>GGC	p.G2407G	RYR1_uc002oiu.2_Silent_p.G2407G|RYR1_uc002oiv.1_5'UTR	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	2407	Cytoplasmic.|6 X approximate repeats.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	GCAGCTTTGGTGAGGAACCGC	0.647													5	127	---	---	---	---	PASS
CCDC61	729440	broad.mit.edu	37	19	46506269	46506269	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46506269C>A	uc002pdw.2	+	3	164	c.164C>A	c.(163-165)ACC>AAC	p.T55N		NM_001080402	NP_001073871			coiled-coil domain containing 61											ovary(1)	1		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		TCTCCAGCAACCTTGGCCATG	0.408													8	111	---	---	---	---	PASS
ZNF611	81856	broad.mit.edu	37	19	53209500	53209500	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53209500G>A	uc002pzz.2	-	7	1125	c.808C>T	c.(808-810)CAC>TAC	p.H270Y	ZNF611_uc010eqc.2_Missense_Mutation_p.H200Y|ZNF611_uc010ydo.1_Missense_Mutation_p.H200Y|ZNF611_uc010ydr.1_Missense_Mutation_p.H201Y|ZNF611_uc010ydp.1_Missense_Mutation_p.H270Y|ZNF611_uc010ydq.1_Missense_Mutation_p.H270Y|ZNF611_uc002qaa.3_Missense_Mutation_p.H200Y	NM_030972	NP_112234	Q8N823	ZN611_HUMAN	zinc finger protein 611 isoform a	270	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TATTGCTCGTGATTAAAGAGC	0.413													49	83	---	---	---	---	PASS
FCAR	2204	broad.mit.edu	37	19	55401272	55401272	+	3'UTR	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55401272C>A	uc002qhr.1	+	5					FCAR_uc002qhs.1_RNA|FCAR_uc002qht.1_3'UTR|FCAR_uc010esi.1_3'UTR|FCAR_uc002qhu.1_3'UTR|FCAR_uc002qhv.1_3'UTR|FCAR_uc002qhw.1_3'UTR|FCAR_uc002qhx.1_3'UTR|FCAR_uc002qhy.1_3'UTR|FCAR_uc002qhz.1_3'UTR|FCAR_uc002qia.1_3'UTR	NM_002000	NP_001991	P24071	FCAR_HUMAN	Fc alpha receptor isoform a precursor						immune response	extracellular region|integral to plasma membrane	IgA binding|receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(193;0.0443)		ACTGTGGAGTCCGACAAAGCT	0.388													8	18	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57330017	57330017	+	Missense_Mutation	SNP	G	T	T	rs80150589	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57330017G>T	uc002qnu.2	-	5	1074	c.723C>A	c.(721-723)CAC>CAA	p.H241Q	ZIM2_uc010ygq.1_5'UTR|ZIM2_uc010ygr.1_5'UTR|ZIM2_uc002qnr.2_Missense_Mutation_p.H116Q|ZIM2_uc002qnq.2_Missense_Mutation_p.H116Q|ZIM2_uc010etp.2_Missense_Mutation_p.H116Q|ZIM2_uc010ygs.1_Missense_Mutation_p.H116Q|PEG3_uc002qnt.2_Missense_Mutation_p.H242Q|PEG3_uc002qnv.2_Missense_Mutation_p.H241Q|PEG3_uc002qnw.2_Missense_Mutation_p.H116Q|PEG3_uc002qnx.2_Missense_Mutation_p.H115Q|PEG3_uc010etr.2_Missense_Mutation_p.H241Q	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	241					apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		GGATTGTGTTGTGAGGTTTCC	0.493													130	299	---	---	---	---	PASS
XRN2	22803	broad.mit.edu	37	20	21309253	21309253	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21309253A>C	uc002wsf.1	+	4	467	c.372A>C	c.(370-372)GAA>GAC	p.E124D	XRN2_uc002wsg.1_Missense_Mutation_p.E48D|XRN2_uc010zsk.1_Missense_Mutation_p.E70D	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	124				SKE -> IKR (in Ref. 1; AAD55138).	cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1						CATCAAAAGAAGGAATGGAAG	0.388													11	154	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47309286	47309286	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47309286G>C	uc002xtw.1	-	8	983	c.960C>G	c.(958-960)ATC>ATG	p.I320M		NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	320	PH.				actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GGGAGCCGTTGATGGATTTGG	0.512													74	215	---	---	---	---	PASS
STAU1	6780	broad.mit.edu	37	20	47731337	47731337	+	3'UTR	SNP	A	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47731337A>T	uc002xud.2	-	14					STAU1_uc002xua.2_3'UTR|STAU1_uc002xub.2_3'UTR|STAU1_uc002xuc.2_3'UTR|STAU1_uc002xue.2_3'UTR|STAU1_uc002xuf.2_3'UTR|STAU1_uc002xug.2_3'UTR	NM_017453	NP_059347	O95793	STAU1_HUMAN	staufen isoform b							microtubule associated complex|rough endoplasmic reticulum|stress granule	double-stranded RNA binding			ovary(4)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			GGTATCAGAAATTCCAAATTT	0.478													117	244	---	---	---	---	PASS
BMP7	655	broad.mit.edu	37	20	55803435	55803435	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55803435C>A	uc010gip.1	-	2	990	c.461G>T	c.(460-462)CGA>CTA	p.R154L	BMP7_uc010giq.1_Missense_Mutation_p.R154L|BMP7_uc002xyc.2_Missense_Mutation_p.R154L	NM_001719	NP_001710	P18075	BMP7_HUMAN	bone morphogenetic protein 7 precursor	154					BMP signaling pathway|cartilage development|cellular response to hypoxia|epithelial to mesenchymal transition|growth|mesonephros development|negative regulation of glomerular mesangial cell proliferation|negative regulation of MAP kinase activity|negative regulation of mitosis|negative regulation of neuron differentiation|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of phosphorylation|negative regulation of striated muscle cell apoptosis|negative regulation of transcription, DNA-dependent|ossification|pathway-restricted SMAD protein phosphorylation|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|protein localization to nucleus|regulation of removal of superoxide radicals|SMAD protein signal transduction|steroid hormone mediated signaling pathway|ureteric bud development	extracellular space	cytokine activity|growth factor activity			skin(1)	1	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			CCGGAACTCTCGATGGTGGTA	0.512													53	76	---	---	---	---	PASS
LAMA5	3911	broad.mit.edu	37	20	60900508	60900508	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60900508A>G	uc002ycq.2	-	41	5460	c.5393T>C	c.(5392-5394)CTC>CCC	p.L1798P		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor	1798	Laminin IV type A.				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CTGTGAGAAGAGGGCACGGAT	0.657													4	49	---	---	---	---	PASS
DNAJC5	80331	broad.mit.edu	37	20	62551440	62551440	+	Intron	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62551440G>A	uc002yhf.2	+						DNAJC5_uc002yhg.1_Intron|DNAJC5_uc002yhh.2_RNA	NM_025219	NP_079495	Q9H3Z4	DNJC5_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5						neurotransmitter secretion|protein folding	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|melanosome|plasma membrane	heat shock protein binding|unfolded protein binding			pancreas(1)	1	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GGACGCACCCGGCTGTGTGGA	0.711													5	65	---	---	---	---	PASS
ADAMTS5	11096	broad.mit.edu	37	21	28337771	28337771	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28337771C>A	uc002ymg.2	-	1	1669	c.940G>T	c.(940-942)GCC>TCC	p.A314S		NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1	314	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						TTCACCACGGCCAGGCGGATG	0.587													11	139	---	---	---	---	PASS
MCM3AP	8888	broad.mit.edu	37	21	47692488	47692488	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47692488C>T	uc002zir.1	-	8	2488	c.2452G>A	c.(2452-2454)GGA>AGA	p.G818R		NM_003906	NP_003897	O60318	MCM3A_HUMAN	minichromosome maintenance complex component 3	818					DNA replication|protein import into nucleus	cytosol|nucleus	DNA binding|nucleotide binding			large_intestine(2)|lung(1)|ovary(1)|skin(1)	5	Breast(49;0.112)					AGGATGTCTCCCTTGTTGAGA	0.498													28	240	---	---	---	---	PASS
CECR2	27443	broad.mit.edu	37	22	17978494	17978494	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17978494G>T	uc010gqw.1	+	3	458	c.332G>T	c.(331-333)GGG>GTG	p.G111V	CECR2_uc010gqv.1_5'UTR|CECR2_uc002zml.2_5'UTR|CECR2_uc002zmm.1_5'UTR	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	153					chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		GACAATTCTGGGGCACTATAT	0.488													63	180	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	18846005	18846005	+	RNA	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18846005G>A	uc002zoe.2	+	5		c.2367G>A			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		TGCGCAGGCCGACACTCACTG	0.617													4	14	---	---	---	---	PASS
SLC7A4	6545	broad.mit.edu	37	22	21385373	21385373	+	Silent	SNP	G	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21385373G>C	uc002zud.2	-	2	797	c.729C>G	c.(727-729)TCC>TCG	p.S243S	SLC7A4_uc002zue.2_Silent_p.S243S	NM_004173	NP_004164	O43246	CTR4_HUMAN	solute carrier family 7 (cationic amino acid	243	Helical; (Potential).				cellular amino acid metabolic process	integral to membrane	basic amino acid transmembrane transporter activity			ovary(1)|lung(1)	2	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CATAGAAGCAGGAGGCAGTGC	0.637													10	20	---	---	---	---	PASS
TFIP11	24144	broad.mit.edu	37	22	26902375	26902375	+	Silent	SNP	A	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26902375A>G	uc003acr.2	-	5	788	c.414T>C	c.(412-414)TCT>TCC	p.S138S	TFIP11_uc003acs.2_Silent_p.S138S|TFIP11_uc003act.2_Silent_p.S138S	NM_012143	NP_036275	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	138					biomineral tissue development	catalytic step 2 spliceosome|cytoplasm|nuclear speck	DNA binding|sequence-specific DNA binding transcription factor activity				0						AGTCCATGAAAGATTTGGTTC	0.448													6	162	---	---	---	---	PASS
TTC28	23331	broad.mit.edu	37	22	28379356	28379356	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28379356T>G	uc003adp.3	-	23	6441	c.6299A>C	c.(6298-6300)AAA>ACA	p.K2100T	LOC284900_uc003ado.2_Intron	NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	2100							binding				0						GATGCTCCCTTTGGAGCTCAC	0.512													6	157	---	---	---	---	PASS
NF2	4771	broad.mit.edu	37	22	30050715	30050715	+	Splice_Site	SNP	G	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30050715G>C	uc003age.3	+	5	959	c.516_splice	c.e5+1	p.R172_splice	NF2_uc003afy.3_Splice_Site_p.R172_splice|NF2_uc003afz.3_Splice_Site_p.R89_splice|NF2_uc003agf.3_Splice_Site_p.R172_splice|NF2_uc003agb.3_Splice_Site_p.R95_splice|NF2_uc003agc.3_Splice_Site_p.R134_splice|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Splice_Site_p.R172_splice|NF2_uc003aga.3_Splice_Site_p.R130_splice|NF2_uc003agh.3_Splice_Site_p.R131_splice|NF2_uc003agi.3_Splice_Site_p.R89_splice|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Splice_Site_p.R134_splice	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1						actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.?(5)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						TCCAAAAAGGGTAAGAGATTA	0.423			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				12	158	---	---	---	---	PASS
LIMK2	3985	broad.mit.edu	37	22	31674430	31674430	+	3'UTR	SNP	C	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31674430C>G	uc003akh.2	+	16					LIMK2_uc003aki.2_3'UTR|LIMK2_uc003akk.2_3'UTR|LIMK2_uc011aln.1_3'UTR	NM_005569	NP_005560	P53671	LIMK2_HUMAN	LIM domain kinase 2 isoform 2a							mitochondrion|nucleus	ATP binding|protein serine/threonine kinase activity|zinc ion binding			ovary(2)	2						CTCCCTAGCCCTGGCCCAGCC	0.667													5	49	---	---	---	---	PASS
