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
DNAJC11	55735	broad.mit.edu	37	1	6741001	6741001	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6741001G>A	uc001aof.2	-	2	275	c.169C>T	c.(169-171)CGA>TGA	p.R57*	DNAJC11_uc010nzt.1_Nonsense_Mutation_p.R19*|DNAJC11_uc001aog.2_Nonsense_Mutation_p.R57*|DNAJC11_uc010nzu.1_Translation_Start_Site	NM_018198	NP_060668	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	57	J.				protein folding		heat shock protein binding|unfolded protein binding			ovary(1)|skin(1)	2	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		TTAAACAGTCGTTCCGCCTGT	0.498													19	141	---	---	---	---	PASS
CYP4X1	260293	broad.mit.edu	37	1	47498916	47498916	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47498916A>C	uc001cqt.2	+	4	618	c.368A>C	c.(367-369)AAA>ACA	p.K123T	CYP4X1_uc001cqr.2_Missense_Mutation_p.K122T|CYP4X1_uc001cqs.2_Missense_Mutation_p.K58T	NM_178033	NP_828847	Q8N118	CP4X1_HUMAN	cytochrome P450, family 4, subfamily X,	123						endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2						TCTCAAGGAAAAGGACTAGCG	0.448													13	61	---	---	---	---	PASS
NFIA	4774	broad.mit.edu	37	1	61921045	61921045	+	3'UTR	SNP	T	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61921045T>C	uc001czw.2	+	11					NFIA_uc001czy.2_3'UTR|NFIA_uc010oos.1_3'UTR|NFIA_uc001czv.2_Silent_p.T497T|NFIA_uc001czx.2_3'UTR|NFIA_uc009wae.2_RNA	NM_001134673	NP_001128145	Q12857	NFIA_HUMAN	nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2						CCTTCTCAACTCTGTAACATG	0.463													7	91	---	---	---	---	PASS
LOC728989	728989	broad.mit.edu	37	1	146493351	146493351	+	Missense_Mutation	SNP	A	G	G	rs141632041	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146493351A>G	uc001epd.2	-	5	636	c.562T>C	c.(562-564)TGG>CGG	p.W188R		NR_024442				SubName: Full=cDNA FLJ59595, highly similar to Homo sapiens phosphodiesterase 4D interacting protein, transcript variant 1, mRNA;												0						TGAAGGAGCCACTCCTGTTTG	0.488													3	21	---	---	---	---	PASS
TCHH	7062	broad.mit.edu	37	1	152080543	152080543	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152080543C>A	uc001ezp.2	-	2	5150	c.5150G>T	c.(5149-5151)CGC>CTC	p.R1717L	TCHH_uc009wne.1_Missense_Mutation_p.R1717L	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1717	23 X 26 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTCCTGGCGGCGCAGCTGCTG	0.567													4	64	---	---	---	---	PASS
RALGPS2	55103	broad.mit.edu	37	1	178753614	178753614	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178753614C>A	uc001glz.2	+	3	457	c.119C>A	c.(118-120)GCT>GAT	p.A40D	RALGPS2_uc001gly.1_Missense_Mutation_p.A40D|RALGPS2_uc010pnb.1_Missense_Mutation_p.A40D	NM_152663	NP_689876	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	40					small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0						AGCTTTGATGCTGTGGTATTC	0.388													8	88	---	---	---	---	PASS
SCCPDH	51097	broad.mit.edu	37	1	246923346	246923346	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246923346A>T	uc001ibr.2	+	8	1248	c.901A>T	c.(901-903)AGG>TGG	p.R301W		NM_016002	NP_057086	Q8NBX0	SCPDH_HUMAN	saccharopine dehydrogenase (putative)	301						midbody	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity			ovary(1)	1	all_cancers(71;6.8e-05)|all_epithelial(71;7.93e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0545)|Lung NSC(105;0.0618)	all_cancers(173;0.0343)	OV - Ovarian serous cystadenocarcinoma(106;0.00323)	GBM - Glioblastoma multiforme(49;0.0896)		GTTCTTTGTGAGGTTTGGAAT	0.323													24	146	---	---	---	---	PASS
TSSC1	7260	broad.mit.edu	37	2	3193089	3193089	+	3'UTR	SNP	A	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3193089A>T	uc002qxj.2	-	9					TSSC1_uc002qxi.2_RNA	NM_003310	NP_003301	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		GGACCTGGATAACCCAGGCCC	0.572													3	12	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61571006	61571006	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61571006T>C	uc002sbe.2	-	16	2466	c.2444A>G	c.(2443-2445)CAC>CGC	p.H815R		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	815					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			TTGTTGGAGGTGAGATGTCAG	0.363													12	134	---	---	---	---	PASS
