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
HMGN2	3151	broad.mit.edu	37	1	26801118	26801118	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26801118G>A	uc001bmp.3	+	5	399	c.197G>A	c.(196-198)GGG>GAG	p.G66E	HMGN2_uc009vsk.2_Missense_Mutation_p.G51E|HMGN2_uc001bmq.3_Missense_Mutation_p.G100R	NM_005517	NP_005508	P05204	HMGN2_HUMAN	high-mobility group nucleosomal binding domain	66					chromatin organization|regulation of transcription, DNA-dependent	chromatin|cytoplasm|nucleus	DNA binding|protein binding				0		all_cancers(24;1.9e-24)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.38e-49)|OV - Ovarian serous cystadenocarcinoma(117;5.38e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.026)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		GGCAAGGAGGGGAATAACCCT	0.413													5	9	---	---	---	---	PASS
SGIP1	84251	broad.mit.edu	37	1	67101650	67101650	+	Silent	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67101650C>T	uc001dcr.2	+	4	340	c.123C>T	c.(121-123)CCC>CCT	p.P41P		NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	41					positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3						ACGAACCACCCTACAATAGCA	0.373													18	71	---	---	---	---	PASS
IL12RB2	3595	broad.mit.edu	37	1	67861487	67861487	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67861487G>C	uc001ddu.2	+	16	2944	c.2304G>C	c.(2302-2304)AAG>AAC	p.K768N	IL12RB2_uc010oqi.1_3'UTR|IL12RB2_uc010oqj.1_3'UTR|IL12RB2_uc010oqk.1_RNA|IL12RB2_uc010oql.1_Missense_Mutation_p.K682N|IL12RB2_uc010oqm.1_3'UTR|IL12RB2_uc010oqn.1_RNA	NM_001559	NP_001550	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2 precursor	768	Cytoplasmic (Potential).				positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3						ATCTGTACAAGGTGCTGGAGA	0.582													19	116	---	---	---	---	PASS
HIST2H2BF	440689	broad.mit.edu	37	1	149398908	149398908	+	RNA	SNP	G	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149398908G>C	uc010pbi.1	-	1		c.322C>G						Q5QNW6	H2B2F_HUMAN	Homo sapiens histone cluster 2, H3, pseudogene 2, mRNA (cDNA clone IMAGE:5190019).						nucleosome assembly	nucleosome|nucleus	DNA binding				0	Breast(34;0.0124)|all_hematologic(923;0.127)					CTCGCGGGACGTGATGGTGGA	0.652													53	88	---	---	---	---	PASS
NUP210L	91181	broad.mit.edu	37	1	154027277	154027277	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154027277T>G	uc001fdw.2	-	24	3344	c.3272A>C	c.(3271-3273)AAA>ACA	p.K1091T	NUP210L_uc009woq.2_5'UTR|NUP210L_uc010peh.1_Missense_Mutation_p.K1091T	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	1091						integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CAGTGTCATTTTCTCTGGAAG	0.368													18	25	---	---	---	---	PASS
NUP210L	91181	broad.mit.edu	37	1	154027278	154027278	+	Nonsense_Mutation	SNP	T	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154027278T>A	uc001fdw.2	-	24	3343	c.3271A>T	c.(3271-3273)AAA>TAA	p.K1091*	NUP210L_uc009woq.2_5'UTR|NUP210L_uc010peh.1_Nonsense_Mutation_p.K1091*	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	1091						integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			AGTGTCATTTTCTCTGGAAGA	0.368													18	23	---	---	---	---	PASS
LAD1	3898	broad.mit.edu	37	1	201354880	201354880	+	Silent	SNP	T	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201354880T>G	uc001gwm.2	-	4	1315	c.1080A>C	c.(1078-1080)CGA>CGC	p.R360R	LAD1_uc009wzu.1_Silent_p.R382R	NM_005558	NP_005549	O00515	LAD1_HUMAN	ladinin 1	360						basement membrane	structural molecule activity				0						TGCTGTAGGTTCGCTGTGTGG	0.537											OREG0014078	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	44	131	---	---	---	---	PASS
LAD1	3898	broad.mit.edu	37	1	201354881	201354881	+	Missense_Mutation	SNP	C	A	A	rs143101113		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201354881C>A	uc001gwm.2	-	4	1314	c.1079G>T	c.(1078-1080)CGA>CTA	p.R360L	LAD1_uc009wzu.1_Missense_Mutation_p.R382L	NM_005558	NP_005549	O00515	LAD1_HUMAN	ladinin 1	360						basement membrane	structural molecule activity				0						GCTGTAGGTTCGCTGTGTGGG	0.537											OREG0014078	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	43	127	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235922372	235922372	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235922372G>A	uc001hxj.2	-	23	6956	c.6781C>T	c.(6781-6783)CGT>TGT	p.R2261C	LYST_uc009xgb.1_RNA|LYST_uc010pxs.1_RNA	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	2261					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			CTTGGCCAACGGCCAACAGCT	0.473									Chediak-Higashi_syndrome				21	45	---	---	---	---	PASS
AKT3	10000	broad.mit.edu	37	1	243859018	243859018	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243859018C>A	uc001iab.1	-	2	128	c.47G>T	c.(46-48)GGA>GTA	p.G16V	AKT3_uc001hzz.1_Missense_Mutation_p.G16V	NM_005465	NP_005456	Q9Y243	AKT3_HUMAN	AKT3 kinase isoform 1	16	PH.				signal transduction	Golgi apparatus|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|lung(1)|breast(1)|central_nervous_system(1)	4	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			TATATATTCTCCTACATGAGG	0.348													4	36	---	---	---	---	PASS
COLEC11	78989	broad.mit.edu	37	2	3691555	3691555	+	Silent	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3691555C>T	uc002qya.2	+	7	811	c.663C>T	c.(661-663)CCC>CCT	p.P221P	COLEC11_uc002qxz.2_Silent_p.P218P|COLEC11_uc002qyb.2_Silent_p.P197P|COLEC11_uc002qyc.2_Silent_p.P197P|COLEC11_uc010ewo.2_Silent_p.P173P|COLEC11_uc010ewp.2_Silent_p.P195P|COLEC11_uc010ewq.2_Silent_p.P171P|COLEC11_uc010ewr.2_Silent_p.P171P|COLEC11_uc010ews.2_Silent_p.P147P	NM_024027	NP_076932	Q9BWP8	COL11_HUMAN	collectin sub-family member 11 isoform a	221	C-type lectin.					collagen	mannose binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		ACCACTCCCCCATGCGGACCT	0.642													37	55	---	---	---	---	PASS
NRBP1	29959	broad.mit.edu	37	2	27663340	27663340	+	Silent	SNP	C	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27663340C>A	uc002rko.2	+	13	1939	c.1107C>A	c.(1105-1107)ATC>ATA	p.I369I	NRBP1_uc002rkq.2_Silent_p.I368I|NRBP1_uc002rkp.2_Silent_p.I369I|NRBP1_uc002rkr.2_Silent_p.I160I|KRTCAP3_uc002rks.2_5'Flank|KRTCAP3_uc010ylr.1_5'Flank|KRTCAP3_uc002rkt.2_5'Flank	NM_013392	NP_037524	Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein	369					ER to Golgi vesicle-mediated transport|gene expression|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cell cortex|endomembrane system|lamellipodium|membrane|nucleoplasm	ATP binding|protein homodimerization activity|protein kinase activity			ovary(2)|lung(1)	3	Acute lymphoblastic leukemia(172;0.155)					TGGCTGAAATCCCTGCAGGAC	0.493													12	30	---	---	---	---	PASS
MTA3	57504	broad.mit.edu	37	2	42909669	42909669	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42909669C>G	uc002rso.1	+	10	1333	c.663C>G	c.(661-663)AGC>AGG	p.S221R	MTA3_uc002rsp.1_Missense_Mutation_p.S221R|MTA3_uc002rsq.2_Missense_Mutation_p.S277R|MTA3_uc002rsr.2_Missense_Mutation_p.S277R	NM_020744	NP_065795	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3	277	SANT.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						CTGAAGCTAGCTTATTTGAAG	0.388													6	17	---	---	---	---	PASS
MSH6	2956	broad.mit.edu	37	2	48032817	48032817	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48032817C>A	uc002rwd.3	+	7	3769	c.3617C>A	c.(3616-3618)GCA>GAA	p.A1206E	MSH6_uc010fbj.2_Missense_Mutation_p.A904E|MSH6_uc010yoi.1_Missense_Mutation_p.A1076E|MSH6_uc010yoj.1_Missense_Mutation_p.A904E	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	1206					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CATGCAACAGCACATTCTCTG	0.294			Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				37	75	---	---	---	---	PASS
MPHOSPH10	10199	broad.mit.edu	37	2	71368393	71368393	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71368393C>G	uc002sht.1	+	7	1692	c.1340C>G	c.(1339-1341)CCT>CGT	p.P447R		NM_005791	NP_005782	O00566	MPP10_HUMAN	M-phase phosphoprotein 10	447					RNA splicing, via transesterification reactions|rRNA processing	chromosome|nucleolus|small nucleolar ribonucleoprotein complex	protein binding			skin(2)|ovary(1)	3						AAAGAAAAACCTAAAGAGGAT	0.338													65	130	---	---	---	---	PASS
RAPH1	65059	broad.mit.edu	37	2	204356027	204356027	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204356027T>G	uc002vad.2	-	3	361	c.136A>C	c.(136-138)AAG>CAG	p.K46Q	RAPH1_uc002vae.2_Missense_Mutation_p.K46Q|RAPH1_uc002vaf.2_Missense_Mutation_p.K46Q	NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains	46					cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10						TCCATGGGCTTGTCAGAATCC	0.318													27	61	---	---	---	---	PASS
OSBPL10	114884	broad.mit.edu	37	3	31921168	31921168	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31921168C>A	uc003cev.2	-	3	817	c.436G>T	c.(436-438)GGA>TGA	p.G146*	OSBPL10_uc011axf.1_Nonsense_Mutation_p.G146*	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10	146	PH.				lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)		AACATCTCTCCATTAGCAGAG	0.468													4	65	---	---	---	---	PASS
CNOT10	25904	broad.mit.edu	37	3	32775009	32775009	+	Nonsense_Mutation	SNP	C	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32775009C>G	uc003cfc.1	+	11	1565	c.1310C>G	c.(1309-1311)TCA>TGA	p.S437*	CNOT10_uc011axi.1_Nonsense_Mutation_p.S209*|CNOT10_uc003cfd.1_Nonsense_Mutation_p.S436*|CNOT10_uc003cfe.1_Nonsense_Mutation_p.S437*|CNOT10_uc010hfv.1_RNA|CNOT10_uc011axj.1_Nonsense_Mutation_p.S497*|CNOT10_uc010hfw.1_Nonsense_Mutation_p.S132*	NM_015442	NP_056257	Q9H9A5	CNOTA_HUMAN	CCR4-NOT transcription complex, subunit 10	437					nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2						GTTTTGGCATCACAGTCTATA	0.289													3	40	---	---	---	---	PASS