USP51	158880	broad.mit.edu	37	X	55514571	55514571	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55514571C>T	uc004dun.1	-	2	881	c.802G>A	c.(802-804)GAA>AAA	p.E268K	USP51_uc011moo.1_Intron	NM_201286	NP_958443	Q70EK9	UBP51_HUMAN	ubiquitin specific protease 51	268	UBP-type.				ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3						TGCTTTGTTTCTGCATGTTTG	0.393													95	187	---	---	---	---	PASS
COL4A5	1287	broad.mit.edu	37	X	107924995	107924995	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107924995C>T	uc004enz.1	+	46	4295	c.4093C>T	c.(4093-4095)CCT>TCT	p.P1365S	COL4A5_uc011mso.1_Missense_Mutation_p.P1362S|COL4A5_uc011msp.1_Missense_Mutation_p.P41S	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor	1359	Triple-helical region.				axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4						CATAGGTCCTCCTGGATTACC	0.463									Alport_syndrome_with_Diffuse_Leiomyomatosis				108	324	---	---	---	---	PASS
ZCCHC16	340595	broad.mit.edu	37	X	111698754	111698754	+	Silent	SNP	C	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111698754C>T	uc004epo.1	+	3	1239	c.798C>T	c.(796-798)CTC>CTT	p.L266L		NM_001004308	NP_001004308	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	266							nucleic acid binding|zinc ion binding			ovary(1)	1						AGCTGCCTCTCACCCCAGCCA	0.547													28	42	---	---	---	---	PASS
MCTS1	28985	broad.mit.edu	37	X	119744919	119744919	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119744919G>A	uc004esx.2	+	5	798	c.450G>A	c.(448-450)ATG>ATA	p.M150I	MCTS1_uc011mub.1_Missense_Mutation_p.M151I	NM_014060	NP_054779	Q9ULC4	MCTS1_HUMAN	malignant T cell amplified sequence 1 isoform 1	150	PUA.				cell cycle|positive regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm	RNA binding				0						TCATGAAGATGTCTGCAGAAG	0.408													17	265	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2602	2602	+	5'Flank	SNP	T	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2602T>C	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		aaggtagcataatcacttgtt	0.239													11	80	---	---	---	---	PASS
TCEB3	6924	broad.mit.edu	37	1	24077207	24077209	+	Intron	DEL	TCT	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24077207_24077209delTCT	uc001bho.2	+							NM_003198	NP_003189	Q14241	ELOA1_HUMAN	elongin A						positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|viral reproduction	integral to membrane	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		AACCTACTTATCTTCTTCTTAAG	0.355													8	6	---	---	---	---	
RUNX3	864	broad.mit.edu	37	1	25271111	25271111	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25271111delT	uc009vrj.2	-						RUNX3_uc001bjr.2_Intron|RUNX3_uc009vrk.2_Intron|RUNX3_uc009vrl.1_Intron	NM_001031680	NP_001026850	Q13761	RUNX3_HUMAN	runt-related transcription factor 3 isoform 1						cell proliferation|induction of apoptosis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|protein phosphorylation|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		acacatggaatagggaggcag	0.000													4	2	---	---	---	---	
ADC	113451	broad.mit.edu	37	1	33557947	33557948	+	Intron	INS	-	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33557947_33557948insG	uc001bwr.2	+						ADC_uc001bws.2_Intron|ADC_uc009vue.2_Intron|ADC_uc001bwt.1_Intron|ADC_uc001bwu.2_Intron|ADC_uc001bwv.2_Intron|ADC_uc001bww.2_Intron|ADC_uc001bwx.1_Intron|ADC_uc001bwz.1_Intron|ADC_uc009vuf.1_Intron|ADC_uc001bwy.1_Intron|ADC_uc009vug.2_Intron	NM_052998	NP_443724	Q96A70	ADC_HUMAN	ODC antizyme inhibitor-2						polyamine biosynthetic process|spermatogenesis	cytosol	arginine decarboxylase activity			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)			L-Arginine(DB00125)|Pyridoxal Phosphate(DB00114)	tTCAGAGTGAAGGGGGGGGTGG	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48414503	48414504	+	IGR	DEL	TC	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48414503_48414504delTC								FOXD2 (508141 upstream) : SKINTL (152883 downstream)																							ATCTGAATCATCTCTCTCACCA	0.470													4	2	---	---	---	---	
FNDC7	163479	broad.mit.edu	37	1	109276272	109276272	+	Intron	DEL	T	-	-	rs6692327		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109276272delT	uc001dvx.2	+						FNDC7_uc010ova.1_Intron	NM_001144937	NP_001138409	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7							extracellular region				ovary(1)|skin(1)	2		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		AAtttctttcttttttttttt	0.144													5	6	---	---	---	---	
SLC22A15	55356	broad.mit.edu	37	1	116531732	116531733	+	Intron	INS	-	TG	TG	rs140553285	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116531732_116531733insTG	uc001egb.3	+						SLC22A15_uc001ega.2_Intron	NM_018420	NP_060890	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15						ion transport	integral to membrane	transmembrane transporter activity			large_intestine(2)	2	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		AGGGCCTTGGAtgtgtgtgtgt	0.391													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116863474	116863474	+	IGR	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116863474delT								C1orf161 (185613 upstream) : ATP1A1 (51530 downstream)																							GAATTTTTGGTTTTTTTTTGT	0.239													4	2	---	---	---	---	
NPHS2	7827	broad.mit.edu	37	1	179520273	179520274	+	3'UTR	INS	-	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179520273_179520274insG	uc001gmq.3	-	8					C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmo.2_Intron|C1orf125_uc001gmp.2_Intron|C1orf125_uc009wxh.2_Intron|NPHS2_uc009wxi.2_3'UTR|C1orf125_uc001gmr.2_RNA	NM_014625	NP_055440	Q9NP85	PODO_HUMAN	podocin						excretion	integral to plasma membrane	protein binding				0						TTTCTATGGCAGGCCCCTTTAC	0.480													6	4	---	---	---	---	
INTS7	25896	broad.mit.edu	37	1	212160993	212160993	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212160993delA	uc001hiw.1	-						INTS7_uc009xdb.1_Intron|INTS7_uc001hix.1_Intron|INTS7_uc001hiy.1_Intron|INTS7_uc010pta.1_Intron	NM_015434	NP_056249	Q9NVH2	INT7_HUMAN	integrator complex subunit 7						snRNA processing	integrator complex	protein binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		CATATAATTCAAAAAAAAAAG	0.289													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	212671231	212671231	+	IGR	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212671231delT								NENF (51512 upstream) : ATF3 (67466 downstream)																							gcttgtgctgtgagatgtggg	0.174													4	2	---	---	---	---	
ITPKB	3707	broad.mit.edu	37	1	226830027	226830027	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226830027delT	uc010pvo.1	-							NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B								ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)				TTTTCTTTTCTTTTTttttta	0.279													2	4	---	---	---	---	
CDC42BPA	8476	broad.mit.edu	37	1	227261514	227261514	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227261514delT	uc001hqr.2	-						CDC42BPA_uc001hqq.2_Intron|CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron|CDC42BPA_uc001hqp.2_Intron|CDC42BPA_uc001hqu.1_Intron	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				CTCCAAATAATTATGACAAAC	0.279													105	48	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245443046	245443046	+	Intron	DEL	T	-	-	rs78944806		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245443046delT	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GTAATCACTCTTTTTTTTTTT	0.333													5	3	---	---	---	---	
KIDINS220	57498	broad.mit.edu	37	2	8931015	8931015	+	Intron	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8931015delC	uc002qzc.2	-						KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Intron|KIDINS220_uc010yiw.1_Intron	NM_020738	NP_065789	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate of 220 kDa						activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ATTGGATCTGCTTTAGAAAGA	0.453													6	12	---	---	---	---	
HS1BP3	64342	broad.mit.edu	37	2	20843410	20843410	+	Intron	DEL	G	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20843410delG	uc002rdw.1	-						HS1BP3_uc002rdx.2_Intron|HS1BP3_uc002rdy.2_Intron	NM_022460	NP_071905	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3						cell communication		phosphatidylinositol binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ggctgggcgtgggggttcaca	0.000													4	2	---	---	---	---	
RASGRP3	25780	broad.mit.edu	37	2	33760756	33760757	+	Intron	INS	-	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33760756_33760757insA	uc002rox.2	+						RASGRP3_uc010ync.1_Intron|RASGRP3_uc002roy.2_Intron	NM_170672	NP_733772	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and						MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity|protein binding|Rap GTPase activator activity|signal transducer activity			lung(3)|ovary(1)|pancreas(1)	5	all_hematologic(175;0.115)					TCATCTCCTGGAAATACTGCAG	0.485													4	2	---	---	---	---	
PSME4	23198	broad.mit.edu	37	2	54148401	54148401	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54148401delT	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|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|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			TAATTAATTGTTTTTTGAAAT	0.264													4	2	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61577152	61577152	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61577152delA	uc002sbe.2	-							NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			GCTTTTGTTTAAAAAAAAAAG	0.284													7	4	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71801334	71801335	+	In_Frame_Ins	INS	-	AGGCGG	AGGCGG			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71801334_71801335insAGGCGG	uc002sie.2	+	30	3557_3558	c.3181_3182insAGGCGG	c.(3181-3183)CAG>CAGGCGGAG	p.1065_1066insAE	DYSF_uc010feg.2_In_Frame_Ins_p.1096_1097insAE|DYSF_uc010feh.2_In_Frame_Ins_p.1051_1052insAE|DYSF_uc002sig.3_In_Frame_Ins_p.1051_1052insAE|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_In_Frame_Ins_p.1065_1066insAE|DYSF_uc010fef.2_In_Frame_Ins_p.1082_1083insAE|DYSF_uc010fei.2_In_Frame_Ins_p.1082_1083insAE|DYSF_uc010fek.2_In_Frame_Ins_p.1083_1084insAE|DYSF_uc010fej.2_In_Frame_Ins_p.1052_1053insAE|DYSF_uc010fel.2_In_Frame_Ins_p.1052_1053insAE|DYSF_uc010feo.2_In_Frame_Ins_p.1097_1098insAE|DYSF_uc010fem.2_In_Frame_Ins_p.1066_1067insAE|DYSF_uc010fen.2_In_Frame_Ins_p.1083_1084insAE|DYSF_uc002sif.2_In_Frame_Ins_p.1066_1067insAE|DYSF_uc010yqy.1_5'Flank	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	1065_1066	Cytoplasmic (Potential).|Arg-rich.					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						GCAGCACAGGCAGGCGGAGGCG	0.639													16	7	---	---	---	---	