LCT	3938	broad.mit.edu	37	2	136566891	136566891	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136566891G>T	uc002tuu.1	-	8	3037	c.3026C>A	c.(3025-3027)GCA>GAA	p.A1009E		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	1009	3.|Extracellular (Potential).|4 X approximate repeats.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)		GATGTTGCTTGCCACCAAGCC	0.493													8	48	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170060531	170060531	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170060531C>A	uc002ues.2	-	42	8179	c.7966G>T	c.(7966-7968)GAA>TAA	p.E2656*		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	2656	EGF-like 10.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	TTAAACTGTTCACAAGGATTG	0.443													18	110	---	---	---	---	PASS
CNTN6	27255	broad.mit.edu	37	3	1363473	1363473	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1363473A>G	uc003boz.2	+	8	1168	c.901A>G	c.(901-903)AAC>GAC	p.N301D	CNTN6_uc011asj.1_Missense_Mutation_p.N229D|CNTN6_uc003bpa.2_Missense_Mutation_p.N301D	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor	301	Ig-like C2-type 3.				axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		CATTGCAAGCAACCTTCGAGG	0.388													21	166	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191480	10191480	+	Missense_Mutation	SNP	T	C	C	rs121913346		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191480T>C	uc003bvc.2	+	3	686	c.473T>C	c.(472-474)CTG>CCG	p.L158P	VHL_uc003bvd.2_Missense_Mutation_p.L117P	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	158	Interaction with Elongin BC complex.		L -> V (in VHLD; type I).|L -> P (in VHLD; type I-II; abolishes release from chaperonin complex and the interaction with Elongin BC complex).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.L158V(8)|p.L158Q(6)|p.L158P(3)|p.L158fs*16(3)|p.V155fs*15(2)|p.L158R(1)|p.L158_K159del(1)|p.L158fs*15(1)|p.T157_K159del(1)|p.Y156*(1)|p.L158fs*6(1)|p.L158fs*1(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTGTATACTCTGAAAGAGCGA	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				6	39	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191481	10191481	+	Silent	SNP	G	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191481G>C	uc003bvc.2	+	3	687	c.474G>C	c.(472-474)CTG>CTC	p.L158L	VHL_uc003bvd.2_Silent_p.L117L	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	158	Interaction with Elongin BC complex.		L -> V (in VHLD; type I).|L -> P (in VHLD; type I-II; abolishes release from chaperonin complex and the interaction with Elongin BC complex).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.L158V(8)|p.L158Q(6)|p.L158P(3)|p.L158fs*16(3)|p.V155fs*15(2)|p.L158R(1)|p.L158_K159del(1)|p.L158fs*15(1)|p.T157_K159del(1)|p.Y156*(1)|p.L158fs*6(1)|p.L158fs*1(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TGTATACTCTGAAAGAGCGAT	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				7	40	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52643348	52643348	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52643348G>A	uc003des.2	-	16	2560	c.2548C>T	c.(2548-2550)CGA>TGA	p.R850*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.R850*|PBRM1_uc003der.2_Nonsense_Mutation_p.R818*|PBRM1_uc003det.2_Nonsense_Mutation_p.R865*|PBRM1_uc003deu.2_Nonsense_Mutation_p.R865*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.R850*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.R850*|PBRM1_uc003dey.2_Nonsense_Mutation_p.R850*|PBRM1_uc003dez.1_Nonsense_Mutation_p.R850*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.R763*|PBRM1_uc003dfa.1_Nonsense_Mutation_p.R196*|PBRM1_uc003dfc.2_Nonsense_Mutation_p.R217*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	850	Bromo 6.				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)		CTTCTTGCTCGTTCCAATACT	0.333			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								13	80	---	---	---	---	PASS
CHRD	8646	broad.mit.edu	37	3	184102984	184102984	+	Silent	SNP	G	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184102984G>T	uc003fov.2	+	14	2022	c.1776G>T	c.(1774-1776)ACG>ACT	p.T592T	CHRD_uc003fow.2_Silent_p.T222T|CHRD_uc003fox.2_Silent_p.T592T|CHRD_uc003foy.2_Silent_p.T222T|CHRD_uc010hyc.2_Silent_p.T182T|CHRD_uc011brr.1_Silent_p.T222T	NM_003741	NP_003732	Q9H2X0	CHRD_HUMAN	chordin precursor	592	CHRD 4.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning|floor plate development|negative regulation of BMP signaling pathway|negative regulation of cell migration|positive regulation of cell adhesion|skeletal system development	extracellular space	cytokine binding			skin(2)|ovary(1)	3	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTCCTGGAACGCCAGGGCCTC	0.567													14	104	---	---	---	---	PASS