LRTM1	57408	broad.mit.edu	37	3	54962027	54962027	+	5'UTR	SNP	G	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54962027G>C	uc003dhl.2	-	1					CACNA2D3_uc003dhf.2_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron	NM_020678	NP_065729	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1							integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		CAGACTCAGAGCCCAGCTTTA	0.463													25	26	---	---	---	---	PASS
ZNF654	55279	broad.mit.edu	37	3	88189697	88189697	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88189697A>G	uc003dqv.2	+	1	1436	c.1237A>G	c.(1237-1239)ATG>GTG	p.M413V	CGGBP1_uc003dqu.2_Intron	NM_018293	NP_060763	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	413					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		AGACCAAAAGATGCCTGACAT	0.343													23	32	---	---	---	---	PASS
NIT2	56954	broad.mit.edu	37	3	100058770	100058770	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100058770C>G	uc003dtv.2	+	3	312	c.238C>G	c.(238-240)CTC>GTC	p.L80V	NIT2_uc011bha.1_Missense_Mutation_p.L80V	NM_020202	NP_064587	Q9NQR4	NIT2_HUMAN	nitrilase family, member 2	80	CN hydrolase.				nitrogen compound metabolic process		omega-amidase activity			ovary(1)	1						CAGCATATATCTCATTGGAGG	0.303													31	27	---	---	---	---	PASS
ADH6	130	broad.mit.edu	37	4	100125313	100125313	+	3'UTR	SNP	A	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100125313A>T	uc003huo.2	-	9					uc003hum.1_Intron|ADH6_uc011cef.1_3'UTR	NM_001102470	NP_001095940	P28332	ADH6_HUMAN	class V alcohol dehydrogenase isoform 1						ethanol oxidation|response to ethanol|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|electron carrier activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)|NADH(DB00157)	AATCATGAAAATTACATCAAA	0.358													27	33	---	---	---	---	PASS
RPS3A	6189	broad.mit.edu	37	4	152022142	152022142	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152022142G>A	uc003ilz.2	+	3	233	c.182G>A	c.(181-183)GGT>GAT	p.G61D	RPS3A_uc011cie.1_Missense_Mutation_p.G61D|SNORD73A_uc003ima.1_5'Flank	NM_001006	NP_000997	P61247	RS3A_HUMAN	ribosomal protein S3a	61					cell differentiation|endocrine pancreas development|induction of apoptosis|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_hematologic(180;0.093)					GCATCTGATGGTCTCAAGGGT	0.348													31	66	---	---	---	---	PASS
SLC23A1	9963	broad.mit.edu	37	5	138715429	138715429	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138715429G>T	uc003leh.2	-	8	960	c.863C>A	c.(862-864)GCA>GAA	p.A288E	SLC23A1_uc003leg.2_Missense_Mutation_p.A292E	NM_005847	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (nucleobase	288					brain development|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|response to toxin|transepithelial L-ascorbic acid transport|water-soluble vitamin metabolic process	apical plasma membrane|cytoplasm|integral to plasma membrane|intracellular organelle|membrane fraction	dehydroascorbic acid transporter activity|L-ascorbate:sodium symporter activity|nucleobase transmembrane transporter activity|protein binding|sodium-dependent L-ascorbate transmembrane transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	ATCGGTTCGTGCCTGGAAGCC	0.592													40	101	---	---	---	---	PASS
HIST1H2AJ	8331	broad.mit.edu	37	6	27782408	27782408	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27782408T>G	uc003njn.1	-	1	111	c.111A>C	c.(109-111)AAA>AAC	p.K37N	HIST1H2BM_uc003njo.2_5'Flank	NM_021066	NP_066544	Q99878	H2A1J_HUMAN	histone cluster 1, H2aj	37					nucleosome assembly	nucleosome|nucleus	DNA binding				0						CATAGTTGCCTTTGCGGAGCA	0.672													23	45	---	---	---	---	PASS
HLA-F	3134	broad.mit.edu	37	6	29694668	29694668	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29694668G>A	uc003nno.3	+	7	1169	c.1045G>A	c.(1045-1047)GTG>ATG	p.V349M	HLA-F_uc011dlx.1_Missense_Mutation_p.V349M|HLA-F_uc011dly.1_RNA|LOC285830_uc003nnp.2_RNA|LOC285830_uc011dlz.1_RNA	NM_001098479	NP_001091949	P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	Error:Variant_position_missing_in_P30511_after_alignment					antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity				0						AGCCTACTCAGTGGTCAGCGG	0.463													42	108	---	---	---	---	PASS
BAT2	7916	broad.mit.edu	37	6	31599818	31599818	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31599818A>C	uc003nvb.3	+	16	3617	c.3368A>C	c.(3367-3369)GAG>GCG	p.E1123A	BAT2_uc011dnv.1_Intron|BAT2_uc003nvc.3_Missense_Mutation_p.E1123A	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	1123	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0						TCAGACAAGGAGGCTCCCACA	0.647													18	46	---	---	---	---	PASS
PRIM2	5558	broad.mit.edu	37	6	57185310	57185310	+	Silent	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57185310C>T	uc003pdx.2	+	3	297	c.210C>T	c.(208-210)TAC>TAT	p.Y70Y	PRIM2_uc003pdv.1_Silent_p.Y70Y|PRIM2_uc003pdw.2_Silent_p.Y70Y	NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2	70					DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CTGAACAATACCAGAGTAAGT	0.308													8	12	---	---	---	---	PASS
MICALL2	79778	broad.mit.edu	37	7	1487214	1487214	+	Silent	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1487214C>T	uc003skj.3	-	4	669	c.522G>A	c.(520-522)AAG>AAA	p.K174K		NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1	174						cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		AGCTTACAGTCTTGGGGGGCG	0.677													12	14	---	---	---	---	PASS
VPS41	27072	broad.mit.edu	37	7	38816289	38816289	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38816289G>A	uc003tgy.2	-	11	898	c.872C>T	c.(871-873)TCA>TTA	p.S291L	VPS41_uc003tgz.2_Missense_Mutation_p.S266L|VPS41_uc010kxn.2_Missense_Mutation_p.S202L	NM_014396	NP_055211	P49754	VPS41_HUMAN	vacuolar protein sorting 41 isoform 1	291					Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4						CGTTTTTTCTGAAATCTCCTT	0.403													12	35	---	---	---	---	PASS
SGCE	8910	broad.mit.edu	37	7	94257637	94257637	+	Silent	SNP	T	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94257637T>A	uc003unl.2	-	3	378	c.267A>T	c.(265-267)ACA>ACT	p.T89T	SGCE_uc003unm.2_Silent_p.T89T|SGCE_uc003unn.2_Silent_p.T89T|SGCE_uc011kic.1_Silent_p.T48T|SGCE_uc011kid.1_Silent_p.T125T	NM_003919	NP_003910	O43556	SGCE_HUMAN	sarcoglycan, epsilon isoform 2	89	Extracellular (Potential).				cell-matrix adhesion|muscle organ development	cytoplasm|cytoskeleton|integral to plasma membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(1)	1	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			CCATTAAATTTGTATTAAATG	0.383													39	37	---	---	---	---	PASS
SERPINE1	5054	broad.mit.edu	37	7	100779089	100779089	+	Intron	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100779089C>T	uc003uxt.2	+						SERPINE1_uc011kkj.1_Intron|SERPINE1_uc003uxu.1_3'UTR	NM_000602	NP_000593	P05121	PAI1_HUMAN	plasminogen activator inhibitor-1 isoform 1						angiogenesis|cellular response to chemical stimulus|cellular response to lipopolysaccharide|chronological cell aging|defense response to Gram-negative bacterium|fibrinolysis|negative regulation of apoptosis|negative regulation of cell adhesion mediated by integrin|negative regulation of fibrinolysis|negative regulation of plasminogen activation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell-matrix adhesion|negative regulation of vascular wound healing|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of interleukin-8 production|positive regulation of leukotriene production involved in inflammatory response|positive regulation of monocyte chemotaxis|positive regulation of receptor-mediated endocytosis|regulation of receptor activity	extracellular matrix|extracellular space|plasma membrane|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)				Atorvastatin(DB01076)|Dimethyl sulfoxide(DB01093)|Drotrecogin alfa(DB00055)|Simvastatin(DB00641)|Tenecteplase(DB00031)|Troglitazone(DB00197)|Urokinase(DB00013)	ACAGGTGAGTCTGGCTCAGGT	0.627													21	59	---	---	---	---	PASS
SDR16C5	195814	broad.mit.edu	37	8	57219234	57219234	+	Splice_Site	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57219234C>T	uc003xsy.1	-	5	1348	c.710_splice	c.e5+1	p.G237_splice	SDR16C5_uc010lyk.1_Splice_Site_p.G237_splice|SDR16C5_uc010lyl.1_Splice_Site_p.G193_splice	NM_138969	NP_620419	Q8N3Y7	RDHE2_HUMAN	epidermal retinal dehydrogenase 2						detection of light stimulus involved in visual perception|keratinocyte proliferation|retinal metabolic process|retinol metabolic process	endoplasmic reticulum membrane|integral to membrane|integral to membrane of membrane fraction	binding|retinol dehydrogenase activity			ovary(1)|central_nervous_system(1)|skin(1)	3						GACATACTTACCCTGTAGTAC	0.289													14	47	---	---	---	---	PASS
ENPP2	5168	broad.mit.edu	37	8	120569905	120569905	+	Silent	SNP	T	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120569905T>C	uc003yot.1	-	25	2534	c.2448A>G	c.(2446-2448)GTA>GTG	p.V816V	ENPP2_uc011lic.1_Silent_p.V354V|ENPP2_uc003yor.1_Silent_p.V451V|ENPP2_uc003yos.1_Silent_p.V868V|ENPP2_uc010mdd.1_Silent_p.V841V	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	autotaxin isoform 2 preproprotein	816					cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TGAGTTCTTCTACCCATTTTG	0.458													48	88	---	---	---	---	PASS
ADCY8	114	broad.mit.edu	37	8	131896886	131896886	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131896886C>T	uc003ytd.3	-	8	2289	c.2033G>A	c.(2032-2034)CGG>CAG	p.R678Q	ADCY8_uc010mds.2_Missense_Mutation_p.R678Q	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	678	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			ATCGCCACTCCGCAAGTCGAT	0.458										HNSCC(32;0.087)			57	65	---	---	---	---	PASS