SULT1C3	442038	broad.mit.edu	37	2	108875465	108875486	+	Intron	DEL	AAACTTGGTCAGGTGATGTTAT	-	-	rs72322214	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108875465_108875486delAAACTTGGTCAGGTGATGTTAT	uc010ywo.1	+							NM_001008743	NP_001008743	Q6IMI6	ST1C3_HUMAN	sulfotransferase family, cytosolic, 1C, member							cytoplasm	alcohol sulfotransferase activity			skin(1)	1						TTCTTGGAGAAAACTTGGTCAGGTGATGTTATAAACAAGATT	0.419													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122565295	122565296	+	IGR	INS	-	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122565295_122565296insT								TSN (39869 upstream) : None (None downstream)																							AACTAGCTCAAttttttttttt	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162136905	162136906	+	IGR	INS	-	TTTC	TTTC			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162136905_162136906insTTTC								TANK (44223 upstream) : PSMD14 (27880 downstream)																							acatttcccattgtatttttct	0.000													4	2	---	---	---	---	
ATF2	1386	broad.mit.edu	37	2	175939224	175939224	+	3'UTR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175939224delA	uc002ujl.2	-	14					ATF2_uc010fqv.2_3'UTR|ATF2_uc002ujv.2_3'UTR|ATF2_uc002ujm.2_3'UTR|ATF2_uc002ujn.2_RNA|ATF2_uc002ujo.2_3'UTR|ATF2_uc002ujp.2_RNA|ATF2_uc002ujq.2_3'UTR|ATF2_uc002ujr.2_RNA|ATF2_uc010fqu.2_3'UTR|ATF2_uc002ujs.2_3'UTR|ATF2_uc002ujt.2_RNA|ATF2_uc002uju.2_RNA|uc002ujk.2_5'Flank	NM_001880	NP_001871	P15336	ATF2_HUMAN	activating transcription factor 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nucleoplasm	protein dimerization activity|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(1)|breast(1)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.125)			AATTTCAAGTAAAAAAAAAAA	0.318													8	4	---	---	---	---	
CCDC141	285025	broad.mit.edu	37	2	179714606	179714609	+	Intron	DEL	AATT	-	-	rs113842328		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179714606_179714609delAATT	uc002unf.1	-							NM_173648	NP_775919	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141								protein binding			ovary(7)|pancreas(2)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			AAAGAAATAGAATTAATTATCACA	0.324													3	6	---	---	---	---	
GULP1	51454	broad.mit.edu	37	2	189434250	189434251	+	Intron	INS	-	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189434250_189434251insT	uc010fru.2	+						GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron|GULP1_uc002uqh.1_5'Flank	NM_016315	NP_057399	Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			CCCCTGCACAGTTTTTTTTTTT	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201965459	201965459	+	IGR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201965459delA								NDUFB3 (14988 upstream) : CFLAR (15357 downstream)																							ttgtctctacaaaaaaagtaa	0.000													4	2	---	---	---	---	
MAGI1	9223	broad.mit.edu	37	3	65864673	65864673	+	Intron	DEL	G	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65864673delG	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hny.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		AGCTCCTGCTGGGGGTTGCAG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	126852088	126852088	+	IGR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126852088delA								PLXNA1 (95860 upstream) : TPRA1 (439820 downstream)																							GCTTCTAGAGAAACCctcctt	0.129													4	2	---	---	---	---	
PPP2R3A	5523	broad.mit.edu	37	3	135821185	135821185	+	Intron	DEL	T	-	-	rs35280203		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135821185delT	uc003eqv.1	+						PPP2R3A_uc011blz.1_Intron|PPP2R3A_uc003eqw.1_Intron	NM_002718	NP_002709	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'',						protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(3)|pancreas(1)|lung(1)|breast(1)|skin(1)	7						GTGTAGCAACttttttttttt	0.169													13	6	---	---	---	---	
KPNA4	3840	broad.mit.edu	37	3	160245537	160245537	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160245537delA	uc003fdn.2	-							NM_002268	NP_002259	O00629	IMA4_HUMAN	karyopherin alpha 4						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			ACTATATACCAAAAAAATGGT	0.289													4	2	---	---	---	---	
ACAP2	23527	broad.mit.edu	37	3	195000334	195000334	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195000334delA	uc003fun.3	-							NM_012287	NP_036419	Q15057	ACAP2_HUMAN	centaurin, beta 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2						GCAATGAAAGAAAAAAAAAAA	0.299													5	4	---	---	---	---	
ABCA11P	79963	broad.mit.edu	37	4	421580	421581	+	Intron	INS	-	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:421580_421581insT	uc003gae.2	-						ABCA11P_uc003gac.2_Intron|ABCA11P_uc003gad.2_Intron|ABCA11P_uc011buv.1_Intron|ABCA11P_uc010ibd.1_Intron					RecName: Full=Putative ATP-binding cassette sub-family A member 11;												0						GAGGGATCATCTGAGCCATTTC	0.356													122	61	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	22312359	22312359	+	IGR	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22312359delC								KCNIP4 (361985 upstream) : GPR125 (76640 downstream)																							GAGACAAGATCTAGGCACAGA	0.323													4	2	---	---	---	---	
DHX15	1665	broad.mit.edu	37	4	24529461	24529461	+	3'UTR	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24529461delC	uc003gqx.2	-	14					DHX15_uc003gqv.2_3'UTR|DHX15_uc003gqw.2_3'UTR	NM_001358	NP_001349	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 15						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)				CATTATCGAACCAACGTGAAG	0.318													38	19	---	---	---	---	
UBA6	55236	broad.mit.edu	37	4	68529846	68529846	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68529846delA	uc003hdg.3	-						UBA6_uc003hdi.2_Intron|UBA6_uc003hdj.2_Intron	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0						GACCATACTTAAAAAAAAAAG	0.274													4	2	---	---	---	---	
CSN1S1	1446	broad.mit.edu	37	4	70812163	70812163	+	3'UTR	DEL	T	-	-	rs139563918		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70812163delT	uc003hep.1	+	16					CSN1S1_uc003heq.1_3'UTR	NM_001890	NP_001881	P47710	CASA1_HUMAN	casein alpha s1 isoform 1							extracellular region	protein binding|transporter activity				0						GTTTACTAAGTTTTCTAGTGG	0.328													4	2	---	---	---	---	
HSPA4L	22824	broad.mit.edu	37	4	128722098	128722098	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128722098delT	uc003ifm.2	+						HSPA4L_uc010iny.1_Intron|HSPA4L_uc011cgr.1_Intron	NM_014278	NP_055093	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like						protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4						TTTAAATTAGTATTCATACTT	0.264													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190653162	190653162	+	IGR	DEL	T	-	-	rs111944048		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190653162delT								None (None upstream) : FRG1 (208812 downstream)																							ccctatcccattttcccaaac	0.144													4	2	---	---	---	---	
PAPD7	11044	broad.mit.edu	37	5	6750912	6750912	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6750912delA	uc003jdx.1	+						PAPD7_uc011cmn.1_Intron|PAPD7_uc010itl.1_Intron	NM_006999	NP_008930	Q5XG87	PAPD7_HUMAN	DNA polymerase sigma						cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding			ovary(1)	1						tttgaagattaaaaaaaaaat	0.353													4	2	---	---	---	---	
GOLPH3	64083	broad.mit.edu	37	5	32135385	32135386	+	Intron	DEL	AC	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32135385_32135386delAC	uc003jhp.1	-							NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3						cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1						ggggtttgttaccaccacagct	0.119													3	3	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38430308	38430308	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38430308delT	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron|EGFLAM_uc003jle.1_Intron|EGFLAM_uc003jlf.1_Intron	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					Gtccttcttattttttatgcg	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	76274851	76274852	+	IGR	DEL	AA	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76274851_76274852delAA								CRHBP (9553 upstream) : AGGF1 (51380 downstream)																							agctttcagtaaccactgccct	0.000													4	2	---	---	---	---	
FAM172A	83989	broad.mit.edu	37	5	93019526	93019526	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93019526delT	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron	NM_032042	NP_114431	Q8WUF8	F172A_HUMAN	hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0						AGGCAAAAAGTTTTTTTTTTA	0.388													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	108826675	108826675	+	IGR	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108826675delT								PJA2 (81000 upstream) : MAN2A1 (198481 downstream)																							ccggggtatatttttttagtc	0.159													4	2	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127680393	127680393	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127680393delT	uc003kuu.2	-						FBN2_uc003kuv.2_Intron	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TCTTATAttcttttttttttt	0.164													6	3	---	---	---	---	
RAPGEF6	51735	broad.mit.edu	37	5	130983109	130983110	+	Intron	INS	-	TT	TT	rs114314479		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130983109_130983110insTT	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TCTACAGCGTCTTTTTTttttt	0.158													5	5	---	---	---	---	
SPOCK1	6695	broad.mit.edu	37	5	136426698	136426699	+	Intron	DEL	AT	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136426698_136426699delAT	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CACAAGAGAAATGAAAATGGGG	0.510													4	2	---	---	---	---	
MYOT	9499	broad.mit.edu	37	5	137211346	137211346	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137211346delA	uc011cye.1	+						MYOT_uc003lbv.2_Intron|MYOT_uc011cyg.1_Intron|MYOT_uc011cyh.1_Intron	NM_001135940	NP_001129412	Q9UBF9	MYOTI_HUMAN	myotilin isoform b						muscle contraction	actin cytoskeleton|sarcolemma|sarcomere	actin binding|structural constituent of muscle			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			tgccaaaaggaaaaaaaaaag	0.129													11	5	---	---	---	---	
CAMK2A	815	broad.mit.edu	37	5	149642895	149642896	+	Intron	DEL	AC	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149642895_149642896delAC	uc003lru.2	-						CAMK2A_uc003lrt.2_Intron|CAMK2A_uc010jhe.2_Intron	NM_171825	NP_741960	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission	cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTGTGCAGCAacacacacacac	0.208													4	2	---	---	---	---	
ANXA6	309	broad.mit.edu	37	5	150509258	150509259	+	Intron	INS	-	TTTG	TTTG	rs144537590	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150509258_150509259insTTTG	uc003ltl.1	-						ANXA6_uc011dcp.1_Intron|ANXA6_uc003ltm.1_Intron|ANXA6_uc003ltn.1_Intron|ANXA6_uc003lto.1_Intron	NM_001155	NP_001146	P08133	ANXA6_HUMAN	annexin VI isoform 1							melanosome	calcium ion binding|calcium-dependent phospholipid binding|protein binding				0		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTCTTACTGTtttgtttgttt	0.163													10	5	---	---	---	---	