ATP13A4	84239	broad.mit.edu	37	3	193188727	193188727	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193188727C>A	uc003ftd.2	-	9	972	c.864G>T	c.(862-864)TTG>TTT	p.L288F	ATP13A4_uc003fte.1_Missense_Mutation_p.L288F|ATP13A4_uc011bsr.1_5'UTR|ATP13A4_uc003ftf.3_5'UTR	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	288	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		TGTTCCCTGTCAAAATTAATA	0.488													18	175	---	---	---	---	PASS
BOD1L	259282	broad.mit.edu	37	4	13605133	13605133	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13605133C>T	uc003gmz.1	-	10	3508	c.3391G>A	c.(3391-3393)GTG>ATG	p.V1131M	BOD1L_uc010idr.1_Missense_Mutation_p.V468M	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	1131							DNA binding			ovary(5)|breast(1)	6						ACTTCAAACACATTTTCAACA	0.388													21	231	---	---	---	---	PASS
GABRB1	2560	broad.mit.edu	37	4	47033947	47033947	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47033947A>C	uc003gxh.2	+	2	471	c.97A>C	c.(97-99)AAC>CAC	p.N33H	GABRB1_uc011bze.1_5'UTR|GABRB1_uc011bzd.1_Missense_Mutation_p.N33H|GABRB1_uc010igg.2_RNA	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	33	Extracellular (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	TGAACCCAGCAACATGTCATA	0.458													25	332	---	---	---	---	PASS
UGT2A1	10941	broad.mit.edu	37	4	70455274	70455274	+	Missense_Mutation	SNP	C	T	T	rs150861593	byFrequency	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70455274C>T	uc003hem.3	-	6	1463	c.1400G>A	c.(1399-1401)CGC>CAC	p.R467H	UGT2A1_uc011caq.1_Missense_Mutation_p.R633H|UGT2A1_uc010ihu.2_Missense_Mutation_p.R467H|UGT2A1_uc010iht.2_Missense_Mutation_p.R423H|UGT2A1_uc010ihs.2_Missense_Mutation_p.R468H	NM_006798	NP_006789	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family,	467	Extracellular (Potential).				detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1						TCCTTTGTGGCGCATGACAAA	0.478													20	185	---	---	---	---	PASS
PCDH10	57575	broad.mit.edu	37	4	134071487	134071487	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134071487A>C	uc003iha.2	+	1	1018	c.192A>C	c.(190-192)TTA>TTC	p.L64F	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Missense_Mutation_p.L64F	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	64	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)		CCCCTTACTTAGACCTCAACC	0.532													18	134	---	---	---	---	PASS
TKTL2	84076	broad.mit.edu	37	4	164393928	164393928	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164393928G>A	uc003iqp.3	-	1	1120	c.959C>T	c.(958-960)GCT>GTT	p.A320V		NM_032136	NP_115512	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	320						cytoplasm	metal ion binding|transketolase activity			ovary(2)|skin(2)|pancreas(1)	5	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				tttctgagtagctatcttgtc	0.199													15	250	---	---	---	---	PASS
SDHAP3	728609	broad.mit.edu	37	5	1574406	1574406	+	RNA	SNP	T	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1574406T>C	uc011cmd.1	-	3		c.440A>G			SDHAP3_uc011cme.1_RNA					Homo sapiens cDNA FLJ58919 complete cds, moderately similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC1.3.5.1).												0						CTCATCAATCTGCACCTGAGG	0.478													3	15	---	---	---	---	PASS
SEPP1	6414	broad.mit.edu	37	5	42804905	42804905	+	Intron	SNP	A	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42804905A>G	uc011cps.1	-						SEPP1_uc011cpt.1_Intron|SEPP1_uc011cpu.1_Intron|SEPP1_uc011cpv.1_RNA|SEPP1_uc003jna.2_Intron			P49908	SEPP1_HUMAN	Homo sapiens cDNA FLJ37321 fis, clone BRAMY2018122.						response to oxidative stress	extracellular region	selenium binding				0						CAATGTCACTATAATATTTTC	0.353													5	28	---	---	---	---	PASS
CSNK1G3	1456	broad.mit.edu	37	5	122911473	122911473	+	Silent	SNP	A	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122911473A>G	uc003ktm.2	+	6	1208	c.489A>G	c.(487-489)GTA>GTG	p.V163V	CSNK1G3_uc003ktl.2_Silent_p.V163V|CSNK1G3_uc003ktn.2_Silent_p.V163V|CSNK1G3_uc003kto.2_Silent_p.V163V|CSNK1G3_uc011cwr.1_Silent_p.V88V|CSNK1G3_uc011cws.1_Silent_p.V50V|CSNK1G3_uc010jda.2_Silent_p.V163V	NM_004384	NP_004375	Q9Y6M4	KC1G3_HUMAN	casein kinase 1, gamma 3 isoform 1	163	Protein kinase.				Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)		ACAGAGATGTAAAACCTGAGA	0.348													12	122	---	---	---	---	PASS