DENND4C	55667	broad.mit.edu	37	9	19371987	19371987	+	Intron	SNP	T	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19371987T>G	uc003znq.2	+						DENND4C_uc011lnc.1_Intron|DENND4C_uc011lnd.1_Intron|DENND4C_uc003znr.2_3'UTR|DENND4C_uc003zns.2_Intron	NM_017925	NP_060395	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C							integral to membrane				ovary(1)|skin(1)	2						TGAACGGCTGTTGTCTTTCTT	0.274													12	62	---	---	---	---	PASS
FRMPD1	22844	broad.mit.edu	37	9	37744497	37744497	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37744497G>T	uc004aag.1	+	16	2512	c.2468G>T	c.(2467-2469)AGC>ATC	p.S823I	FRMPD1_uc004aah.1_Missense_Mutation_p.S823I	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	823						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		AGACAGCCAAGCAGGAGGGGA	0.537													4	118	---	---	---	---	PASS
HIATL1	84641	broad.mit.edu	37	9	97220627	97220627	+	Nonsense_Mutation	SNP	G	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97220627G>T	uc004aur.2	+	11	1419	c.1150G>T	c.(1150-1152)GGA>TGA	p.G384*	HIATL1_uc011luh.1_Missense_Mutation_p.W286L	NM_032558	NP_115947	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1	384	Extracellular (Potential).				transmembrane transport	integral to membrane|plasma membrane	protein binding|transporter activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)				GATCATAACTGGAATAAGAGG	0.448													5	113	---	---	---	---	PASS
ZBTB26	57684	broad.mit.edu	37	9	125681478	125681478	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125681478C>A	uc004bnj.2	-	2	948	c.736G>T	c.(736-738)GGC>TGC	p.G246C	ZBTB26_uc004bnk.2_Missense_Mutation_p.G246C	NM_020924	NP_065975	Q9HCK0	ZBT26_HUMAN	zinc finger and BTB domain containing 26	246					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTATCACTGCCTGTATAAGAA	0.433													57	101	---	---	---	---	PASS
YME1L1	10730	broad.mit.edu	37	10	27431334	27431334	+	Missense_Mutation	SNP	C	G	G	rs143591480		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27431334C>G	uc001iti.2	-	5	765	c.583G>C	c.(583-585)GAT>CAT	p.D195H	YME1L1_uc001itj.2_Missense_Mutation_p.D138H|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_RNA	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1	195					protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						TACTGAAGATCTGAACAAATG	0.318													47	112	---	---	---	---	PASS
KCNK7	10089	broad.mit.edu	37	11	65360885	65360885	+	Intron	SNP	G	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65360885G>T	uc001oes.2	-						KCNK7_uc001oeq.2_Intron|KCNK7_uc001oer.2_Intron|KCNK7_uc001oeu.2_3'UTR	NM_033347	NP_203133	Q9Y2U2	KCNK7_HUMAN	potassium channel, subfamily K, member 7 isoform							integral to membrane	potassium channel activity|voltage-gated ion channel activity				0						GTGATTTATGGGAGTCCTAGT	0.617													4	67	---	---	---	---	PASS
TTC12	54970	broad.mit.edu	37	11	113194723	113194723	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113194723A>C	uc001pnu.2	+	4	335	c.230A>C	c.(229-231)GAA>GCA	p.E77A	TTC12_uc001pnv.2_Missense_Mutation_p.E77A|TTC12_uc001pnw.2_RNA|TTC12_uc001pnx.2_5'UTR	NM_017868	NP_060338	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	77							binding			pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		CAGAGTGCAGAAGAAATAAAC	0.323													10	26	---	---	---	---	PASS
FAM55D	54827	broad.mit.edu	37	11	114451052	114451052	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114451052C>T	uc001ppc.2	-	5	1082	c.901G>A	c.(901-903)GTT>ATT	p.V301I	FAM55D_uc001ppd.2_Missense_Mutation_p.V17I	NM_001077639	NP_001071107	Q6UWF7	FA55D_HUMAN	hypothetical protein LOC54827 isoform 1	301						extracellular region				ovary(2)|skin(2)	4		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.82e-06)|Epithelial(105;0.000129)|all cancers(92;0.000938)		TTCATTGCAACTGTTTCTTCT	0.408													33	65	---	---	---	---	PASS
MIR614	693199	broad.mit.edu	37	12	13068802	13068802	+	RNA	SNP	G	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13068802G>T	hsa-mir-614|MI0003627	+			c.40G>T			uc001rbb.3_RNA																	0						GCAGGGGCAGGCCAGCCCTGC	0.443													5	107	---	---	---	---	PASS
NACA	4666	broad.mit.edu	37	12	57118311	57118311	+	5'UTR	SNP	A	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57118311A>C	uc001slz.2	-	2					NACA_uc001sly.2_Intron|NACA_uc009zoy.1_Intron|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Intron|NACA_uc001smb.2_5'UTR|NACA_uc010squ.1_Intron	NM_001113201	NP_001106672	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha						interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1						GGCATTTCTGAAGGAAGGGAA	0.512			T	BCL6	NHL								7	12	---	---	---	---	PASS
HSP90B1	7184	broad.mit.edu	37	12	104332226	104332226	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104332226A>G	uc001tkb.1	+	7	1069	c.964A>G	c.(964-966)AAG>GAG	p.K322E	HSP90B1_uc010swg.1_5'UTR|HSP90B1_uc009zui.1_Intron	NM_003299	NP_003290	P14625	ENPL_HUMAN	heat shock protein 90kDa beta, member 1	322					actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm	ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding			ovary(2)|skin(1)	3					Rifabutin(DB00615)	aaagaaACCAAAGACTAAAAA	0.229													14	40	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19414102	19414102	+	RNA	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19414102C>T	uc010tcj.1	-	1		c.32008G>A				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						GAATTTTTACCAAAGATTGAT	0.274													4	11	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19414287	19414287	+	RNA	SNP	G	T	T	rs4037774	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19414287G>T	uc010tcj.1	-	1		c.31823C>A				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						TTTTCTTGTTGTAAGGTGCAT	0.274													3	21	---	---	---	---	PASS
PABPN1	8106	broad.mit.edu	37	14	23794554	23794554	+	3'UTR	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23794554G>A	uc001wjk.2	+	7					PABPN1_uc001wjh.3_3'UTR	NM_004643	NP_004634	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1						modification by virus of host mRNA processing|mRNA 3'-end processing|muscle contraction|nuclear mRNA splicing, via spliceosome|poly(A)+ mRNA export from nucleus|termination of RNA polymerase II transcription|viral infectious cycle	cytoplasm|nucleoplasm|ribonucleoprotein complex	nucleotide binding|protein binding|RNA binding			ovary(2)	2	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)		aaaaaaaaaagaattaaaaaa	0.299													10	16	---	---	---	---	PASS
DHRS4	10901	broad.mit.edu	37	14	24424160	24424160	+	Intron	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24424160C>T	uc001wla.2	+						C14orf167_uc001wkz.2_5'Flank|C14orf167_uc001wky.2_5'Flank|C14orf167_uc001wkx.2_5'Flank|C14orf167_uc010akx.1_RNA|DHRS4_uc010aky.2_Intron|DHRS4_uc001wlb.2_Intron|DHRS4_uc010akz.2_Intron|DHRS4_uc001wlc.3_Intron|DHRS4L2_uc001wld.3_Intron|DHRS4L2_uc001wle.3_Intron	NM_021004	NP_066284	Q9BTZ2	DHRS4_HUMAN	peroxisomal short-chain alcohol dehydrogenase							mitochondrion|nuclear membrane|peroxisome	binding|carbonyl reductase (NADPH) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	aattcaaacccgggcagtctt	0.303													14	35	---	---	---	---	PASS
EIF2S1	1965	broad.mit.edu	37	14	67831709	67831709	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67831709G>T	uc001xjg.2	+	2	366	c.225G>T	c.(223-225)AGG>AGT	p.R75S		NM_004094	NP_004085	P05198	IF2A_HUMAN	eukaryotic translation initiation factor 2,	75	S1 motif.					cytosol|eukaryotic translation initiation factor 2 complex|polysome|stress granule	protein binding|ribosome binding|translation initiation factor activity			ovary(1)	1				all cancers(60;0.000683)|OV - Ovarian serous cystadenocarcinoma(108;0.00579)|BRCA - Breast invasive adenocarcinoma(234;0.00937)		TTGTCATTAGGGTGGACAAAG	0.328													6	137	---	---	---	---	PASS
HHIPL1	84439	broad.mit.edu	37	14	100129224	100129224	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100129224C>G	uc010avs.2	+	6	1579	c.1514C>G	c.(1513-1515)TCC>TGC	p.S505C	HHIPL1_uc001ygl.1_Missense_Mutation_p.S505C	NM_001127258	NP_001120730	Q96JK4	HIPL1_HUMAN	HHIP-like protein 1 isoform a	505					carbohydrate metabolic process	extracellular region|membrane	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding|scavenger receptor activity			skin(2)	2		Melanoma(154;0.128)				CGTCTGATGTCCCTCCAAGAG	0.512													30	79	---	---	---	---	PASS
MAP1A	4130	broad.mit.edu	37	15	43821953	43821953	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43821953G>T	uc001zrt.2	+	5	8608	c.8141G>T	c.(8140-8142)CGA>CTA	p.R2714L		NM_002373	NP_002364	P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2714						cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(3)|breast(3)|pancreas(2)|skin(1)	9		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TTCTTCCGTCGAGTGCGTGCA	0.582													4	109	---	---	---	---	PASS
TSC2	7249	broad.mit.edu	37	16	2132493	2132493	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2132493G>A	uc002con.2	+	32	3977	c.3871G>A	c.(3871-3873)GTT>ATT	p.V1291I	TSC2_uc010bsd.2_Intron|TSC2_uc002coo.2_Intron|TSC2_uc010uvv.1_Intron|TSC2_uc010uvw.1_Intron|TSC2_uc002cop.2_Missense_Mutation_p.V1047I|TSC2_uc002coq.2_5'Flank|TSC2_uc002cor.2_5'Flank	NM_000548	NP_000539	P49815	TSC2_HUMAN	tuberous sclerosis 2 isoform 1	1291					cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)				GCACAGGAGCGTTTCCTGGGC	0.647			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				52	119	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	32191961	32191961	+	RNA	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32191961G>A	uc010vfv.1	-	6		c.887C>T								Homo sapiens cDNA FLJ60890 complete cds, moderately similar to HECT domain and RCC1-like domain-containing protein 2.																		GCTCTGGAACGTTTGCAGCAA	0.532													5	21	---	---	---	---	PASS