GALNT10	55568	broad.mit.edu	37	5	153769852	153769853	+	Intron	INS	-	C	C	rs145987985	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153769852_153769853insC	uc003lvh.2	+						GALNT10_uc010jic.2_Intron|GALNT10_uc010jid.2_Intron|uc003lvi.2_RNA	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			ctgagtcactaattccatcaaa	0.000													5	3	---	---	---	---	
RNF130	55819	broad.mit.edu	37	5	179442665	179442666	+	Intron	INS	-	G	G	rs67220158		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179442665_179442666insG	uc003mll.1	-						RNF130_uc003mlm.1_Intron|MIR340_hsa-mir-340|MI0000802_5'Flank|uc003mln.2_5'Flank	NM_018434	NP_060904	Q86XS8	GOLI_HUMAN	ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ggaaaggagtaggaaaggagta	0.000													7	5	---	---	---	---	
BTNL8	79908	broad.mit.edu	37	5	180376489	180376490	+	Intron	INS	-	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180376489_180376490insG	uc003mmp.2	+						BTNL8_uc003mmq.2_Intron|BTNL8_uc011dhg.1_Intron|BTNL8_uc010jll.2_Intron|BTNL8_uc010jlm.2_Intron|BTNL8_uc011dhh.1_Intron	NM_001040462	NP_001035552	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8 isoform 2 precursor							integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAACGGGAGACGGGGGGGTCTT	0.550													6	4	---	---	---	---	
KDM1B	221656	broad.mit.edu	37	6	18163378	18163378	+	Intron	DEL	T	-	-	rs35989887		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18163378delT	uc003ncn.1	+							NM_153042	NP_694587	Q8NB78	KDM1B_HUMAN	amine oxidase (flavin containing) domain 1						multicellular organismal development|regulation of DNA methylation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-monomethyl-K4 specific)|oxidoreductase activity|zinc ion binding			skin(1)	1						CTGCCAtttcttttttttttt	0.204													10	5	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51748098	51748100	+	Intron	DEL	ATT	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51748098_51748100delATT	uc003pah.1	-						PKHD1_uc010jzn.1_Intron|PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						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)					AGCTTTTAAAATTATTGATTAAG	0.369													9	7	---	---	---	---	
DDX43	55510	broad.mit.edu	37	6	74104495	74104496	+	5'UTR	INS	-	G	G	rs141245018	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74104495_74104496insG	uc003pgw.2	+	1					OOEP_uc003pgv.3_5'UTR|DDX43_uc011dyn.1_RNA	NM_018665	NP_061135	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43							intracellular	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4						AGAGCGTGGGCGGGGGGGCTAG	0.619											OREG0003901	type=REGULATORY REGION|Gene=DDX43|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168112753	168112753	+	IGR	DEL	C	-	-	rs113873331		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168112753delC								TCP10 (314755 upstream) : C6orf123 (72468 downstream)																							tgagcaggggcgctgagcaga	0.000													4	2	---	---	---	---	
OCM	654231	broad.mit.edu	37	7	5922471	5922471	+	Intron	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5922471delC	uc003spe.3	+							NM_001097622	NP_001091091	P0CE72	ONCO_HUMAN	oncomodulin								calcium ion binding				0		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0978)|OV - Ovarian serous cystadenocarcinoma(56;2.11e-14)		TGCAAAGAttctttttttttt	0.239													6	3	---	---	---	---	
OCM	654231	broad.mit.edu	37	7	5923319	5923320	+	Intron	INS	-	AAAC	AAAC	rs149728613	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5923319_5923320insAAAC	uc003spe.3	+							NM_001097622	NP_001091091	P0CE72	ONCO_HUMAN	oncomodulin								calcium ion binding				0		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0978)|OV - Ovarian serous cystadenocarcinoma(56;2.11e-14)		ccctgtctcaaaaacaaacaaa	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24823544	24823544	+	IGR	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24823544delC								DFNA5 (25905 upstream) : OSBPL3 (12621 downstream)																							gtttgagatgccccaggggat	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25900996	25900996	+	IGR	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25900996delT								NPVF (632891 upstream) : MIR148A (88543 downstream)																							gctccttaactttttttttta	0.119													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	51589208	51589208	+	IGR	DEL	T	-	-	rs112840594		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51589208delT								COBL (204693 upstream) : None (None downstream)																							TCCCTGATGCTTTGAGTTGGT	0.408													3	3	---	---	---	---	
GTF2IP1	2970	broad.mit.edu	37	7	74613973	74613973	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74613973delT	uc003ubw.2	-						GTF2IP1_uc003ubx.3_Intron					SubName: Full=cDNA FLJ61347, highly similar to General transcription factor II-I;												0						cttcttcttcttttttttttt	0.164													7	5	---	---	---	---	
FAM185A	222234	broad.mit.edu	37	7	102413122	102413122	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102413122delA	uc011klf.1	+						FAM185A_uc011klg.1_Intron|FAM185A_uc011klh.1_Intron	NM_001145268	NP_001138740	Q8N0U4	F185A_HUMAN	hypothetical protein LOC222234 isoform 1												0						TTCTCTGaagaaaaaaaaaag	0.259													3	3	---	---	---	---	
COG5	10466	broad.mit.edu	37	7	106924377	106924377	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106924377delT	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4						CATAGTAACCttttttttttt	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117080631	117080631	+	IGR	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117080631delT								ASZ1 (13054 upstream) : CFTR (39386 downstream)																							TTTTCACACATTTTTTTCTTG	0.358													4	2	---	---	---	---	
WRN	7486	broad.mit.edu	37	8	31009847	31009847	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31009847delA	uc003xio.3	+						WRN_uc010lvk.2_Intron	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein						base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		actccatctcaaaaaaaaaaa	0.119			Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				3	4	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99592216	99592216	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99592216delA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		GGGCTTGTTTAAAAAAAAAAC	0.308													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101887341	101887341	+	IGR	DEL	G	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101887341delG								PABPC1 (153026 upstream) : YWHAZ (43463 downstream)																							aagacagagtgggggttttgg	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	104090029	104090030	+	IGR	INS	-	G	G	rs150328671	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104090029_104090030insG								ATP6V1C1 (4745 upstream) : C8orf56 (55162 downstream)																							AGGACTAACCTGGCTGGGAATG	0.411													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144138674	144138674	+	IGR	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144138674delT								C8orf31 (2954 upstream) : LY6H (100658 downstream)																							attatttttattttttttttt	0.159													8	5	---	---	---	---	
ADAMTSL1	92949	broad.mit.edu	37	9	18769193	18769193	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18769193delA	uc003zne.3	+							NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)		GACTGCCGGCAAAAAACCCCA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68421236	68421236	+	IGR	DEL	T	-	-	rs67952768		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68421236delT								FAM27B (627047 upstream) : MIR1299 (581003 downstream)																							CCCGGGGATCTCCTTAAAATG	0.448													4	2	---	---	---	---	
CENPP	401541	broad.mit.edu	37	9	95369483	95369484	+	Intron	INS	-	T	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95369483_95369484insT	uc004arz.2	+						CENPP_uc010mqx.2_Intron|CENPP_uc004asj.2_Intron	NM_001012267	NP_001012267	Q6IPU0	CENPP_HUMAN	centromere protein P						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2						attgaagtttgttttttttatc	0.020													4	2	---	---	---	---	
KCNT1	57582	broad.mit.edu	37	9	138657196	138657215	+	Intron	DEL	GCCATCCTCTCCCCAGGACT	-	-	rs71505365		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138657196_138657215delGCCATCCTCTCCCCAGGACT	uc011mdq.1	+						KCNT1_uc011mdr.1_Intron|KCNT1_uc010nbf.2_Intron|KCNT1_uc004cgo.1_Intron	NM_020822	NP_065873	Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1							membrane	binding|calcium-activated potassium channel activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		GCCCAGAGACGCCATCCTCTCCCCAGGACTGCCATCCTCT	0.632													3	4	---	---	---	---	
COBRA1	25920	broad.mit.edu	37	9	140161635	140161639	+	Intron	DEL	GGGCT	-	-	rs3936177	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140161635_140161639delGGGCT	uc004cmm.3	+							NM_015456	NP_056271	Q8WX92	NELFB_HUMAN	cofactor of BRCA1						negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleoplasm	protein binding				0	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.137)	OV - Ovarian serous cystadenocarcinoma(145;9.42e-05)|Epithelial(140;0.000766)		GGTCGGTgtggggctgaggtggggc	0.551													8	7	---	---	---	---	
COBRA1	25920	broad.mit.edu	37	9	140161642	140161647	+	Intron	DEL	GGTGGG	-	-	rs115604241	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140161642_140161647delGGTGGG	uc004cmm.3	+							NM_015456	NP_056271	Q8WX92	NELFB_HUMAN	cofactor of BRCA1						negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleoplasm	protein binding				0	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.137)	OV - Ovarian serous cystadenocarcinoma(145;9.42e-05)|Epithelial(140;0.000766)		gtggggctgaggtggggctgaggtgg	0.563													9	7	---	---	---	---	
BEND7	222389	broad.mit.edu	37	10	13522595	13522596	+	Intron	INS	-	TTAG	TTAG	rs143590690	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13522595_13522596insTTAG	uc001imm.2	-						BEND7_uc001imn.2_Intron|BEND7_uc001imo.3_Intron	NM_152751	NP_689964	Q8N7W2	BEND7_HUMAN	BEN domain containing 7 isoform 1								protein binding			ovary(1)|breast(1)	2						TGAGGAAGCTCTTAGAAATTAC	0.272													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	19563792	19563792	+	IGR	DEL	T	-	-	rs113669056		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19563792delT								ARL5B (596852 upstream) : PLXDC2 (541580 downstream)																							atggatatagtttctggtttt	0.030													2	5	---	---	---	---	
ARHGAP21	57584	broad.mit.edu	37	10	24939895	24939895	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24939895delA	uc001isb.2	-						ARHGAP21_uc009xkl.1_Intron|ARHGAP21_uc001isc.1_Intron|ARHGAP21_uc001isd.1_Intron	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21						signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8						ctgaggagacaaaaaaaaaaa	0.000													4	3	---	---	---	---	