UBTD2	92181	broad.mit.edu	37	5	171661293	171661293	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171661293T>C	uc003mbp.1	-	2	266	c.140A>G	c.(139-141)GAT>GGT	p.D47G		NM_152277	NP_689490	Q8WUN7	UBTD2_HUMAN	dendritic cell-derived ubiquitin-like protein	47						cytoplasm					0	Renal(175;0.000159)|Lung NSC(126;0.00976)|all_lung(126;0.0156)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TAGTTGTCCATCTGTCATAGG	0.428													8	145	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176637818	176637818	+	Silent	SNP	A	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176637818A>C	uc003mfr.3	+	5	2556	c.2418A>C	c.(2416-2418)ATA>ATC	p.I806I	NSD1_uc003mft.3_Silent_p.I537I|NSD1_uc003mfs.1_Silent_p.I703I|NSD1_uc011dfx.1_Silent_p.I454I	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	806					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		CCCCAGTTATAAATGAGGAGT	0.408			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			20	73	---	---	---	---	PASS
ATXN1	6310	broad.mit.edu	37	6	16326679	16326679	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16326679G>C	uc003nbt.2	-	8	2834	c.1863C>G	c.(1861-1863)AGC>AGG	p.S621R	ATXN1_uc010jpi.2_Missense_Mutation_p.S621R|ATXN1_uc010jpj.1_Intron	NM_000332	NP_000323	P54253	ATX1_HUMAN	ataxin 1	621	Interaction with USP7.|RNA-binding.|AXH.				cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CCGGGCTATGGCTGTCTTCAA	0.552													5	70	---	---	---	---	PASS
BAI3	577	broad.mit.edu	37	6	69349081	69349081	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69349081T>C	uc003pev.3	+	3	962	c.514T>C	c.(514-516)TGT>CGT	p.C172R	BAI3_uc010kak.2_Missense_Mutation_p.C172R	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	172	Extracellular (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				CCATGTATTATGTACTTGGTT	0.413													10	149	---	---	---	---	PASS
MANEA	79694	broad.mit.edu	37	6	96053648	96053648	+	Nonsense_Mutation	SNP	C	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96053648C>G	uc003poo.1	+	5	896	c.756C>G	c.(754-756)TAC>TAG	p.Y252*		NM_024641	NP_078917	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	252	Catalytic (Probable).|Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	glycoprotein endo-alpha-1,2-mannosidase activity			ovary(2)|breast(1)	3		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		CGGCCTTTTACAGGTACAAGA	0.353													10	147	---	---	---	---	PASS
KIAA0146	23514	broad.mit.edu	37	8	48309113	48309113	+	Silent	SNP	T	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48309113T>C	uc003xqd.2	+	6	712	c.703T>C	c.(703-705)TTG>CTG	p.L235L	KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Silent_p.L235L|KIAA0146_uc010lxs.2_5'UTR|KIAA0146_uc011ldc.1_Silent_p.L165L|KIAA0146_uc011ldd.1_Silent_p.L175L|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_RNA|KIAA0146_uc011lde.1_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514	235											0		Lung NSC(58;0.175)				AGAGACCATTTTGCATACACC	0.398													29	226	---	---	---	---	PASS
DCAF4L2	138009	broad.mit.edu	37	8	88885732	88885732	+	Silent	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88885732G>A	uc003ydz.2	-	1	565	c.468C>T	c.(466-468)GCC>GCT	p.A156A		NM_152418	NP_689631	Q8NA75	DC4L2_HUMAN	WD repeat domain 21C	156										ovary(1)	1						GGAGCAGCACGGCACAGCTTG	0.552													12	93	---	---	---	---	PASS
TRAPPC9	83696	broad.mit.edu	37	8	141415691	141415691	+	Silent	SNP	A	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141415691A>G	uc003yvj.2	-	6	1127	c.993T>C	c.(991-993)ATT>ATC	p.I331I	TRAPPC9_uc003yvh.2_Silent_p.I429I|TRAPPC9_uc003yvi.1_Silent_p.I322I	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform	331					cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						TGTAATAGGAAATCGCCTCTT	0.398													12	46	---	---	---	---	PASS
FLJ46321	389763	broad.mit.edu	37	9	84607804	84607804	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84607804A>T	uc004amn.2	+	4	2466	c.2419A>T	c.(2419-2421)ACT>TCT	p.T807S		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	807						integral to membrane					0						AGACCTAGAAACTCATATGAT	0.468													11	87	---	---	---	---	PASS