GAS8	2622	broad.mit.edu	37	16	90099333	90099333	+	Splice_Site	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90099333G>A	uc002fqi.1	+	4	617	c.495_splice	c.e4+1	p.L165_splice	GAS8_uc010vps.1_Splice_Site_p.L140_splice|GAS8_uc002fqh.2_Splice_Site_p.L82_splice|GAS8_uc010vpt.1_Splice_Site_p.L165_splice|GAS8_uc010vpu.1_Splice_Site_p.L82_splice|GAS8_uc010vpv.1_Splice_Site_p.L136_splice|GAS8_uc010cjc.1_Splice_Site_p.L82_splice|GAS8_uc010vpw.1_Splice_Site_p.L82_splice|GAS8_uc002fqj.1_Splice_Site	NM_001481	NP_001472	O95995	GAS8_HUMAN	growth arrest-specific 8						negative regulation of cell proliferation|sperm motility	cilium|Golgi apparatus|microtubule|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		CCTGCGGCTGGTAGGTGTGGC	0.428													8	17	---	---	---	---	PASS
C17orf75	64149	broad.mit.edu	37	17	30665271	30665271	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30665271T>G	uc002hhg.2	-	4	478	c.447A>C	c.(445-447)GAA>GAC	p.E149D		NM_022344	NP_071739	Q9HAS0	NJMU_HUMAN	hypothetical protein LOC64149	149					spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			AGACCACATATTCTGAAGGGT	0.403													48	117	---	---	---	---	PASS
CDK12	51755	broad.mit.edu	37	17	37650846	37650846	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37650846G>A	uc010cvv.2	+	5	2904	c.2318G>A	c.(2317-2319)CGT>CAT	p.R773H	CDK12_uc010wef.1_Missense_Mutation_p.R772H|CDK12_uc002hrw.3_Missense_Mutation_p.R773H	NM_016507	NP_057591	Q9NYV4	CDK12_HUMAN	Cdc2-related kinase, arginine/serine-rich	773	Protein kinase.				mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1)	19						ACAGCCATTCGTGAAATCAAA	0.264										TCGA Ovarian(9;0.13)			7	26	---	---	---	---	PASS
CNTNAP1	8506	broad.mit.edu	37	17	40844591	40844591	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40844591G>C	uc002iay.2	+	17	2821	c.2605G>C	c.(2605-2607)GAG>CAG	p.E869Q	CNTNAP1_uc010wgs.1_RNA	NM_003632	NP_003623	P78357	CNTP1_HUMAN	contactin associated protein 1 precursor	869	Laminin G-like 3.|Extracellular (Potential).				axon guidance|cell adhesion	paranode region of axon	receptor activity|receptor binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(3)|breast(3)|upper_aerodigestive_tract(1)|lung(1)	8		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		AGACGACTTTGAGTTCAATGA	0.587													39	132	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630855	44630855	+	3'UTR	SNP	G	C	C	rs144516284	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630855G>C	uc002iks.2	-	4					LRRC37A2_uc002ikn.1_Intron|ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Intron	NM_001113738	NP_001107210	Q8IVW1	ARL17_HUMAN	hypothetical protein LOC51326 isoform a						protein transport|vesicle-mediated transport	Golgi apparatus	GTP binding				0						cttctcttttgagacggagtt	0.139													4	90	---	---	---	---	PASS
HELZ	9931	broad.mit.edu	37	17	65184580	65184580	+	Silent	SNP	T	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65184580T>C	uc010wqk.1	-	12	1204	c.1017A>G	c.(1015-1017)CAA>CAG	p.Q339Q	HELZ_uc002jfv.3_RNA|HELZ_uc002jfx.3_Silent_p.Q339Q	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					CTAATCCATTTTGGGCCATCT	0.383													134	286	---	---	---	---	PASS
C17orf62	79415	broad.mit.edu	37	17	80401837	80401837	+	3'UTR	SNP	T	C	C	rs11557531	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80401837T>C	uc002kez.2	-	6					C17orf62_uc002kex.2_Silent_p.P54P|C17orf62_uc002key.2_Silent_p.P54P|C17orf62_uc002kfa.2_3'UTR|C17orf62_uc010dir.2_3'UTR|C17orf62_uc002kfb.3_3'UTR|C17orf62_uc002kfc.3_3'UTR|C17orf62_uc002kfd.3_Silent_p.P54P|C17orf62_uc002kfe.3_Silent_p.P54P	NM_001100407	NP_001093877	Q9BQA9	CQ062_HUMAN	hypothetical protein LOC79415 isoform a							integral to membrane	protein binding				0	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GAATGTGCCATGGGTCCTGTG	0.687													11	297	---	---	---	---	PASS
LOC727896	727896	broad.mit.edu	37	18	2945478	2945478	+	3'UTR	SNP	C	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2945478C>A	uc010wyu.1	-	1					LPIN2_uc002klo.2_Intron	NR_026659				Homo sapiens cDNA clone IMAGE:4614712, containing frame-shift errors.												0						ATGACAGCAGCAAGCCACCAC	0.388													9	9	---	---	---	---	PASS
DLGAP1	9229	broad.mit.edu	37	18	3502638	3502638	+	Silent	SNP	A	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3502638A>G	uc002kmf.2	-	9	2644	c.2577T>C	c.(2575-2577)CCT>CCC	p.P859P	DLGAP1_uc010wyz.1_Silent_p.P859P|DLGAP1_uc002kme.1_Silent_p.P557P|DLGAP1_uc010dkn.2_Silent_p.P567P|DLGAP1_uc010wyw.1_Silent_p.P565P|DLGAP1_uc010wyx.1_Silent_p.P581P|DLGAP1_uc010wyy.1_Silent_p.P543P|DLGAP1_uc002kmg.2_Silent_p.P557P	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform	859					synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				GATGAGCATTAGGATTCTGCA	0.388													36	64	---	---	---	---	PASS
ZCCHC2	54877	broad.mit.edu	37	18	60241796	60241796	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60241796A>G	uc002lip.3	+	13	2482	c.2482A>G	c.(2482-2484)ACA>GCA	p.T828A	ZCCHC2_uc002lio.2_RNA|ZCCHC2_uc002liq.2_Missense_Mutation_p.T298A	NM_017742	NP_060212	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	828					cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding			lung(1)|prostate(1)	2						TGAGAGCTGCACAGTTAACAT	0.498													38	56	---	---	---	---	PASS
SMARCA4	6597	broad.mit.edu	37	19	11098575	11098575	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11098575G>C	uc002mqf.3	+	6	1377	c.1093G>C	c.(1093-1095)GAG>CAG	p.E365Q	SMARCA4_uc010dxp.2_Missense_Mutation_p.E365Q|SMARCA4_uc010dxo.2_Missense_Mutation_p.E365Q|SMARCA4_uc002mqg.1_Missense_Mutation_p.E365Q|SMARCA4_uc010dxq.2_Missense_Mutation_p.E365Q|SMARCA4_uc010dxr.2_Missense_Mutation_p.E365Q|SMARCA4_uc002mqj.3_Missense_Mutation_p.E365Q|SMARCA4_uc010dxs.2_Missense_Mutation_p.E365Q|SMARCA4_uc002mqe.2_Missense_Mutation_p.E365Q	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	365					chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CGACCCTGTGGAGATCCTGCA	0.692			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				11	20	---	---	---	---	PASS
ZNF208	7757	broad.mit.edu	37	19	22155223	22155223	+	Silent	SNP	T	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22155223T>C	uc002nqp.2	-	5	2462	c.2313A>G	c.(2311-2313)AAA>AAG	p.K771K	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTGAGGGCCATTTATAGGCTT	0.373													3	85	---	---	---	---	PASS
ZNF615	284370	broad.mit.edu	37	19	52496685	52496685	+	Silent	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52496685G>A	uc002pye.1	-	6	1936	c.1644C>T	c.(1642-1644)GGC>GGT	p.G548G	ZNF615_uc002pyf.1_Silent_p.G559G|ZNF615_uc002pyg.1_Silent_p.G440G|ZNF615_uc002pyh.1_Silent_p.G559G|ZNF615_uc010epi.1_Silent_p.G555G|ZNF615_uc010ydg.1_Silent_p.G553G	NM_198480	NP_940882	Q8N8J6	ZN615_HUMAN	zinc finger protein 615	548	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TCTCAGTGAAGCCTTTTCCAC	0.448													59	108	---	---	---	---	PASS
ZNF616	90317	broad.mit.edu	37	19	52618981	52618981	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52618981C>T	uc002pym.2	-	4	1719	c.1436G>A	c.(1435-1437)CGA>CAA	p.R479Q	ZNF616_uc002pyn.2_RNA	NM_178523	NP_848618	Q08AN1	ZN616_HUMAN	zinc finger protein 616	479	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		AGCTGCAAGTCGTGAATGTAT	0.418													52	128	---	---	---	---	PASS
ZNF551	90233	broad.mit.edu	37	19	58198816	58198816	+	Silent	SNP	T	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58198816T>C	uc002qpw.3	+	3	1348	c.1125T>C	c.(1123-1125)TAT>TAC	p.Y375Y	ZNF551_uc002qpv.3_Silent_p.Y318Y|ZNF776_uc002qpx.2_Intron	NM_138347	NP_612356	Q7Z340	ZN551_HUMAN	zinc finger protein 551	391	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AAAGGCCTTATCAGTGCTGTG	0.448													42	63	---	---	---	---	PASS
N6AMT1	29104	broad.mit.edu	37	21	30257617	30257617	+	Silent	SNP	G	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30257617G>T	uc002ymo.1	-	1	77	c.51C>A	c.(49-51)GGC>GGA	p.G17G	N6AMT1_uc002ymp.1_Silent_p.G17G|N6AMT1_uc002ymq.1_RNA	NM_013240	NP_037372	Q9Y5N5	HEMK2_HUMAN	N-6 adenine-specific DNA methyltransferase 1	17					positive regulation of cell growth	protein complex	nucleic acid binding|protein binding|protein methyltransferase activity				0						CGCTGAAGGCGCCGCGGCCCA	0.682													8	94	---	---	---	---	PASS
RCAN1	1827	broad.mit.edu	37	21	35893781	35893781	+	Intron	SNP	C	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35893781C>G	uc002yue.2	-						RCAN1_uc002yuc.2_Intron|RCAN1_uc002yud.2_Intron|RCAN1_uc002yub.2_Intron|RCAN1_uc011adx.1_Missense_Mutation_p.R146P	NM_004414	NP_004405	P53805	RCAN1_HUMAN	calcipressin 1 isoform a						blood circulation|calcium-mediated signaling|central nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0						CCCTCCCACCCGAGGGCCCTG	0.602													15	29	---	---	---	---	PASS
PCNT	5116	broad.mit.edu	37	21	47769001	47769001	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47769001C>A	uc002zji.3	+	7	1215	c.1108C>A	c.(1108-1110)CAA>AAA	p.Q370K	PCNT_uc002zjj.2_Missense_Mutation_p.Q252K|PCNT_uc010gqk.1_RNA	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	370	Glu-rich.|Potential.				cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					TGCAAAGCATCAATCAGAAAT	0.343													42	159	---	---	---	---	PASS