ANK3	288	broad.mit.edu	37	10	61815229	61815229	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61815229delT	uc001jky.2	-						ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						TACTTGGAACTTTTTTTTTTA	0.284													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	82713975	82713975	+	IGR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82713975delA								SH2D4B (307659 upstream) : NRG3 (921095 downstream)																							gtcctcctccaaaaaaagaga	0.000													4	2	---	---	---	---	
AGAP11	119385	broad.mit.edu	37	10	88753100	88753100	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88753100delT	uc001kee.2	+						AGAP11_uc001kef.2_5'Flank	NM_133447	NP_597704	Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0						ATGAGTTTACTTTTTTTTTTA	0.303													6	3	---	---	---	---	
FAM22D	728130	broad.mit.edu	37	10	89118409	89118409	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89118409delA	uc001kes.2	+						FAM22D_uc009xte.1_Intron	NM_001009610	NP_001009610	Q5VT03	FA22D_HUMAN	hypothetical protein LOC728130												0						TGCCTGGGGGAATACACCGTG	0.532													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91738926	91738926	+	IGR	DEL	A	-	-	rs76395084		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91738926delA								KIF20B (204226 upstream) : HTR7 (761652 downstream)																							TTTCTAGTGGAAAAAAAAAAA	0.353													7	6	---	---	---	---	
IDE	3416	broad.mit.edu	37	10	94239368	94239369	+	Intron	DEL	GT	-	-	rs3831274		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94239368_94239369delGT	uc001kia.2	-						IDE_uc010qnp.1_Intron|IDE_uc001khz.2_Intron	NM_004969	NP_004960	P14735	IDE_HUMAN	insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	gtgtgtgtgagtgtgtgtgtgt	0.317													4	3	---	---	---	---	
GBF1	8729	broad.mit.edu	37	10	104140752	104140752	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104140752delA	uc001kux.1	+						GBF1_uc001kuy.1_Intron|GBF1_uc001kuz.1_Intron	NM_004193	NP_004184	Q92538	GBF1_HUMAN	golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		attccatctcaaaaaaaaaaa	0.234													12	7	---	---	---	---	
ADD3	120	broad.mit.edu	37	10	111877423	111877423	+	Intron	DEL	T	-	-	rs141428623		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111877423delT	uc001kyt.3	+						ADD3_uc001kys.3_Intron|ADD3_uc001kyu.2_Intron|ADD3_uc001kyv.2_Intron|ADD3_uc001kyw.2_Intron	NM_016824	NP_058432	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma) isoform a							cytoskeleton	actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton			ovary(2)|skin(2)|large_intestine(1)	5		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		GGAATCGTGATTTTTTTTTTT	0.249													7	4	---	---	---	---	
ADD3	120	broad.mit.edu	37	10	111882229	111882229	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111882229delT	uc001kyt.3	+						ADD3_uc001kys.3_Intron|ADD3_uc001kyu.2_Intron|ADD3_uc001kyv.2_Intron|ADD3_uc001kyw.2_Intron|ADD3_uc001kyx.2_5'Flank	NM_016824	NP_058432	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma) isoform a							cytoskeleton	actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton			ovary(2)|skin(2)|large_intestine(1)	5		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		AAATGTCGTGTTTTTttttta	0.194													6	3	---	---	---	---	
GFRA1	2674	broad.mit.edu	37	10	118014359	118014359	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118014359delA	uc001lcj.2	-						GFRA1_uc001lci.2_Intron|GFRA1_uc009xyr.2_Intron	NM_005264	NP_005255	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1 isoform a						axon guidance	anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity			ovary(1)|pancreas(1)	2		Lung NSC(174;0.21)		all cancers(201;0.0337)		GCTAGTATTCAAAAAAACAGC	0.458													4	2	---	---	---	---	
FAM53B	9679	broad.mit.edu	37	10	126392779	126392780	+	Intron	DEL	AG	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126392779_126392780delAG	uc001lhv.1	-						FAM53B_uc001lhu.1_Intron|FAM53B_uc001lhw.2_Intron|uc001lhx.2_RNA	NM_014661	NP_055476	Q14153	FA53B_HUMAN	hypothetical protein LOC9679											ovary(1)|pancreas(1)	2		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		AGCAGCAGCCAGAGAGAGAGTA	0.436													4	2	---	---	---	---	
KRTAP5-5	439915	broad.mit.edu	37	11	1649551	1649552	+	5'Flank	INS	-	C	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1649551_1649552insC	uc001lty.2	+							NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5							keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AAGCAAATGTATCAAGCACTGG	0.510													5	3	---	---	---	---	
KRTAP5-5	439915	broad.mit.edu	37	11	1649552	1649553	+	5'Flank	INS	-	GGAGG	GGAGG			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1649552_1649553insGGAGG	uc001lty.2	+							NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5							keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AGCAAATGTATCAAGCACTGGG	0.510													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44344310	44344311	+	IGR	DEL	AC	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44344310_44344311delAC								ALX4 (12594 upstream) : CD82 (242830 downstream)																							TTAATAAAAAACACACACACCT	0.406													4	2	---	---	---	---	
FNBP4	23360	broad.mit.edu	37	11	47768072	47768072	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47768072delT	uc009ylv.2	-						FNBP4_uc001ngj.2_Intron|FNBP4_uc001ngl.2_Intron	NM_015308	NP_056123	Q8N3X1	FNBP4_HUMAN	formin binding protein 4											ovary(1)	1						TAAAAACGACttttttttttt	0.164													3	4	---	---	---	---	
TMEM132A	54972	broad.mit.edu	37	11	60697734	60697734	+	Intron	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60697734delC	uc001nqj.2	+						TMEM132A_uc001nqi.2_Intron|TMEM132A_uc001nqk.2_Intron|TMEM132A_uc001nql.1_Intron	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1						CCCTGGAGGGCCCCCAAATGC	0.358													4	2	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	5865798	5865798	+	Intron	DEL	G	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5865798delG	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						catggtccgtgggtgggcctg	0.000													4	2	---	---	---	---	
PLBD1	79887	broad.mit.edu	37	12	14659645	14659645	+	Intron	DEL	T	-	-	rs78906132		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14659645delT	uc001rcc.1	-							NM_024829	NP_079105	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1						lipid catabolic process	extracellular region	hydrolase activity				0						TTACAGATGATTTTTTTTTTT	0.274													4	2	---	---	---	---	
DENND5B	160518	broad.mit.edu	37	12	31555178	31555181	+	Intron	DEL	AGTA	-	-	rs67565625		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31555178_31555181delAGTA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2						ccctgaaaataGTAGGAGAAGACC	0.289													4	5	---	---	---	---	
SENP1	29843	broad.mit.edu	37	12	48468838	48468839	+	Intron	INS	-	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48468838_48468839insA	uc001rqx.2	-						SENP1_uc001rqw.2_Intron|SENP1_uc001rqy.2_Intron|SENP1_uc001rqz.2_Intron|SENP1_uc009zkx.2_Intron	NM_014554	NP_055369	Q9P0U3	SENP1_HUMAN	sentrin/SUMO-specific protease 1						activation of caspase activity|induction of apoptosis by extracellular signals|protein desumoylation|proteolysis	cytoplasm|nucleus	endopeptidase activity|SUMO-specific protease activity			pancreas(2)|lung(1)	3		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				aaagaaaacttaaaaaaaaaaa	0.000													4	3	---	---	---	---	
TFCP2	7024	broad.mit.edu	37	12	51510404	51510404	+	Intron	DEL	T	-	-	rs147560823		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51510404delT	uc001rxw.2	-						TFCP2_uc001rxv.1_Intron|TFCP2_uc009zlx.1_Intron|TFCP2_uc001rxx.2_Intron|TFCP2_uc009zly.1_Intron	NM_005653	NP_005644	Q12800	TFCP2_HUMAN	transcription factor CP2						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						AGATATAATCttttttttttt	0.124													4	2	---	---	---	---	
SLC4A8	9498	broad.mit.edu	37	12	51878694	51878694	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51878694delT	uc001rys.1	+						SLC4A8_uc001rym.2_Intron|SLC4A8_uc001ryn.2_Intron|SLC4A8_uc001ryo.2_Intron|SLC4A8_uc010snj.1_Intron|SLC4A8_uc001ryr.2_Intron	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate						bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)		gaaggtgatatttgagttgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54993959	54993960	+	IGR	INS	-	G	G	rs139332872	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54993959_54993960insG								PPP1R1A (11516 upstream) : GLYCAM1 (8011 downstream)																							ttgtggccagacgtgggattct	0.000													4	6	---	---	---	---	
YEATS4	8089	broad.mit.edu	37	12	69777044	69777044	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69777044delA	uc001sux.2	+							NM_006530	NP_006521	O95619	YETS4_HUMAN	glioma-amplified sequence-41						histone H2A acetylation|histone H4 acetylation|mitosis|positive regulation of transcription, DNA-dependent|regulation of growth	NuA4 histone acetyltransferase complex|nuclear matrix	DNA binding|protein C-terminus binding|sequence-specific DNA binding transcription factor activity|structural constituent of cytoskeleton				0	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			attctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SYT1	6857	broad.mit.edu	37	12	79702391	79702392	+	Intron	DEL	AA	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79702391_79702392delAA	uc001sys.2	+						SYT1_uc001syt.2_Intron|SYT1_uc001syu.2_Intron|SYT1_uc001syv.2_Intron	NM_001135805	NP_001129277	P21579	SYT1_HUMAN	synaptotagmin I						detection of calcium ion|glutamate secretion|neurotransmitter secretion|protein homooligomerization	cell junction|chromaffin granule membrane|clathrin sculpted acetylcholine transport vesicle membrane|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|clathrin sculpted glutamate transport vesicle membrane|clathrin sculpted monoamine transport vesicle membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	1-phosphatidylinositol binding|low-density lipoprotein particle receptor binding|metal ion binding|syntaxin-1 binding|transporter activity			skin(3)|pancreas(2)|ovary(1)	6						agaaagaaagaaaaagaaagaa	0.109													6	3	---	---	---	---	
CUX2	23316	broad.mit.edu	37	12	111747683	111747684	+	Intron	DEL	CT	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111747683_111747684delCT	uc001tsa.1	+							NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						ctcgctctccctctctctctct	0.000													4	2	---	---	---	---	
ATXN2	6311	broad.mit.edu	37	12	111892734	111892735	+	Intron	DEL	CG	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111892734_111892735delCG	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsg.2_Intron|ATXN2_uc001tsl.1_3'UTR	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2						CGGACCAAACCGGCTTCCCTCC	0.550													16	21	---	---	---	---	
RNF10	9921	broad.mit.edu	37	12	121003122	121003124	+	Intron	DEL	TCA	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121003122_121003124delTCA	uc001typ.3	+						RNF10_uc010szk.1_Intron|RNF10_uc001tyq.3_Intron	NM_014868	NP_055683	Q8N5U6	RNF10_HUMAN	ring finger protein 10						negative regulation of Schwann cell proliferation|positive regulation of myelination|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription regulatory region DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTTCATCTGTTCATCTAGTCCAG	0.394													39	24	---	---	---	---	