RGS3	5998	broad.mit.edu	37	9	116345959	116345959	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116345959C>T	uc004bhq.2	+	21	2476	c.2267C>T	c.(2266-2268)CCA>CTA	p.P756L	RGS3_uc004bhs.2_Missense_Mutation_p.P646L|RGS3_uc004bht.2_Missense_Mutation_p.P475L|RGS3_uc010muy.2_Intron|RGS3_uc004bhv.2_Missense_Mutation_p.P77L|RGS3_uc010muz.1_Missense_Mutation_p.P95L|RGS3_uc004bhw.2_Intron|RGS3_uc011lxh.1_Missense_Mutation_p.P66L|RGS3_uc004bhx.2_Missense_Mutation_p.P77L|RGS3_uc004bhy.1_Missense_Mutation_p.P66L|RGS3_uc004bhz.2_Missense_Mutation_p.P98L	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	756	Pro-rich.				inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3						CCTCCAGGCCCAGATGCTCCG	0.622													6	135	---	---	---	---	PASS
NUP214	8021	broad.mit.edu	37	9	134077067	134077067	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134077067G>C	uc004cag.2	+	30	5666	c.5555G>C	c.(5554-5556)GGT>GCT	p.G1852A	NUP214_uc004cah.2_Missense_Mutation_p.G1842A|NUP214_uc004cai.2_Missense_Mutation_p.G1282A|NUP214_uc010mzg.2_RNA|NUP214_uc011mcg.1_Missense_Mutation_p.G678A	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa	1852	Pro/Ser/Thr-rich.|11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.				carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TCTGTGTTTGGTCAAGCAGCC	0.353			T	DEK|SET|ABL1	AML|T-ALL								11	133	---	---	---	---	PASS
BICC1	80114	broad.mit.edu	37	10	60588657	60588657	+	3'UTR	SNP	C	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60588657C>A	uc001jki.1	+	21						NM_001080512	NP_001073981	Q9H694	BICC1_HUMAN	bicaudal C homolog 1						multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4						GGTAGCAGCACCCTCTTGGCA	0.537													10	33	---	---	---	---	PASS
KIAA1598	57698	broad.mit.edu	37	10	118661447	118661447	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118661447G>C	uc009xyw.2	-	16	2000	c.1502C>G	c.(1501-1503)ACC>AGC	p.T501S	KIAA1598_uc001lcz.3_Intron|KIAA1598_uc010qso.1_Missense_Mutation_p.T441S|KIAA1598_uc010qsp.1_Missense_Mutation_p.T501S|KIAA1598_uc010qsq.1_Missense_Mutation_p.T441S|KIAA1598_uc001lcy.3_Missense_Mutation_p.T471S	NM_001127211	NP_001120683	A0MZ66	SHOT1_HUMAN	shootin1 isoform a	501					axon guidance	axon					0				all cancers(201;0.00494)		GGACTCTGAGGTGGCTAATAT	0.403													4	47	---	---	---	---	PASS
TRIM6-TRIM34	445372	broad.mit.edu	37	11	5624933	5624933	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5624933T>G	uc001mbf.2	+	2	719	c.475T>G	c.(475-477)TTC>GTC	p.F159V	HBG2_uc001mak.1_Intron|TRIM6_uc009yeo.1_Missense_Mutation_p.F105V|TRIM6_uc010qzj.1_5'UTR|TRIM6_uc001mbc.1_Missense_Mutation_p.F131V|TRIM6_uc001mbe.2_5'UTR|TRIM6_uc010qzk.1_Intron|TRIM6_uc010qzl.1_Intron|TRIM6_uc001mbd.2_Missense_Mutation_p.F159V|TRIM6_uc001mbg.1_5'Flank|TRIM6_uc009yep.1_5'Flank	NM_001003819	NP_001003819	B2RNG4	B2RNG4_HUMAN	tripartite motif-containing 6 and tripartite	159						intracellular	zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;1.01e-08)|BRCA - Breast invasive adenocarcinoma(625;0.145)		TCACCACACGTTCCTCGTGGA	0.532													8	74	---	---	---	---	PASS
OR56A5	390084	broad.mit.edu	37	11	5988973	5988973	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5988973A>G	uc010qzu.1	-	1	752	c.752T>C	c.(751-753)ATC>ACC	p.I251T		NM_001146033	NP_001139505	P0C7T3	O56A5_HUMAN	olfactory receptor, family 56, subfamily A,	251	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	olfactory receptor activity				0						GAAGAAGAGGATGAGGATGAA	0.483													6	12	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108141874	108141874	+	Splice_Site	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108141874G>A	uc001pkb.1	+	19	3306	c.2921_splice	c.e19+1	p.S974_splice	ATM_uc009yxr.1_Splice_Site_p.S974_splice|ATM_uc009yxs.1_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		AACCACTATCGTAAGAAATTA	0.323			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			10	100	---	---	---	---	PASS
ALG9	79796	broad.mit.edu	37	11	111724387	111724387	+	Silent	SNP	G	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111724387G>T	uc001pmb.2	-	8	873	c.774C>A	c.(772-774)GCC>GCA	p.A258A	ALG9_uc001ply.2_Silent_p.A87A|ALG9_uc001plz.2_Silent_p.A87A|ALG9_uc010rwm.1_Silent_p.A258A|ALG9_uc010rwn.1_Silent_p.A212A|ALG9_uc010rwo.1_Silent_p.A86A|ALG9_uc009yyh.1_Silent_p.A153A	NM_001077690	NP_001071158	Q9H6U8	ALG9_HUMAN	asparagine-linked glycosylation 9 protein	258	Helical; (Potential).				dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity			large_intestine(1)|ovary(1)	2		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)		ATAGTATGAGGGCCATCAGCG	0.388													9	120	---	---	---	---	PASS