PCNT	5116	broad.mit.edu	37	21	47769614	47769614	+	Silent	SNP	G	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47769614G>T	uc002zji.3	+	8	1331	c.1224G>T	c.(1222-1224)CTG>CTT	p.L408L	PCNT_uc002zjj.2_Silent_p.L290L|PCNT_uc010gqk.1_RNA	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	408	Glu-rich.|Potential.				cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					TTAGGAACCTGGAGAGTCATC	0.498													6	171	---	---	---	---	PASS
APOL6	80830	broad.mit.edu	37	22	36055229	36055229	+	Silent	SNP	C	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36055229C>A	uc003aoe.2	+	3	912	c.618C>A	c.(616-618)ACC>ACA	p.T206T	APOL6_uc003aod.2_RNA	NM_030641	NP_085144	Q9BWW8	APOL6_HUMAN	apolipoprotein L6	206					lipoprotein metabolic process	cytoplasm|extracellular region	lipid binding|lipid transporter activity				0						GTCTTCTGACCACTGGCCAAG	0.537													4	81	---	---	---	---	PASS
PNPLA3	80339	broad.mit.edu	37	22	44342402	44342402	+	3'UTR	SNP	A	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44342402A>G	uc003bei.1	+	9					PNPLA3_uc010gzm.1_Intron	NM_025225	NP_079501	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3						triglyceride biosynthetic process|triglyceride catabolic process	integral to membrane	diolein transacylation activity|mono-olein transacylation activity|phospholipase A2 activity|triglyceride lipase activity				0		Ovarian(80;0.024)|all_neural(38;0.0416)				AGTTGGTTTTATGAAAAGCTA	0.502											OREG0026623	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	11	---	---	---	---	PASS
CERK	64781	broad.mit.edu	37	22	47116101	47116101	+	Silent	SNP	G	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47116101G>A	uc003bia.2	-	3	368	c.261C>T	c.(259-261)CAC>CAT	p.H87H		NM_022766	NP_073603	Q8TCT0	CERK1_HUMAN	ceramide kinase	87	Required for binding to sulfatide and phosphoinositides.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TCTTTACACAGTGAACTGCAC	0.522													24	30	---	---	---	---	PASS
MAP3K15	389840	broad.mit.edu	37	X	19478148	19478148	+	5'UTR	SNP	G	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19478148G>T	uc004czk.1	-	4					MAP3K15_uc004czj.1_5'UTR	NM_001001671	NP_001001671	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase								ATP binding|MAP kinase kinase kinase activity|metal ion binding			ovary(3)|lung(2)|stomach(1)|skin(1)	7	Hepatocellular(33;0.183)					TGATGTCTGAGGTCAGAACCT	0.483													4	56	---	---	---	---	PASS
ACRC	93953	broad.mit.edu	37	X	70823781	70823781	+	Missense_Mutation	SNP	G	C	C	rs141229655	byFrequency	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70823781G>C	uc004eae.2	+	8	1155	c.654G>C	c.(652-654)AAG>AAC	p.K218N	BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	218	Asp/Ser-rich.					nucleus				ovary(3)	3	Renal(35;0.156)					CCGACGACAAGAGTGATGATT	0.502													6	204	---	---	---	---	PASS
TMEM187	8269	broad.mit.edu	37	X	153247610	153247610	+	Missense_Mutation	SNP	G	T	T	rs139864308	byFrequency	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153247610G>T	uc004fjq.2	+	2	631	c.97G>T	c.(97-99)GTG>TTG	p.V33L	hsa-mir-3202-2|MI0014253_5'Flank	NM_003492	NP_003483	Q14656	TM187_HUMAN	transmembrane protein 187	33						integral to membrane|transport vesicle					0	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGTGTTTCCGTGCAAGTGGG	0.637													37	30	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	7913	7913	+	RNA	SNP	T	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:7913T>C	uc004cou.3	+	1		c.328T>C			uc011mfi.1_5'Flank|uc004cov.3_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP42.																		GAACCTACGAGTACACCGACT	0.502													17	284	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	8113	8113	+	RNA	SNP	C	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:8113C>A	uc004cou.3	+	1		c.528C>A			uc011mfi.1_5'Flank|uc004cov.3_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP42.																		GATGCAATTCCCGGACGTCTA	0.473													6	267	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15858	15858	+	3'UTR	SNP	T	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15858T>C	uc004coy.2	+	1					uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		AACTATCTCCCTAATTGAAAA	0.388													4	166	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16945236	16945239	+	RNA	DEL	TTAT	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16945236_16945239delTTAT	uc010ocf.1	-	4		c.918_921delATAA			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						AGGCATTACCTTATTTAAAGTTCA	0.373													8	4	---	---	---	---	
ESPNP	284729	broad.mit.edu	37	1	17034614	17034615	+	Intron	INS	-	CC	CC			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17034614_17034615insCC	uc001azn.1	-						ESPNP_uc010ocj.1_Intron	NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						TCAGCGCCTCACCCCCTCCGAG	0.728													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	50871283	50871284	+	IGR	INS	-	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50871283_50871284insC								ELAVL4 (203743 upstream) : DMRTA2 (11945 downstream)																							CTGCATAGGTTCCTTGGTGTGC	0.401													30	13	---	---	---	---	
GPA33	10223	broad.mit.edu	37	1	167026111	167026112	+	Intron	INS	-	GGCA	GGCA			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167026111_167026112insGGCA	uc001gea.1	-							NM_005814	NP_005805	Q99795	GPA33_HUMAN	transmembrane glycoprotein A33 precursor							integral to plasma membrane	receptor activity				0						tgtggtgtgtggtgtgtgtggt	0.000													4	2	---	---	---	---	
CD34	947	broad.mit.edu	37	1	208084199	208084200	+	Intron	INS	-	G	G	rs150714878	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208084199_208084200insG	uc001hgw.1	-						CD34_uc001hgx.1_Intron|CD34_uc010psj.1_Intron	NM_001025109	NP_001020280	P28906	CD34_HUMAN	CD34 antigen isoform a						cell-cell adhesion|leukocyte migration|regulation of immune response	integral to membrane	carbohydrate binding			ovary(1)	1						GCGCTGGCCCCGGGGGGAAGCA	0.683													3	4	---	---	---	---	
DISP1	84976	broad.mit.edu	37	1	223165176	223165177	+	Intron	INS	-	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223165176_223165177insT	uc001hnu.1	+							NM_032890	NP_116279	Q96F81	DISP1_HUMAN	dispatched A						diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)		GTGAGATTTTCTTTTTTTTTTT	0.317													4	2	---	---	---	---	
AHCTF1	25909	broad.mit.edu	37	1	247087043	247087044	+	Intron	DEL	GT	-	-	rs74456165		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247087043_247087044delGT	uc001ibv.1	-							NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS						cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			gcgtgcatgcgtgtgtgtgtgt	0.361													3	3	---	---	---	---	
TAF1B	9014	broad.mit.edu	37	2	9983579	9983594	+	5'UTR	DEL	TTTCCGGCCGGAAGCT	-	-	rs62621835	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9983579_9983594delTTTCCGGCCGGAAGCT	uc002qzz.2	+	1					TAF1B_uc010exc.2_5'UTR|TAF1B_uc002qzy.3_5'UTR|TAF1B_uc010yja.1_5'UTR|TAF1B_uc010exd.2_5'UTR	NM_005680	NP_005671	Q53T94	TAF1B_HUMAN	TBP-associated factor 1B						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGATCTCGCGTTTCCGGCCGGAAGCTTCTCCAGCCT	0.708													3	8	---	---	---	---	
RAD51AP2	729475	broad.mit.edu	37	2	17696274	17696275	+	Intron	INS	-	A	A	rs34060092		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17696274_17696275insA	uc002rcl.1	-						RAD51AP2_uc010exn.1_Intron	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CTTCTTGCTGGAAAAAAAAAAA	0.307													3	5	---	---	---	---	
XDH	7498	broad.mit.edu	37	2	31628978	31628979	+	Intron	INS	-	TTTAA	TTTAA			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31628978_31628979insTTTAA	uc002rnv.1	-							NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase						purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)	taaatctcatgtttaattgtaa	0.109													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129098917	129098919	+	IGR	DEL	GTG	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129098917_129098919delGTG								HS6ST1 (22746 upstream) : None (None downstream)																							ggtattggtagtggtggtgatgg	0.103													5	4	---	---	---	---	
DYTN	391475	broad.mit.edu	37	2	207574185	207574186	+	Intron	DEL	AC	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207574185_207574186delAC	uc002vbr.1	-							NM_001093730	NP_001087199	A2CJ06	DYTN_HUMAN	dystrotelin							plasma membrane	zinc ion binding			ovary(1)|central_nervous_system(1)	2				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		acacacacagacacacacacac	0.188													4	2	---	---	---	---	
PER2	8864	broad.mit.edu	37	2	239186719	239186720	+	Intron	INS	-	TCTCTCTG	TCTCTCTG	rs149341285	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239186719_239186720insTCTCTCTG	uc002vyc.2	-						PER2_uc010znv.1_Intron|PER2_uc010znw.1_Intron|PER2_uc010fyx.1_5'Flank	NM_022817	NP_073728	O15055	PER2_HUMAN	period 2						circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		TCTTTCTTTCTTCTCTCTGTCT	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	26990550	26990557	+	IGR	DEL	AGGAAGGG	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26990550_26990557delAGGAAGGG								LRRC3B (238287 upstream) : NEK10 (161838 downstream)																							gggaggaggaaggaagggaggaagggag	0.062													4	2	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52610585	52610585	+	Frame_Shift_Del	DEL	T	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52610585delT	uc003des.2	-	22	3675	c.3663delA	c.(3661-3663)GAAfs	p.E1221fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.E1221fs|PBRM1_uc003der.2_Frame_Shift_Del_p.E1189fs|PBRM1_uc003det.2_Frame_Shift_Del_p.E1236fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.E1236fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.E1221fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.E1196fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.E1196fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.E1220fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1221	BAH 2.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GGCAGGTTTCTTCCAGATTAC	0.303			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								29	39	---	---	---	---	