WDR66	144406	broad.mit.edu	37	12	122369918	122369918	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122369918delA	uc009zxk.2	+							NM_144668	NP_653269	Q8TBY9	WDR66_HUMAN	WD repeat domain 66								calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		CCTTGGAACTAAAAGCAAGCC	0.368													18	9	---	---	---	---	
CCDC92	80212	broad.mit.edu	37	12	124427761	124427762	+	Intron	INS	-	A	A	rs148378755	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124427761_124427762insA	uc001ufw.1	-						CCDC92_uc001ufv.1_Intron|CCDC92_uc001ufx.1_Intron|CCDC92_uc001ufy.1_Intron	NM_025140	NP_079416	Q53HC0	CCD92_HUMAN	coiled-coil domain containing 92												0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.0002)|OV - Ovarian serous cystadenocarcinoma(86;0.000222)|all cancers(50;0.00129)|BRCA - Breast invasive adenocarcinoma(302;0.242)		ATGAGGATGATATAAGGCATTC	0.490													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	23344892	23344892	+	IGR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23344892delA								None (None upstream) : SGCG (410168 downstream)																							TCCAACTAACAAGGGACAACA	0.348													4	2	---	---	---	---	
FRY	10129	broad.mit.edu	37	13	32606131	32606132	+	Intron	INS	-	T	T	rs67814768		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32606131_32606132insT	uc001utx.2	+						FRY_uc010tdw.1_Intron|uc001utw.2_5'Flank	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		cttttcttttcttttctctttc	0.272													8	4	---	---	---	---	
FRY	10129	broad.mit.edu	37	13	32606136	32606137	+	Intron	INS	-	TT	TT	rs11272632		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32606136_32606137insTT	uc001utx.2	+						FRY_uc010tdw.1_Intron|uc001utw.2_5'Flank	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		cttttcttttctctttctttct	0.277													8	4	---	---	---	---	
COG3	83548	broad.mit.edu	37	13	46099393	46099393	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46099393delT	uc001vak.2	+						COG3_uc010tfv.1_Intron|COG3_uc010aci.2_Intron	NM_031431	NP_113619	Q96JB2	COG3_HUMAN	component of golgi transport complex 3						ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity			breast(1)|skin(1)	2		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		GAAGGAAGAATTTTTTTTTTT	0.358													5	3	---	---	---	---	
FAM124A	220108	broad.mit.edu	37	13	51855526	51855526	+	3'UTR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51855526delA	uc001vfg.1	+	4					FAM124A_uc001vff.1_3'UTR	NM_145019	NP_659456	Q86V42	F124A_HUMAN	hypothetical protein LOC220108											central_nervous_system(1)	1		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		TTTGCCTACCACCCACTCTTA	0.463													4	2	---	---	---	---	
SCEL	8796	broad.mit.edu	37	13	78167395	78167396	+	Intron	DEL	GT	-	-	rs66470060		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78167395_78167396delGT	uc001vki.2	+						SCEL_uc001vkj.2_Intron|SCEL_uc010thx.1_Intron	NM_144777	NP_659001	O95171	SCEL_HUMAN	sciellin isoform 1						embryo development|keratinocyte differentiation	cornified envelope|cytoplasm|membrane	protein binding|zinc ion binding			ovary(4)|breast(1)	5		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		ACAGAGGGGAgtgtgtgtgtgt	0.272													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22520546	22520547	+	Intron	INS	-	GA	GA			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22520546_22520547insGA	uc001wbw.2	+						uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																		TGTGTGTGTGTgagagagagag	0.252													4	2	---	---	---	---	
C14orf106	55320	broad.mit.edu	37	14	45708728	45708728	+	Intron	DEL	G	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45708728delG	uc001wwf.2	-						C14orf106_uc010anh.2_Intron	NM_018353	NP_060823	Q6P0N0	M18BP_HUMAN	chromosome 14 open reading frame 106						cell division|CenH3-containing nucleosome assembly at centromere|mitosis	chromosome, centromeric region|nucleoplasm	DNA binding				0						gtaagtgagagggaataagtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	77352628	77352628	+	IGR	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77352628delT								C14orf166B (15983 upstream) : C14orf4 (138260 downstream)																							GTGACAGGGATTTTTTTTTTT	0.418													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	93162378	93162379	+	IGR	INS	-	TC	TC			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93162378_93162379insTC								RIN3 (7046 upstream) : LGMN (7778 downstream)																							ttcttctttcttctctctctct	0.000													4	2	---	---	---	---	
MOAP1	64112	broad.mit.edu	37	14	93650048	93650050	+	In_Frame_Del	DEL	TTC	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93650048_93650050delTTC	uc001ybj.2	-	3	908_910	c.538_540delGAA	c.(538-540)GAAdel	p.E180del	C14orf109_uc001ybk.3_5'Flank|C14orf109_uc010auo.2_5'Flank	NM_022151	NP_071434	Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	180				EEE->AAA: No effect on RASSF1-binding; interacts with BAX in the absence of RASSF1.	activation of caspase activity|apoptotic nuclear change	cytoplasm	protein homodimerization activity			skin(2)|ovary(1)	3		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		agcgtccaaattcttcttctcct	0.000													42	35	---	---	---	---	
SERPINA11	256394	broad.mit.edu	37	14	94919223	94919223	+	5'Flank	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94919223delT	uc001ydd.1	-							NM_001080451	NP_001073920	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1						regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			kidney(1)	1				COAD - Colon adenocarcinoma(157;0.211)		GGAAGGGCTCTTTTTTTTCAA	0.448													4	2	---	---	---	---	
EML1	2009	broad.mit.edu	37	14	100345171	100345174	+	Intron	DEL	CTGT	-	-	rs55988713		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100345171_100345174delCTGT	uc001ygs.2	+						EML1_uc010avt.1_Intron|EML1_uc010tww.1_Intron|EML1_uc001ygq.2_Intron|EML1_uc001ygr.2_Intron	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				GGTGGAAAAACTGTCACTCAGATT	0.441													3	3	---	---	---	---	
GOLGA8G	283768	broad.mit.edu	37	15	28771709	28771709	+	Intron	DEL	G	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28771709delG	uc001zbu.2	-						GOLGA8G_uc001zbt.3_Intron|GOLGA8G_uc001zbv.2_Intron|GOLGA8F_uc010uah.1_Intron|uc002cdz.2_5'Flank	NM_001012420	NP_001012420			golgi autoantigen, golgin subfamily a, 8G												0		all_lung(180;1.98e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;4.69e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0201)|GBM - Glioblastoma multiforme(186;0.0503)|Lung(196;0.171)		aaaaaaaaaagaaaagaaaag	0.483													4	3	---	---	---	---	
CHRFAM7A	89832	broad.mit.edu	37	15	30664654	30664655	+	Intron	INS	-	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30664654_30664655insA	uc001zdt.1	-						DKFZP434L187_uc001zds.2_Intron|CHRFAM7A_uc001zdu.1_Intron|CHRFAM7A_uc010azn.2_Intron	NM_139320	NP_647536	Q494W8	CRFM7_HUMAN	CHRNA7-FAM7A fusion isoform 1							integral to membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity			skin(1)	1		all_lung(180;3.42e-11)|Breast(32;0.000153)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		tgcaaagtgctaaaaaaaaaaa	0.104													6	3	---	---	---	---	
ATPBD4	89978	broad.mit.edu	37	15	35834829	35834829	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35834829delA	uc001zja.2	-						ATPBD4_uc001ziz.2_5'Flank|ATPBD4_uc001zjb.2_Intron	NM_080650	NP_542381	Q7L8W6	ATBD4_HUMAN	ATP binding domain 4 isoform 1												0		all_epithelial(112;2.11e-09)|Lung NSC(122;2.38e-08)|all_lung(180;3.65e-07)		all cancers(64;9.9e-19)|GBM - Glioblastoma multiforme(113;2.01e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)		ATTACAATGCAAAAAAAACCC	0.308													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	40442944	40442944	+	IGR	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40442944delT								BMF (41869 upstream) : BUB1B (10266 downstream)																							tgtgttgcaattatctttcca	0.000													4	2	---	---	---	---	
SECISBP2L	9728	broad.mit.edu	37	15	49319807	49319807	+	Intron	DEL	A	-	-	rs7177172	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49319807delA	uc001zxe.1	-						SECISBP2L_uc001zxd.1_Intron|SECISBP2L_uc010bep.1_Intron|SECISBP2L_uc010beq.1_Intron	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like											breast(1)|skin(1)	2						AAACCTTATTAtttttttttt	0.129													9	4	---	---	---	---	
GLDN	342035	broad.mit.edu	37	15	51698140	51698140	+	3'UTR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51698140delA	uc002aba.2	+	10					GLDN_uc002abb.2_3'UTR	NM_181789	NP_861454	Q6ZMI3	GLDN_HUMAN	gliomedin						cell differentiation|nervous system development	collagen|integral to membrane|plasma membrane				ovary(2)	2				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)		cacagtgcctaaaatattgac	0.090													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	61335981	61335981	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61335981delT	uc002agx.2	-							NM_134261	NP_599023	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						AAGGGTTTTATTTTTTTTTAA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	68111944	68111944	+	IGR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68111944delA								MAP2K5 (12493 upstream) : LBXCOR1 (5997 downstream)																							TCAGCAGCGGAACCGGGTCTG	0.602													4	2	---	---	---	---	
CCDC33	80125	broad.mit.edu	37	15	74535081	74535081	+	Intron	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74535081delC	uc002axo.2	+							NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5						CCAGGGAGGACAAGGACACCC	0.617													4	2	---	---	---	---	
NMRAL1	57407	broad.mit.edu	37	16	4523926	4523926	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4523926delA	uc002cwm.2	-						NMRAL1_uc002cwn.2_Intron|NMRAL1_uc002cwo.2_Intron|NMRAL1_uc002cwp.2_Intron|HMOX2_uc010bts.2_5'Flank|HMOX2_uc002cwr.3_5'Flank|HMOX2_uc002cwq.3_5'Flank|HMOX2_uc002cws.3_5'Flank	NM_020677	NP_065728	Q9HBL8	NMRL1_HUMAN	NmrA-like family domain containing 1							nucleus|perinuclear region of cytoplasm	binding			kidney(1)	1						aactccgtccaaaaaaaaaaa	0.279													5	5	---	---	---	---	
ABAT	18	broad.mit.edu	37	16	8861848	8861848	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8861848delA	uc002czc.3	+						ABAT_uc002czd.3_Intron|ABAT_uc010buh.2_Intron|ABAT_uc010bui.2_Intron	NM_020686	NP_065737	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase precursor						behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	TTTGTGACTTAAAAAAAAAAA	0.199													13	6	---	---	---	---	