GPRC5D	55507	broad.mit.edu	37	12	13093773	13093773	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13093773G>C	uc010shp.1	-	3	974	c.974C>G	c.(973-975)CCC>CGC	p.P325R		NM_018654	NP_061124	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, family C, group 5,	325	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		CTCTTGTGTGGGATCAACAGT	0.378													10	178	---	---	---	---	PASS
GLS2	27165	broad.mit.edu	37	12	56865561	56865561	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56865561C>A	uc001slj.2	-	17	1927	c.1648G>T	c.(1648-1650)GAC>TAC	p.D550Y	GLS2_uc009zos.2_RNA|GLS2_uc001slk.2_Missense_Mutation_p.D285Y|GLS2_uc009zot.2_Missense_Mutation_p.D211Y	NM_013267	NP_037399	Q9UI32	GLSL_HUMAN	glutaminase 2 precursor	550	ANK 1.				cellular amino acid biosynthetic process|glutamate secretion|glutamine metabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity|protein binding	p.D550E(1)		ovary(1)|central_nervous_system(1)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	CCTCACCTGTCCTTGGCAAAA	0.493													24	266	---	---	---	---	PASS
PPM1H	57460	broad.mit.edu	37	12	63042320	63042320	+	Silent	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63042320G>A	uc001srk.3	-	10	1643	c.1494C>T	c.(1492-1494)GAC>GAT	p.D498D		NM_020700	NP_065751	Q9ULR3	PPM1H_HUMAN	protein phosphatase 1H (PP2C domain containing)	498	PP2C-like.						phosphoprotein phosphatase activity			lung(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		CAGAAATGTCGTCTCCTGAGC	0.527													7	99	---	---	---	---	PASS
GCN1L1	10985	broad.mit.edu	37	12	120586152	120586152	+	Splice_Site	SNP	T	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120586152T>C	uc001txo.2	-	37	4560	c.4547_splice	c.e37-1	p.G1516_splice		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCACTGACCCTGTGGATAGCA	0.562													7	36	---	---	---	---	PASS
RNF219	79596	broad.mit.edu	37	13	79212988	79212988	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79212988T>G	uc001vkw.1	-	4	578	c.519A>C	c.(517-519)AAA>AAC	p.K173N	RNF219_uc010afb.1_5'UTR|RNF219_uc010afc.2_Missense_Mutation_p.K173N	NM_024546	NP_078822	Q5W0B1	RN219_HUMAN	ring finger protein 219	173	Potential.						zinc ion binding			large_intestine(2)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		CATCTTTCACTTTTTCATAGA	0.313													20	157	---	---	---	---	PASS
ACIN1	22985	broad.mit.edu	37	14	23533399	23533399	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23533399G>C	uc001wit.3	-	12	3012	c.2684C>G	c.(2683-2685)TCT>TGT	p.S895C	ACIN1_uc001wio.3_RNA|ACIN1_uc001wip.3_Missense_Mutation_p.S137C|ACIN1_uc001wiq.3_Missense_Mutation_p.S137C|ACIN1_uc001wir.3_Missense_Mutation_p.S168C|ACIN1_uc001wis.3_Missense_Mutation_p.S576C|ACIN1_uc010akg.2_Missense_Mutation_p.S882C	NM_014977	NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	895					apoptotic chromosome condensation|erythrocyte differentiation|positive regulation of monocyte differentiation	cytosol	ATPase activity|enzyme binding|nucleic acid binding|nucleotide binding			ovary(2)|large_intestine(1)|skin(1)	4	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		AGAGATGCGAGAGTCATCAGC	0.562													16	83	---	---	---	---	PASS
PABPN1	8106	broad.mit.edu	37	14	23794554	23794554	+	3'UTR	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									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													8	34	---	---	---	---	PASS
PRKCH	5583	broad.mit.edu	37	14	61920051	61920051	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61920051G>A	uc001xfn.2	+	7	1245	c.940G>A	c.(940-942)GGA>AGA	p.G314R	PRKCH_uc010tsa.1_Missense_Mutation_p.G153R	NM_006255	NP_006246	P24723	KPCL_HUMAN	protein kinase C, eta	314					intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		TCTCCAACCCGGAAATATTTC	0.483													5	96	---	---	---	---	PASS