STXBP5L	9515	broad.mit.edu	37	3	121097745	121097746	+	Intron	DEL	AT	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121097745_121097746delAT	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		TATGTTAAACATATTAAATTTT	0.366													16	25	---	---	---	---	
KNG1	3827	broad.mit.edu	37	3	186435632	186435635	+	Intron	DEL	CCAC	-	-	rs10575985		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186435632_186435635delCCAC	uc011bsa.1	+						KNG1_uc003fqr.2_Intron	NM_001102416	NP_001095886	P01042	KNG1_HUMAN	kininogen 1 isoform 1						blood coagulation, intrinsic pathway|elevation of cytosolic calcium ion concentration|inflammatory response|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|positive regulation of renal sodium excretion|positive regulation of urine volume|smooth muscle contraction|vasodilation	extracellular space|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding			skin(1)	1	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)	Ouabain(DB01092)	cccaccaccaccacccaccaccca	0.162													5	3	---	---	---	---	
C4orf36	132989	broad.mit.edu	37	4	87812447	87812448	+	Intron	DEL	AA	-	-	rs71657593		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87812447_87812448delAA	uc003hqe.3	-							NM_144645	NP_653246	Q96KX1	CD036_HUMAN	hypothetical protein LOC132989												0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00141)		AGCAGTTGCCaaaaaaaaaaaa	0.252													6	3	---	---	---	---	
DKK2	27123	broad.mit.edu	37	4	108184982	108184983	+	Intron	INS	-	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108184982_108184983insA	uc010ilw.1	-									Q9UBU2	DKK2_HUMAN	Homo sapiens dickkopf-2 mRNA, complete cds.						multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		AGAGAAAAGCCAAAATATGTTA	0.134													4	2	---	---	---	---	
ENPEP	2028	broad.mit.edu	37	4	111409738	111409745	+	Frame_Shift_Del	DEL	AATCTTTT	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111409738_111409745delAATCTTTT	uc003iab.3	+	2	1028_1035	c.686_693delAATCTTTT	c.(685-693)AAATCTTTTfs	p.K229fs		NM_001977	NP_001968	Q07075	AMPE_HUMAN	glutamyl aminopeptidase	229_231	Extracellular (Potential).				cell migration|cell proliferation|cell-cell signaling|proteolysis	integral to plasma membrane	aminopeptidase activity|metalloexopeptidase activity|zinc ion binding			skin(3)|ovary(1)|breast(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)	L-Glutamic Acid(DB00142)	GATGCCAGGAAATCTTTTCCTTGTTTTG	0.394													31	16	---	---	---	---	
SRFBP1	153443	broad.mit.edu	37	5	121297441	121297442	+	5'Flank	INS	-	AA	AA	rs2972696	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121297441_121297442insAA	uc003kst.1	+							NM_152546	NP_689759	Q8NEF9	SRFB1_HUMAN	serum response factor binding protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	perinuclear region of cytoplasm					0		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		cacacacacacaAACCGAATCT	0.406													3	7	---	---	---	---	
CTNNA1	1495	broad.mit.edu	37	5	138253221	138253224	+	Intron	DEL	TTTA	-	-	rs66467400		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138253221_138253224delTTTA	uc003ldh.2	+						CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron|CTNNA1_uc003ldl.2_Intron	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1						adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TAGTACAGTTTTTATTTGTTTTAT	0.314													7	9	---	---	---	---	
HAVCR2	84868	broad.mit.edu	37	5	156534163	156534164	+	Intron	DEL	AC	-	-	rs34492239		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156534163_156534164delAC	uc003lwk.1	-						HAVCR2_uc003lwl.2_Intron	NM_032782	NP_116171	Q8TDQ0	HAVR2_HUMAN	T cell immunoglobulin mucin 3 precursor							integral to membrane					0	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ccttgcgaaaacacagattgct	0.119													3	4	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168173703	168173703	+	Intron	DEL	T	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168173703delT	uc003mab.2	-						SLIT3_uc010jjg.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			gtggtgtgggtgtggtggtgt	0.000													4	2	---	---	---	---	
PBX2	5089	broad.mit.edu	37	6	32157697	32157697	+	5'UTR	DEL	G	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32157697delG	uc003oav.1	-	1					PBX2_uc003oaw.2_5'UTR	NM_002586	NP_002577	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2								transcription factor binding			ovary(1)	1						GTCCATAGCTGGGGGGGGGCC	0.602													10	5	---	---	---	---	
CD2AP	23607	broad.mit.edu	37	6	47522510	47522510	+	Intron	DEL	A	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47522510delA	uc003oyw.2	+							NM_012120	NP_036252	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein						cell division|mitosis|protein complex assembly|signal transduction|substrate-dependent cell migration, cell extension	cytoplasm|filamentous actin|nucleolus|plasma membrane|ruffle	SH3 domain binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			CAGGTAGACtattttttaaaa	0.284													21	11	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51946933	51946933	+	Intron	DEL	A	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51946933delA	uc003pah.1	-						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)					AACTCTTTGCAAAAAAAAACA	0.368													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1335027	1335028	+	IGR	INS	-	GT	GT			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1335027_1335028insGT								UNCX (58415 upstream) : MICALL2 (138968 downstream)																							tgggtctatgggtgtgtgtgtg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	31404676	31404676	+	IGR	DEL	A	-	-	rs35317967		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31404676delA								NEUROD6 (24138 upstream) : CCDC129 (149009 downstream)																							actctgtctcaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98409055	98409057	+	IGR	DEL	TAG	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98409055_98409057delTAG								NPTX2 (149874 upstream) : TMEM130 (35055 downstream)																							gtagtggtgatagtggtgatggt	0.000													13	6	---	---	---	---	
IFRD1	3475	broad.mit.edu	37	7	112113108	112113123	+	Intron	DEL	TGTGTGTGTGTGTGTA	-	-	rs71755364		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112113108_112113123delTGTGTGTGTGTGTGTA	uc003vgh.2	+						IFRD1_uc011kmn.1_Intron|IFRD1_uc003vgj.2_Intron|IFRD1_uc011kmo.1_Intron|IFRD1_uc011kmp.1_Intron|IFRD1_uc003vgk.2_Intron	NM_001007245	NP_001007246	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1						multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2						tgtgtgtgtgtgtgtgtgtgtgtgtatatatgtgtc	0.208													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150606882	150606883	+	IGR	INS	-	G	G	rs111959480		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150606882_150606883insG								ABP1 (48503 upstream) : KCNH2 (35167 downstream)																							tgtgtgtgtgtggtgtgtgtgt	0.000													6	5	---	---	---	---	
UBXN2B	137886	broad.mit.edu	37	8	59358815	59358818	+	Intron	DEL	TATT	-	-	rs147054459		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59358815_59358818delTATT	uc003xtl.2	+							NM_001077619	NP_001071087	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B							cytosol|endoplasmic reticulum|Golgi apparatus|nucleus				ovary(2)	2						AAATATGTGGTATTTAAACAGTCT	0.250													8	4	---	---	---	---	
ASPH	444	broad.mit.edu	37	8	62437930	62437931	+	Intron	INS	-	AC	AC	rs58731265		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62437930_62437931insAC	uc003xuj.2	-						ASPH_uc011leg.1_Intron	NM_004318	NP_004309	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	cacacacacatacacacacGCT	0.307													4	2	---	---	---	---	
BNC2	54796	broad.mit.edu	37	9	16616815	16616818	+	Intron	DEL	AAGA	-	-	rs7470257	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16616815_16616818delAAGA	uc003zml.2	-						BNC2_uc011lmw.1_Intron|BNC2_uc003zmm.2_Intron|BNC2_uc003zmq.1_Intron|BNC2_uc003zmr.1_Intron|BNC2_uc003zmp.1_Intron|BNC2_uc010mij.1_Intron|BNC2_uc003zmu.1_Intron|BNC2_uc010mim.1_Intron|BNC2_uc010min.1_Intron|BNC2_uc003zmo.1_Intron|BNC2_uc003zms.1_Intron|BNC2_uc010mik.1_Intron|BNC2_uc010mil.1_Intron|BNC2_uc003zmt.1_Intron	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)		ggaaggaaggaagaaaggaaggaa	0.162													4	3	---	---	---	---	
MOBKL2B	79817	broad.mit.edu	37	9	27359377	27359377	+	Intron	DEL	G	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27359377delG	uc003zqn.2	-							NM_024761	NP_079037	Q86TA1	MOL2B_HUMAN	MOB1, Mps One Binder kinase activator-like 2B								metal ion binding|protein binding			ovary(1)|pleura(1)	2		all_neural(11;9.12e-11)		Lung(218;6.54e-05)|LUSC - Lung squamous cell carcinoma(38;0.000397)		gtgtgtgtgtggggggggggg	0.169													8	4	---	---	---	---	