IQCK	124152	broad.mit.edu	37	16	19830814	19830815	+	Intron	DEL	AA	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19830814_19830815delAA	uc002dgr.2	+						IQCK_uc002dgs.2_Intron|IQCK_uc010vat.1_Intron|IQCK_uc010bwc.2_Intron|IQCK_uc010vau.1_Intron	NM_153208	NP_694940	Q8N0W5	IQCK_HUMAN	IQ motif containing K											skin(1)	1						gactccatctaaaaaaaaaaaa	0.158													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	53044990	53044990	+	IGR	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53044990delC								TOX3 (463276 upstream) : CHD9 (43955 downstream)																							TTCATGCTTACCATGTGCTAA	0.413													4	2	---	---	---	---	
CES1	1066	broad.mit.edu	37	16	55845084	55845085	+	Intron	INS	-	G	G	rs138015167	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55845084_55845085insG	uc002eim.2	-						CES1_uc010ccf.2_Intron|CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	ATGAATCAAATGGGCTTATATC	0.347													13	6	---	---	---	---	
CES1	1066	broad.mit.edu	37	16	55845123	55845123	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55845123delA	uc002eim.2	-						CES1_uc010ccf.2_Intron|CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	CAAAGTTTACAAAAAAAAAAA	0.289													6	3	---	---	---	---	
CNOT1	23019	broad.mit.edu	37	16	58571103	58571106	+	Frame_Shift_Del	DEL	TACT	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58571103_58571106delTACT	uc002env.2	-	39	5726_5729	c.5433_5436delAGTA	c.(5431-5436)GAAGTAfs	p.E1811fs	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Frame_Shift_Del_p.E1806fs|CNOT1_uc010vik.1_Frame_Shift_Del_p.E768fs	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1811_1812					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TGGATCGCACTACTTCCATCAGCT	0.422													108	50	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80591277	80591277	+	IGR	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80591277delC								DYNLRB2 (6738 upstream) : CDYL2 (46401 downstream)																							tcacagattgcccaaggtcaa	0.090													4	2	---	---	---	---	
PABPN1L	390748	broad.mit.edu	37	16	88931363	88931364	+	Intron	INS	-	GGGAG	GGGAG	rs141563331	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88931363_88931364insGGGAG	uc010vpe.1	-						PABPN1L_uc010vpd.1_Intron|PABPN1L_uc002fmi.2_Intron|PABPN1L_uc002fmj.2_Intron	NM_001080487	NP_001073956	A6NDY0	EPAB2_HUMAN	similar to poly(A)binding protein nuclear-like							cytoplasm	nucleotide binding|RNA binding				0						ggggaggggcagggaggggagg	0.554													18	12	---	---	---	---	
MYH8	4626	broad.mit.edu	37	17	10308044	10308045	+	Intron	DEL	AC	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10308044_10308045delAC	uc002gmm.2	-						uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						TGCAGGCTTTacacacacacac	0.307									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				4	2	---	---	---	---	
SLC47A1	55244	broad.mit.edu	37	17	19456031	19456031	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19456031delA	uc002gvy.1	+						SLC47A1_uc010vyy.1_Intron|SLC47A1_uc002gvx.2_Intron|SLC47A1_uc010vyz.1_Intron|SLC47A1_uc010cqp.1_Intron|SLC47A1_uc010cqq.1_Intron|SLC47A1_uc010vza.1_5'Flank|SLC47A1_uc010vzb.1_5'Flank	NM_018242	NP_060712	Q96FL8	S47A1_HUMAN	solute carrier family 47, member 1							integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)					tggagtttccaaggttgggaa	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	30424190	30424190	+	IGR	DEL	T	-	-	rs112375622		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30424190delT								LRRC37B (43673 upstream) : RHOT1 (45283 downstream)																							cttttctttcttttttttttt	0.119													4	3	---	---	---	---	
CCL23	6368	broad.mit.edu	37	17	34340465	34340465	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34340465delT	uc002hkt.1	-						CCL23_uc002hks.1_Intron	NM_145898	NP_665905	P55773	CCL23_HUMAN	small inducible cytokine A23 isoform CKbeta8						cell-cell signaling|cellular calcium ion homeostasis|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response|negative regulation of cell proliferation	extracellular space	chemokine activity|heparin binding				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	Treprostinil(DB00374)	TTTTTTTTTCTTTTTTTTTTC	0.507													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	37195476	37195491	+	Intron	DEL	TGTGTGTGTGTGTGTG	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37195476_37195491delTGTGTGTGTGTGTGTG	uc002hrd.1	+											Homo sapiens cDNA FLJ43826 fis, clone TESTI4002703.																		GGGgtgtgcttgtgtgtgtgtgtgtgtgtgtgtgtg	0.264													7	4	---	---	---	---	
VPS25	84313	broad.mit.edu	37	17	40927064	40927065	+	Intron	INS	-	T	T	rs151270458	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40927064_40927065insT	uc002ibi.2	+							NM_032353	NP_115729	Q9BRG1	VPS25_HUMAN	vacuolar protein sorting 25						cellular membrane organization|endosome transport|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endosome membrane|nucleoplasm					0		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		GTTCATGATACtttttttttgg	0.163													3	3	---	---	---	---	
NPEPPS	9520	broad.mit.edu	37	17	45660377	45660377	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45660377delT	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010dba.1_Intron	NM_006310	NP_006301	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0						TTTTTCTTTCTTTTttttttt	0.035													11	6	---	---	---	---	
RHBDF2	79651	broad.mit.edu	37	17	74500404	74500405	+	5'Flank	INS	-	T	T	rs148915512	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74500404_74500405insT	uc002jrq.1	-						RHBDF2_uc002jrp.1_5'Flank	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1						negative regulation of protein secretion|protein transport|proteolysis	endoplasmic reticulum membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity				0						GGAGGCTGCTGTGTGTCTGGAT	0.540													4	3	---	---	---	---	
SMCHD1	23347	broad.mit.edu	37	18	2707351	2707351	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2707351delT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0						TTCCAAAAGGTTTTTTTTTTT	0.284													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11625310	11625311	+	IGR	INS	-	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11625310_11625311insA								FAM38B (923331 upstream) : GNAL (63825 downstream)																							atctcaggaagaaaaaaaaaaa	0.198													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	12303610	12303610	+	IGR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12303610delA								CIDEA (26018 upstream) : TUBB6 (4630 downstream)																							gactccgtctaaaaaaaaaaa	0.169													10	5	---	---	---	---	
POLI	11201	broad.mit.edu	37	18	51797526	51797527	+	Intron	INS	-	AAAG	AAAG	rs149280018	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51797526_51797527insAAAG	uc002lfj.3	+						POLI_uc010xds.1_Intron|POLI_uc002lfk.3_Intron|POLI_uc002lfl.1_5'UTR	NM_007195	NP_009126	Q9UNA4	POLI_HUMAN	DNA polymerase iota						DNA repair|DNA replication	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding|protein binding			ovary(2)|kidney(1)	3				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		ACGCAGTGCACAAACAGTAATT	0.361								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					8	10	---	---	---	---	
CDH20	28316	broad.mit.edu	37	18	59002108	59002109	+	Intron	INS	-	T	T	rs144314471	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59002108_59002109insT	uc002lif.2	+							NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)				ACCAGGAACAATTTTTTTTCTG	0.446													6	5	---	---	---	---	
CCDC102B	79839	broad.mit.edu	37	18	66503861	66503862	+	Intron	INS	-	A	A	rs149330255	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66503861_66503862insA	uc002lkk.2	+						CCDC102B_uc002lki.2_Intron|CCDC102B_uc002lkj.1_Intron	NM_001093729	NP_001087198	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				aagactctgtcaaaaataaaaa	0.119													8	4	---	---	---	---	
DPP9	91039	broad.mit.edu	37	19	4720052	4720053	+	Intron	INS	-	C	C	rs140547317	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4720052_4720053insC	uc002mba.2	-						DPP9_uc002mbb.2_Intron|DPP9_uc002mbc.2_Intron	NM_139159	NP_631898	Q86TI2	DPP9_HUMAN	dipeptidylpeptidase 9						proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		GCTCCAGGCAGCCCCCCAAGCC	0.649													16	7	---	---	---	---	
UHRF1	29128	broad.mit.edu	37	19	4929124	4929125	+	Intron	INS	-	C	C	rs148082424	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4929124_4929125insC	uc002mbo.2	+						UHRF1_uc010xik.1_Intron|UHRF1_uc010duf.2_Intron|UHRF1_uc002mbp.2_Intron	NM_001048201	NP_001041666	Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains						cell cycle|cell proliferation|DNA repair|regulation of transcription from RNA polymerase II promoter	nucleus	acid-amino acid ligase activity|methyl-CpG binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		GATGCAGATTGCCCCCCCCCCA	0.609													13	13	---	---	---	---	
MBD3L5	284428	broad.mit.edu	37	19	7031004	7031005	+	Intron	INS	-	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7031004_7031005insA	uc010xjl.1	+							NM_001136507	NP_001129979	A6NJ08	MB3L5_HUMAN	hypothetical protein LOC284428												0						AAACAAAAAACAAAAAAAATTA	0.337													4	2	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7174422	7174422	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7174422delT	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TCATTTCAGGTTTTGAGGCAG	0.463													4	2	---	---	---	---	
ARHGEF18	23370	broad.mit.edu	37	19	7494015	7494017	+	Intron	DEL	CCC	-	-	rs67217673		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7494015_7494017delCCC	uc010xjm.1	+						ARHGEF18_uc002mgh.2_Intron	NM_015318	NP_056133	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)				CTCTGAGGCTCCCCCCTGGTATG	0.631													2	4	---	---	---	---	
ARHGEF18	23370	broad.mit.edu	37	19	7494057	7494058	+	Intron	INS	-	A	A	rs148438719	by1000genomes	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7494057_7494058insA	uc010xjm.1	+						ARHGEF18_uc002mgh.2_Intron	NM_015318	NP_056133	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)				GTATAGGGTACAAAATGTGGCA	0.609													7	6	---	---	---	---	
HNRNPM	4670	broad.mit.edu	37	19	8520630	8520630	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8520630delT	uc010dwe.2	+						HNRNPM_uc010dwc.1_Intron|HNRNPM_uc010xke.1_Intron|HNRNPM_uc010dwd.2_Intron	NM_005968	NP_005959	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0						ttgttttgtgttttttttttg	0.368													4	3	---	---	---	---	
CACNA1A	773	broad.mit.edu	37	19	13322506	13322507	+	Intron	DEL	AT	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13322506_13322507delAT	uc010dze.2	-						CACNA1A_uc010xnd.1_Intron|CACNA1A_uc002mwx.3_Intron|CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc002mwv.3_Intron	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	acagctgcacatgtgtgtgcat	0.173													0	6	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17739775	17739776	+	Intron	DEL	CA	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17739775_17739776delCA	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						tgcacagactcacacacacaca	0.153													4	2	---	---	---	---	