EIF5	1983	broad.mit.edu	37	14	103805214	103805214	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103805214T>A	uc001ymq.2	+	8	1250	c.728T>A	c.(727-729)CTC>CAC	p.L243H	EIF5_uc001ymr.2_Missense_Mutation_p.L243H|EIF5_uc001yms.2_Missense_Mutation_p.L243H|EIF5_uc001ymt.2_Missense_Mutation_p.L243H|EIF5_uc001ymu.2_Missense_Mutation_p.L243H	NM_001969	NP_001960	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	243	W2.				regulation of translational initiation|RNA metabolic process	cytosol	GTP binding|GTPase activity|translation initiation factor activity			pancreas(1)|breast(1)|skin(1)	3		Melanoma(154;0.155)	Epithelial(46;0.182)			GTCAATATCCTCTTTGATTTT	0.383													6	107	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105417156	105417156	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105417156C>A	uc010axc.1	-	7	4752	c.4632G>T	c.(4630-4632)CAG>CAT	p.Q1544H	AHNAK2_uc001ypx.2_Missense_Mutation_p.Q1444H	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1544						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CAGAAGGGGGCTGTATGCTCA	0.657													7	150	---	---	---	---	PASS
SLC24A1	9187	broad.mit.edu	37	15	65945096	65945096	+	Silent	SNP	C	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65945096C>T	uc010ujf.1	+	9	3287	c.3000C>T	c.(2998-3000)GAC>GAT	p.D1000D	SLC24A1_uc010ujd.1_3'UTR|SLC24A1_uc010uje.1_Silent_p.D982D|SLC24A1_uc010ujg.1_Silent_p.D970D|SLC24A1_uc010ujh.1_Silent_p.D982D|SLC24A1_uc010uji.1_Silent_p.D327D	NM_004727	NP_004718	O60721	NCKX1_HUMAN	solute carrier family 24	1000	Alpha-2.|Extracellular (Potential).				response to light intensity|visual perception	integral to plasma membrane|membrane fraction|outer membrane	calcium, potassium:sodium antiporter activity|protein binding|symporter activity				0						GCCTGGGAGACATGGCTGTGT	0.473													7	137	---	---	---	---	PASS
THSD4	79875	broad.mit.edu	37	15	72039333	72039333	+	Silent	SNP	C	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72039333C>T	uc002atb.1	+	12	2272	c.2193C>T	c.(2191-2193)TGC>TGT	p.C731C	THSD4_uc002ate.2_Silent_p.C371C	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	731	TSP type-1 2.					proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2						CCAGCACCTGCCAACTCAAGA	0.657													3	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	102295539	102295539	+	5'Flank	SNP	A	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102295539A>C	uc002bxo.2	-						uc002bxq.2_5'Flank|uc002bxr.2_5'Flank|uc010usk.1_5'Flank|uc002bxs.2_5'Flank|uc002bxu.1_5'Flank|uc002bxv.1_5'Flank|uc002bxw.1_5'Flank|uc002bxy.1_5'Flank|uc002byb.1_5'Flank|uc002byc.2_5'Flank|uc002byh.2_5'Flank|uc002byj.2_5'Flank|uc002byl.1_5'Flank|uc010usl.1_RNA|uc010usm.1_5'Flank|uc002byr.2_5'Flank|uc002bys.2_5'Flank|uc002byv.2_5'Flank|uc002byx.3_5'Flank|uc002bza.2_5'Flank|uc002bzb.2_5'Flank|uc002bzc.1_5'Flank|uc002bzd.2_5'Flank|uc002bze.2_5'Flank|uc002bzg.2_5'Flank|uc002bzi.1_5'Flank|uc002bzj.2_5'Flank|uc002bzl.2_5'Flank|uc002bzm.2_5'Flank|uc002bzo.2_5'Flank|uc002bzp.2_5'Flank|uc002bzq.2_5'Flank|uc002bzr.2_5'Flank|uc002bzt.2_5'Flank|uc010usp.1_5'Flank|uc002bzu.2_5'Flank|uc002bzv.3_5'Flank|uc010usq.1_5'Flank|uc010usr.1_5'Flank|uc010uss.1_5'Flank|uc002bzz.2_5'Flank					DQ593630																		TCGCGTCGGAACCTGCAGACA	0.607													2	4	---	---	---	---	PASS
ANKS4B	257629	broad.mit.edu	37	16	21261470	21261470	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21261470G>A	uc010bwp.1	+	2	626	c.583G>A	c.(583-585)GGG>AGG	p.G195R	CRYM_uc010bwq.1_Intron	NM_145865	NP_665872	Q8N8V4	ANS4B_HUMAN	harmonin-interacting ankyrin-repeat containing	195										ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0565)		TGGCACATTCGGGTCACTATC	0.498													18	70	---	---	---	---	PASS
PKD1L2	114780	broad.mit.edu	37	16	81157278	81157278	+	Silent	SNP	C	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81157278C>G	uc002fgh.1	-	39	6462	c.6462G>C	c.(6460-6462)CTG>CTC	p.L2154L	PKD1L2_uc002fgf.1_5'UTR|PKD1L2_uc002fgg.1_RNA	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	2154	Helical; (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						TCTCTAGCGTCAGCGTGACAA	0.592													8	140	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	21731270	21731270	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21731270T>C	uc002gyy.3	+	2	697	c.572T>C	c.(571-573)ATC>ACC	p.I191T						SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																		ATCCCCCCGATCAGCAGAGGC	0.547													4	77	---	---	---	---	PASS
XYLT2	64132	broad.mit.edu	37	17	48433278	48433278	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48433278G>A	uc002iqo.2	+	6	1334	c.1225G>A	c.(1225-1227)GTG>ATG	p.V409M	XYLT2_uc010dbo.2_RNA	NM_022167	NP_071450	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	409	Lumenal (Potential).				glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			pancreas(1)	1	Breast(11;7.18e-19)					ACGCAGCTTTGTGGAGTATGT	0.602													13	45	---	---	---	---	PASS