CEP110	11064	broad.mit.edu	37	9	123939699	123939699	+	3'UTR	DEL	T	-	-	rs75910820		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123939699delT	uc004bkx.1	+	42					CEP110_uc004blb.1_3'UTR|CEP110_uc010mvp.1_3'UTR	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						TGGCTGAGCCTTTTTTTTTTT	0.289													4	3	---	---	---	---	
GSN	2934	broad.mit.edu	37	9	124064505	124064506	+	Intron	INS	-	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124064505_124064506insT	uc004blf.1	+						GSN_uc004bld.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_Intron	NM_000177	NP_000168	P06396	GELS_HUMAN	gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3						GCAGACCTTTGGGGCATGGTCC	0.436													44	28	---	---	---	---	
GAPVD1	26130	broad.mit.edu	37	9	128069548	128069548	+	Intron	DEL	A	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128069548delA	uc010mwx.2	+						GAPVD1_uc004bpo.2_Intron|GAPVD1_uc011lzs.1_Intron|GAPVD1_uc004bpp.2_Intron|GAPVD1_uc004bpq.2_Intron|GAPVD1_uc004bpr.2_Intron|GAPVD1_uc004bps.2_Intron|GAPVD1_uc010mwy.1_Intron	NM_015635	NP_056450	Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1						endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4						actttgtctcaaaaaaaaaaa	0.104													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132172566	132172568	+	IGR	DEL	ACA	-	-	rs78168144		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132172566_132172568delACA								C9orf106 (87684 upstream) : C9orf50 (201938 downstream)																							catcaacatcacaaccaccacca	0.049													5	3	---	---	---	---	
LCN6	158062	broad.mit.edu	37	9	139642171	139642172	+	Intron	INS	-	C	C			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139642171_139642172insC	uc004ciy.2	-						LCN10_uc004ciw.2_Intron|uc004ciz.1_RNA	NM_198946	NP_945184	P62502	LCN6_HUMAN	lipocalin 6 precursor						single fertilization	extracellular region	binding				0	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)		caaccctccagcctccagcctt	0.079													7	4	---	---	---	---	
MRC1	4360	broad.mit.edu	37	10	17951301	17951301	+	Intron	DEL	T	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17951301delT	uc001ipk.2	+							NM_002438	NP_002429	P22897	MRC1_HUMAN	mannose receptor C type 1 precursor						receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0						tttttataaattttttttttt	0.299													4	3	---	---	---	---	
FAR1	84188	broad.mit.edu	37	11	13721790	13721790	+	Intron	DEL	A	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13721790delA	uc001mld.2	+						FAR1_uc009ygp.2_Intron	NM_032228	NP_115604	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1						ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2						CCTTGGTGGGAAAAAAATGGT	0.264													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	51593175	51593175	+	IGR	DEL	G	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51593175delG								OR4C46 (76966 upstream) : None (None downstream)																							agaccacaaagtggtgcaaat	0.000													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115846591	115846592	+	IGR	INS	-	GTGC	GTGC	rs28469321		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115846591_115846592insGTGC								CADM1 (471350 upstream) : BUD13 (772296 downstream)																							tgtgtgtgtgtgCGCGCGCGCG	0.510													5	3	---	---	---	---	
SIK3	23387	broad.mit.edu	37	11	116719685	116719686	+	Intron	INS	-	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116719685_116719686insA	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron|SIK3_uc001ppw.2_Intron|SIK3_uc001ppx.2_Intron	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						tctcaaaaaagaaaaaaaaaga	0.233													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124144174	124144175	+	IGR	INS	-	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124144174_124144175insT								OR8G2 (47864 upstream) : OR8D1 (35562 downstream)																							TCCATCATTCCTTTTTTTTTTT	0.411													4	2	---	---	---	---	
SLC6A12	6539	broad.mit.edu	37	12	312226	312232	+	Intron	DEL	TTTTTTT	-	-	rs71951905		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:312226_312232delTTTTTTT	uc001qhz.2	-						SLC6A12_uc001qia.2_Intron|SLC6A12_uc001qib.2_Intron|SLC6A12_uc009zdh.1_Intron|SLC6A12_uc009zdi.1_Intron	NM_003044	NP_003035	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter						cellular nitrogen compound metabolic process|neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			ttttcttttcttttttttttttttttt	0.174													3	3	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6167366	6167366	+	Intron	DEL	G	-	-	rs11313234		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6167366delG	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	GGCTGCAAAAGGGGGGGCGGG	0.393													4	6	---	---	---	---	
DDX11	1663	broad.mit.edu	37	12	31255772	31255773	+	Intron	INS	-	G	G	rs149786035	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31255772_31255773insG	uc001rjt.1	+						DDX11_uc001rjr.1_Intron|DDX11_uc001rjs.1_Intron|DDX11_uc001rju.1_Intron|DDX11_uc001rjv.1_Intron|DDX11_uc001rjw.1_Intron|DDX11_uc009zjn.1_Intron|DDX11_uc009zjo.1_Intron	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					ACAGTCGGAGAGGCTGAGGGAA	0.604										Multiple Myeloma(12;0.14)			7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31920776	31920779	+	IGR	DEL	AAGG	-	-	rs142707641		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31920776_31920779delAAGG								AMN1 (38668 upstream) : H3F3C (23342 downstream)																							ggaaggaagaaaggaaggaaggaa	0.000													4	2	---	---	---	---	
SLC17A8	246213	broad.mit.edu	37	12	100774908	100774915	+	Intron	DEL	CATCTCAG	-	-	rs68046331		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100774908_100774915delCATCTCAG	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						TAGCTCCTCCcatctcagcatctcagca	0.221													5	3	---	---	---	---	
TDG	6996	broad.mit.edu	37	12	104380496	104380497	+	Intron	INS	-	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104380496_104380497insA	uc001tkg.2	+						TDG_uc009zuk.2_Intron|TDG_uc010swi.1_Intron|TDG_uc010swj.1_Intron	NM_003211	NP_003202	Q13569	TDG_HUMAN	thymine-DNA glycosylase						depyrimidination|mismatch repair	nucleoplasm	damaged DNA binding|mismatched DNA binding|protein binding|pyrimidine-specific mismatch base pair DNA N-glycosylase activity			ovary(3)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(302;0.00114)		gtctcaaaaagaaaaaaaaaaa	0.025								BER_DNA_glycosylases					5	3	---	---	---	---	
RAD9B	144715	broad.mit.edu	37	12	110944649	110944649	+	Intron	DEL	T	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110944649delT	uc001trf.3	+						RAD9B_uc001trg.3_Intron|RAD9B_uc010sya.1_Intron|RAD9B_uc001tre.3_Intron|RAD9B_uc001trd.3_Intron	NM_152442	NP_689655	Q6WBX8	RAD9B_HUMAN	RAD9 homolog B						cell cycle checkpoint|DNA repair|DNA replication	nucleoplasm	protein binding			pancreas(1)|skin(1)	2						AGTATTATCCttttttttttt	0.164													6	3	---	---	---	---	
DDX55	57696	broad.mit.edu	37	12	124103024	124103025	+	Intron	INS	-	T	T			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124103024_124103025insT	uc001ufi.2	+						DDX55_uc001ufh.2_Intron|DDX55_uc001ufk.2_Intron|DDX55_uc001ufl.2_5'Flank	NM_020936	NP_065987	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		gtgaaatctgatttttaaaTTT	0.208											OREG0022230	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132024812	132024812	+	IGR	DEL	T	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132024812delT								LOC116437 (327337 upstream) : SFRS8 (170823 downstream)																							atgatggtgatgatggtggtg	0.000													4	2	---	---	---	---	
FOXO1	2308	broad.mit.edu	37	13	41133599	41133601	+	Intron	DEL	TTA	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41133599_41133601delTTA	uc001uxl.3	-						FOXO1_uc010acc.1_Intron	NM_002015	NP_002006	Q12778	FOXO1_HUMAN	forkhead box O1						anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|lung(1)|central_nervous_system(1)	948		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		TTCCTCGCTTTTAAGTTCTATTT	0.429													50	24	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35829629	35829630	+	IGR	INS	-	AC	AC			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35829629_35829630insAC								KIAA0391 (42956 upstream) : NFKBIA (41087 downstream)																							TGTGTGTGAATacacacacaca	0.114													4	3	---	---	---	---	
PPP1R13B	23368	broad.mit.edu	37	14	104208221	104208222	+	Frame_Shift_Ins	INS	-	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104208221_104208222insG	uc001yof.1	-	11	2010_2011	c.1727_1728insC	c.(1726-1728)TCAfs	p.S576fs	PPP1R13B_uc010awv.1_RNA|PPP1R13B_uc001yog.1_Frame_Shift_Ins_p.S443fs	NM_015316	NP_056131	Q96KQ4	ASPP1_HUMAN	apoptosis-stimulating protein of p53, 1	576	Pro-rich.				apoptosis|induction of apoptosis|negative regulation of cell cycle	cytoplasm|nucleus|plasma membrane	protein binding			ovary(1)	1		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				ATATGGAACTTGAATTCACTGT	0.510													113	51	---	---	---	---	
RTF1	23168	broad.mit.edu	37	15	41757131	41757132	+	Intron	INS	-	GT	GT	rs147115092	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41757131_41757132insGT	uc001zny.2	+							NM_015138	NP_055953	Q92541	RTF1_HUMAN	Paf1/RNA polymerase II complex component						histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		ACCTGTTTTGAgtgtgtgtgtg	0.243													4	2	---	---	---	---	
TPSAB1	7177	broad.mit.edu	37	16	1291717	1291718	+	Intron	INS	-	G	G			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1291717_1291718insG	uc002ckz.2	+						TPSAB1_uc010uux.1_Intron	NM_003294	NP_003285	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1 precursor						defense response|proteolysis	extracellular space	protein binding|serine-type endopeptidase activity				0		Hepatocellular(780;0.00369)				CTGGGGACAGTGGAGGTGGGGC	0.703													3	4	---	---	---	---	