PIK3R2	5296	broad.mit.edu	37	19	18271038	18271039	+	Intron	INS	-	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18271038_18271039insG	uc002nia.1	+						PIK3R2_uc002nib.1_Intron|PIK3R2_uc010ebi.1_Intron	NM_005027	NP_005018	O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2						fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|negative regulation of anti-apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	GTPase activator activity|phosphatidylinositol 3-kinase regulator activity|protein binding			lung(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)	6						CCACCTAGTCTGTGAAGTTGTG	0.292													4	3	---	---	---	---	
TSHZ3	57616	broad.mit.edu	37	19	31770731	31770731	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31770731delA	uc002nsy.3	-							NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537						negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					ggagagaaagaaaaaaaaaaG	0.284													7	5	---	---	---	---	
ZNF780B	163131	broad.mit.edu	37	19	40553533	40553533	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40553533delA	uc002omu.2	-						ZNF780B_uc002omv.2_Intron	NM_001005851	NP_001005851	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					AACTATGTTTAAAAAAAAAAA	0.249													14	10	---	---	---	---	
ZNF543	125919	broad.mit.edu	37	19	57838235	57838235	+	Intron	DEL	G	-	-	rs10549195		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57838235delG	uc002qoi.1	+							NM_213598	NP_998763	Q08ER8	ZN543_HUMAN	zinc finger protein 543						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)|pancreas(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CTCCCCGCCCGCCCCCCCCCA	0.338													2	4	---	---	---	---	
TP53TG5	27296	broad.mit.edu	37	20	44006414	44006414	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44006414delA	uc002xny.2	-						SYS1-DBNDD2_uc002xnx.2_Intron	NM_014477	NP_055292	Q9Y2B4	T53G5_HUMAN	TP53-target gene 5 protein						intracellular signal transduction|negative regulation of cell growth	cytoplasm|nucleus				central_nervous_system(1)	1						tgactctaccaaaaaaaaaaa	0.000													8	5	---	---	---	---	
DPM1	8813	broad.mit.edu	37	20	49565404	49565404	+	Intron	DEL	T	-	-	rs35950937		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49565404delT	uc002xvw.1	-						DPM1_uc002xvv.1_5'Flank|DPM1_uc002xvx.1_Intron	NM_003859	NP_003850	O60762	DPM1_HUMAN	dolichyl-phosphate mannosyltransferase 1						C-terminal protein lipidation|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|protein N-linked glycosylation via asparagine|protein O-linked mannosylation	dolichol-phosphate-mannose synthase complex|endoplasmic reticulum membrane|membrane fraction	dolichyl-phosphate beta-D-mannosyltransferase activity|dolichyl-phosphate-mannose-protein mannosyltransferase activity|protein binding			ovary(1)	1						GTAGCTAACAttttttttttt	0.139													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53691714	53691715	+	IGR	DEL	GA	-	-	rs71196482		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53691714_53691715delGA								DOK5 (424005 upstream) : CBLN4 (880782 downstream)																							AGGATCATTTGacacacacaca	0.327													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	62745117	62745118	+	IGR	DEL	AC	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62745117_62745118delAC								NPBWR2 (6933 upstream) : MYT1 (38026 downstream)																							TGACTGCAGTacacacacacac	0.342													5	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11059172	11059175	+	Intron	DEL	CTAT	-	-	rs56885467		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11059172_11059175delCTAT	uc002yit.1	-						BAGE_uc002yiw.1_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)		TGGGAAATGACTATCTAACATAAA	0.373													4	2	---	---	---	---	
RBM11	54033	broad.mit.edu	37	21	15598941	15598941	+	Intron	DEL	A	-	-	rs72206436		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15598941delA	uc002yjo.3	+						RBM11_uc002yjn.3_Intron|RBM11_uc002yjp.3_Intron	NM_144770	NP_658983	P57052	RBM11_HUMAN	RNA binding motif protein 11								nucleotide binding|RNA binding				0				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		accctgtctcaaaaaaaaaaa	0.090													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26436431	26436431	+	IGR	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26436431delT								None (None upstream) : NCRNA00158 (321703 downstream)																							ctgcatcatgtttttcttctt	0.070													4	2	---	---	---	---	
TIAM1	7074	broad.mit.edu	37	21	32586008	32586008	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32586008delA	uc002yow.1	-						TIAM1_uc011adk.1_Intron|TIAM1_uc011adl.1_Intron|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						TGACAGTTGGAAAAAAAAAAG	0.274													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	41037977	41037977	+	IGR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41037977delA								B3GALT5 (3162 upstream) : IGSF5 (79357 downstream)																							ACCAGGACTGAAAAAAAAGAA	0.303													4	2	---	---	---	---	
PRDM15	63977	broad.mit.edu	37	21	43220665	43220665	+	3'UTR	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43220665delA	uc002yzp.2	-	25					PRDM15_uc002yzo.2_3'UTR	NM_001040424	NP_001035514	P57071	PRD15_HUMAN	PR domain containing 15 isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AAATAAAGTTAAAAAAAAAAA	0.343													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16955063	16955065	+	IGR	DEL	ATT	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16955063_16955065delATT								OR11H1 (505259 upstream) : CCT8L2 (116583 downstream)																							TATGTCTCTCATTATTTTGGTAA	0.187													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17442495	17442495	+	IGR	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17442495delC								HSFYL1 (132270 upstream) : GAB4 (334 downstream)																							GCATAGCAGACCCCCCTTCAC	0.657													4	2	---	---	---	---	
C22orf42	150297	broad.mit.edu	37	22	32550002	32550003	+	Intron	INS	-	CA	CA	rs111234718		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32550002_32550003insCA	uc003amd.2	-							NM_001010859	NP_001010859	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42											ovary(1)|skin(1)	2						tgagaccttTTcacacacacac	0.099													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	44731107	44731108	+	IGR	DEL	GT	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44731107_44731108delGT								KIAA1644 (22376 upstream) : LDOC1L (157342 downstream)																							TGGGGATGTGGtgtgtgtgtgt	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48423877	48423877	+	IGR	DEL	C	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48423877delC								TBC1D22A (854155 upstream) : FAM19A5 (461411 downstream)																							CCTTAATTTTCCCATTAGGAG	0.502													4	2	---	---	---	---	
ARSA	410	broad.mit.edu	37	22	51067347	51067349	+	5'Flank	DEL	TGT	-	-	rs34043300		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51067347_51067349delTGT	uc003bnb.3	-						ARSA_uc003bna.3_5'Flank|ARSA_uc003bnc.3_5'Flank|ARSA_uc003bnd.3_5'Flank|ARSA_uc003bmz.3_5'Flank|ARSA_uc010hbf.2_5'Flank	NM_001085426	NP_001078895	P15289	ARSA_HUMAN	arylsulfatase A isoform a precursor							lysosome	arylsulfatase activity|calcium ion binding|cerebroside-sulfatase activity			pancreas(1)|skin(1)	2		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)	atgtgtgtggtgttgggtgtgtg	0.074													0	8	---	---	---	---	
PIR	8544	broad.mit.edu	37	X	15415874	15415875	+	Intron	INS	-	T	T	rs34607296		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15415874_15415875insT	uc004cwu.2	-						PIR_uc004cwv.2_Intron	NM_003662	NP_003653	O00625	PIR_HUMAN	pirin						transcription from RNA polymerase II promoter	cytoplasm|nucleus	metal ion binding|protein binding|quercetin 2,3-dioxygenase activity|transcription cofactor activity			ovary(1)	1	Hepatocellular(33;0.183)					TGAATCCTGCGTGTGTTTCCAT	0.292													7	4	---	---	---	---	
WDR13	64743	broad.mit.edu	37	X	48456721	48456721	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48456721delT	uc004dkh.1	+						WDR13_uc010nif.1_Intron|WDR13_uc004dki.1_Intron|WDR13_uc004dkj.1_Intron|WDR13_uc004dkk.1_Intron|WDR13_uc004dkl.3_5'UTR|WDR13_uc011mme.1_5'Flank	NM_017883	NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13 protein							cytoplasm|nucleus				ovary(2)	2						TCCCCTAGACTTTTTTTTTTT	0.517													4	2	---	---	---	---	
CACNA1F	778	broad.mit.edu	37	X	49090939	49090940	+	5'Flank	INS	-	G	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49090939_49090940insG	uc004dnb.2	-						CACNA1F_uc010nip.2_5'Flank|CCDC22_uc011mna.1_5'Flank|CCDC22_uc004dnc.1_5'Flank|CCDC22_uc004dnd.1_5'Flank	NM_005183	NP_005174	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)	AGGAGCGAGAAGGGGACGCGGC	0.545													4	2	---	---	---	---	
LOC550643	550643	broad.mit.edu	37	X	56790254	56790254	+	Intron	DEL	T	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56790254delT	uc004dut.3	+							NR_015367				Homo sapiens hypothetical protein LOC550643, mRNA (cDNA clone IMAGE:5285100).												0						CTCCTCTGTCTTTTTTTTTGT	0.488											OREG0019814	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	X	71047904	71047904	+	IGR	DEL	G	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71047904delG								BCYRN1 (98942 upstream) : NHSL2 (83034 downstream)																							tctggaagctgggtctacaag	0.000													4	2	---	---	---	---	
CHM	1121	broad.mit.edu	37	X	85152446	85152446	+	Intron	DEL	A	-	-	rs143677864		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85152446delA	uc004eet.2	-						CHM_uc011mqz.1_Intron	NM_000390	NP_000381	P24386	RAE1_HUMAN	choroideremia isoform a						intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)				GTGTGCGTGTACAAGAGCACT	0.478													3	5	---	---	---	---	
ODZ1	10178	broad.mit.edu	37	X	123838709	123838709	+	Intron	DEL	A	-	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123838709delA	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23						GGTTAGGAAGAAAAAAAAAAA	0.353													5	3	---	---	---	---	
SMARCA1	6594	broad.mit.edu	37	X	128620788	128620790	+	Intron	DEL	TGA	-	-	rs113612790		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128620788_128620790delTGA	uc004eun.3	-						SMARCA1_uc004eup.3_Intron|SMARCA1_uc011muk.1_Intron|SMARCA1_uc011mul.1_Intron	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated						ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding			ovary(3)|skin(1)	4						cagcaAAAATtgatgatgatgat	0.113													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	134313588	134313589	+	IGR	INS	-	A	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134313588_134313589insA								CXorf48 (7837 upstream) : ZNF75D (69300 downstream)																							TTTAATGAAAGAAAAAAAAAAG	0.213													4	2	---	---	---	---	