MLST8	64223	broad.mit.edu	37	16	2255805	2255805	+	Intron	DEL	G	-	-	rs3214648		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2255805delG	uc002coz.2	+						MLST8_uc002coy.2_Intron|MLST8_uc002cpa.2_Intron|MLST8_uc002cpb.2_Intron|MLST8_uc010uvx.1_Intron|MLST8_uc002cpc.2_Intron|MLST8_uc002cpd.2_Intron|MLST8_uc002cpe.2_5'UTR|MLST8_uc010uvy.1_5'UTR|MLST8_uc002cpg.2_5'UTR|MLST8_uc002cph.2_RNA|MLST8_uc002cpf.2_5'UTR	NM_022372	NP_071767	Q9BVC4	LST8_HUMAN	G protein beta subunit-like						insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|T cell costimulation	cytosol	protein binding				0						CTGCGGAGGTGGGGGGGGGAC	0.512													12	6	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14700252	14700252	+	Intron	DEL	G	-	-	rs62037478		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14700252delG	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						aagaccctgagggaaaaaaaa	0.139													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	18487052	18487055	+	IGR	DEL	CGAG	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18487052_18487055delCGAG								XYLT1 (922314 upstream) : NOMO2 (24128 downstream)																							GGCGCTCCCACGAGGAGGTTCTCG	0.711													3	4	---	---	---	---	
GOT2	2806	broad.mit.edu	37	16	58767917	58767918	+	Intron	DEL	GT	-	-	rs143852021		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58767917_58767918delGT	uc002eof.1	-						GOT2_uc010vim.1_Intron	NM_002080	NP_002071	P00505	AATM_HUMAN	aspartate aminotransferase 2 precursor						aspartate catabolic process|fatty acid transport|gluconeogenesis|response to ethanol	mitochondrial matrix|plasma membrane	L-aspartate:2-oxoglutarate aminotransferase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	TGGCAGAAAAGTGTGTGTGTGT	0.639													7	6	---	---	---	---	
MYBBP1A	10514	broad.mit.edu	37	17	4443460	4443470	+	Intron	DEL	GAGGGTCCTGT	-	-	rs3833100	by1000genomes	TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4443460_4443470delGAGGGTCCTGT	uc002fyb.3	-						MYBBP1A_uc002fxz.3_Intron|MYBBP1A_uc002fya.3_Intron|MYBBP1A_uc010vsa.1_Intron	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2						nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NLS-dependent protein nuclear import complex|nucleolus	DNA binding|DNA-directed DNA polymerase activity|transcription factor binding			ovary(1)|skin(1)	2						AGGCTCCTGCGAGGGTCCTGTGAGGGTCCTA	0.455													10	5	---	---	---	---	
ETV4	2118	broad.mit.edu	37	17	41609864	41609865	+	Intron	INS	-	A	A			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41609864_41609865insA	uc002idw.2	-						ETV4_uc002idv.2_5'Flank|ETV4_uc010wih.1_Intron|ETV4_uc010czh.2_Intron|ETV4_uc010wii.1_Intron|ETV4_uc002idx.2_Intron|ETV4_uc010wij.1_Intron	NM_001986	NP_001977	P43268	ETV4_HUMAN	ets variant gene 4 (E1A enhancer binding						positive regulation of transcription, DNA-dependent	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/ETV4(6)	bone(4)|soft_tissue(2)|ovary(1)	7		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)		gaccccatttcaaaaaaaaaaa	0.124			T	EWSR1|TMPRSS2|DDX5|KLK2|CANT1	Ewing sarcoma|Prostate carcinoma								4	2	---	---	---	---	
HELZ	9931	broad.mit.edu	37	17	65163956	65163957	+	Intron	INS	-	CT	CT			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65163956_65163957insCT	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TTACATCAAAAATATATAAAAA	0.292													25	11	---	---	---	---	
TTYH2	94015	broad.mit.edu	37	17	72218928	72218928	+	Intron	DEL	T	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72218928delT	uc002jkc.2	+						TTYH2_uc010wqw.1_Intron	NM_032646	NP_116035	Q9BSA4	TTYH2_HUMAN	tweety 2 isoform 1							chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4						ATGTTGTCCCTTTTTTTTTTT	0.522													9	5	---	---	---	---	
ZNF93	81931	broad.mit.edu	37	19	20028754	20028754	+	Intron	DEL	T	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20028754delT	uc002non.2	+						ZNF93_uc002nom.2_Intron	NM_031218	NP_112495	P35789	ZNF93_HUMAN	zinc finger protein 93							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1						TCCTTCTTTCTTTTTTtttct	0.020													4	3	---	---	---	---	
RYR1	6261	broad.mit.edu	37	19	39027506	39027506	+	Intron	DEL	G	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39027506delG	uc002oit.2	+						RYR1_uc002oiu.2_Intron|RYR1_uc002oiv.1_Intron	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1						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)	GGGACGTGGAGGGGAGGGAGG	0.458													10	6	---	---	---	---	
GLTSCR2	29997	broad.mit.edu	37	19	48249118	48249124	+	Intron	DEL	GTCGGGG	-	-	rs6146540		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48249118_48249124delGTCGGGG	uc002phm.2	+						GLTSCR2_uc002phk.2_Intron|GLTSCR2_uc002phl.2_Intron|GLTSCR2_uc010elj.2_Intron	NM_015710	NP_056525	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2							nucleolus				central_nervous_system(1)	1		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		GCGTGGACTCgtcgggggtcgggggtc	0.560													5	3	---	---	---	---	
TEAD2	8463	broad.mit.edu	37	19	49858274	49858275	+	Intron	INS	-	CATG	CATG			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49858274_49858275insCATG	uc002pnj.2	-						TEAD2_uc002png.2_Intron|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		atacatacatacatgcatacat	0.203													3	3	---	---	---	---	
KLK14	43847	broad.mit.edu	37	19	51581198	51581198	+	3'UTR	DEL	C	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51581198delC	uc002pvs.1	-	7						NM_022046	NP_071329	Q9P0G3	KLK14_HUMAN	kallikrein 14 preproprotein						epidermis morphogenesis|fertilization|negative regulation of G-protein coupled receptor protein signaling pathway|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis|seminal clot liquefaction	extracellular space	serine-type endopeptidase activity			skin(1)	1		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		ggcctggactcctgggtcctg	0.184													23	10	---	---	---	---	
SIGLEC5	8778	broad.mit.edu	37	19	52132021	52132022	+	Intron	DEL	GT	-	-	rs34312547		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52132021_52132022delGT	uc002pxe.2	-							NM_003830	NP_003821	O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5 precursor						cell adhesion	integral to membrane	sugar binding			skin(2)|breast(1)|central_nervous_system(1)	4		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		gtgtatgtgcgtgtgtgtgtgg	0.000													4	3	---	---	---	---	
SEC23B	10483	broad.mit.edu	37	20	18485750	18485751	+	5'Flank	INS	-	A	A	rs74180905		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18485750_18485751insA	uc002wqz.1	+						SEC23B_uc002wra.1_5'Flank|SEC23B_uc002wrb.1_5'Flank|SEC23B_uc010zsb.1_5'Flank|SEC23B_uc002wrc.1_5'Flank	NM_006363	NP_006354	Q15437	SC23B_HUMAN	Sec23 homolog B						ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1						GCCTCATTCAGAAAAAAAAAAA	0.371													4	2	---	---	---	---	
RALGAPB	57148	broad.mit.edu	37	20	37182420	37182421	+	Intron	INS	-	AA	AA	rs11472819		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37182420_37182421insAA	uc002xiw.2	+						RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Intron	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2						agcccagtctcaaaaaaaaaaa	0.104													2	4	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62074712	62074714	+	Intron	DEL	CAT	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62074712_62074714delCAT	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	ccaccaccaccatcaccatcatc	0.000													7	5	---	---	---	---	
PRDM15	63977	broad.mit.edu	37	21	43222047	43222047	+	Intron	DEL	A	-	-			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43222047delA	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AGCGAGAAACAAAAACAAGAA	0.363													7	5	---	---	---	---	
SF3A1	10291	broad.mit.edu	37	22	30734627	30734627	+	Intron	DEL	C	-	-	rs5844903		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30734627delC	uc003ahl.2	-							NM_005877	NP_005868	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa isoform 1						nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|U2-type spliceosomal complex	protein binding|RNA binding			ovary(3)|large_intestine(1)|pancreas(1)	5						GAGAGAGGTTCCCACTTGCAT	0.527													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	43172335	43172336	+	IGR	INS	-	TTTTTTTTTT	TTTTTTTTTT			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43172335_43172336insTTTTTTTTTT								A4GALT (55049 upstream) : ARFGAP3 (20196 downstream)																							AATTACTTGGCTTTTTTTTTTT	0.351													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	50777749	50777750	+	IGR	INS	-	GT	GT			TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50777749_50777750insGT								FAM116B (12260 upstream) : SAPS2 (4010 downstream)																							ttgtgggtgtagtgtgtgtggt	0.000													3	4	---	---	---	---	
SYTL5	94122	broad.mit.edu	37	X	37913837	37913838	+	Intron	DEL	GT	-	-	rs71844138		TCGA-A3-3322-01A-01D-0966-08	TCGA-A3-3322-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37913837_37913838delGT	uc004ddu.2	+						SYTL5_uc004ddv.2_Intron|SYTL5_uc004ddx.2_Intron	NM_001163335	NP_001156807	Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5 isoform 1						intracellular protein transport	membrane	metal ion binding|Rab GTPase binding			skin(1)	1						GGGCTCTGGGgtgtgtgtgtgt	0.243													4	4	---	---	---	---	