ITGB4	3691	broad.mit.edu	37	17	73729634	73729634	+	Silent	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73729634G>A	uc002jpg.2	+	13	1705	c.1518G>A	c.(1516-1518)GAG>GAA	p.E506E	ITGB4_uc002jph.2_Silent_p.E506E|ITGB4_uc010dgo.2_Silent_p.E506E|ITGB4_uc002jpi.3_Silent_p.E506E|ITGB4_uc010dgp.1_Silent_p.E506E|ITGB4_uc002jpj.2_Silent_p.E506E|ITGB4_uc010wsh.1_Silent_p.E61E	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	506	II.|Extracellular (Potential).|Cysteine-rich tandem repeats.				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCCTGCGGGAGGGCGAGGACA	0.637													4	42	---	---	---	---	PASS
SEC14L1	6397	broad.mit.edu	37	17	75209464	75209464	+	Silent	SNP	C	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75209464C>T	uc002jto.2	+	16	2199	c.1932C>T	c.(1930-1932)TGC>TGT	p.C644C	SEC14L1_uc010dhc.2_Silent_p.C644C|SEC14L1_uc010wth.1_Silent_p.C644C|SEC14L1_uc002jtm.2_Silent_p.C644C|SEC14L1_uc010wti.1_Silent_p.C610C|SEC14L1_uc010wtj.1_Missense_Mutation_p.R133C|SEC14L1_uc002jtr.2_Silent_p.C38C	NM_003003	NP_002994	Q92503	S14L1_HUMAN	SEC14 (S. cerevisiae)-like 1 isoform a	644	GOLD.				transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2						TGCCTGCGTGCGCCGCCAGCA	0.607													3	33	---	---	---	---	PASS
CTDP1	9150	broad.mit.edu	37	18	77477938	77477938	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77477938A>T	uc002lnh.1	+	10	2486	c.2339A>T	c.(2338-2340)AAG>ATG	p.K780M	CTDP1_uc002lni.1_Missense_Mutation_p.K780M|CTDP1_uc010drd.1_Missense_Mutation_p.K780M	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	780					positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		AACACGGGGAAGCTCATCAGG	0.697													10	75	---	---	---	---	PASS
CTDP1	9150	broad.mit.edu	37	18	77477956	77477956	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77477956C>T	uc002lnh.1	+	10	2504	c.2357C>T	c.(2356-2358)GCC>GTC	p.A786V	CTDP1_uc002lni.1_Missense_Mutation_p.A786V|CTDP1_uc010drd.1_Missense_Mutation_p.A786V	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	786					positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		AGGACGGGCGCCCGGGGGCCC	0.677													7	62	---	---	---	---	PASS
ZNF136	7695	broad.mit.edu	37	19	12298092	12298092	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12298092G>A	uc002mti.2	+	4	999	c.899G>A	c.(898-900)AGA>AAA	p.R300K	ZNF136_uc010xmh.1_Missense_Mutation_p.R234K	NM_003437	NP_003428	P52737	ZN136_HUMAN	zinc finger protein 136	300	C2H2-type 6.				negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|transcription corepressor activity|zinc ion binding			ovary(1)|pancreas(1)	2						ATACATGAAAGAACCCATACT	0.423													7	78	---	---	---	---	PASS
ZNF44	51710	broad.mit.edu	37	19	12383395	12383395	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12383395G>A	uc010xmj.1	-	5	2024	c.1819C>T	c.(1819-1821)CCC>TCC	p.P607S	ZNF44_uc002mtl.2_Intron|ZNF44_uc010dyr.1_Intron|ZNF44_uc010xmi.1_RNA|ZNF44_uc002mtn.3_RNA|ZNF44_uc010dys.2_Missense_Mutation_p.P559S	NM_001164276	NP_001157748	P15621	ZNF44_HUMAN	zinc finger protein 44 isoform 1	607					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		CATTCATAGGGTCTTTCTCCA	0.438													6	38	---	---	---	---	PASS
ZNF585B	92285	broad.mit.edu	37	19	37676023	37676023	+	3'UTR	SNP	A	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37676023A>C	uc002ofq.2	-	5					uc002ofp.1_5'Flank|ZNF585B_uc002ofr.1_3'UTR	NM_152279	NP_689492	Q52M93	Z585B_HUMAN	zinc finger protein 585B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGACATTCTGATGTGGTCATT	0.473													3	18	---	---	---	---	PASS
PSG3	5671	broad.mit.edu	37	19	43244635	43244635	+	5'UTR	SNP	C	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43244635C>T	uc002oue.2	-	1					PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG3_uc010eil.2_5'UTR	NM_021016	NP_066296	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3						defense response|female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)				CCTCCTTCTGCGCTGAGCCTC	0.607													4	55	---	---	---	---	PASS
ZNF587	84914	broad.mit.edu	37	19	58352661	58352661	+	Intron	SNP	T	A	A	rs148810844	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58352661T>A	uc002qqb.2	+						uc002qqh.1_Missense_Mutation_p.F157I|ZNF587_uc010yhh.1_Intron|ZNF587_uc002qqi.1_Intron|uc010yhj.1_Missense_Mutation_p.F207I|ZNF587_uc002qqj.1_Intron	NM_032828	NP_116217	Q96SQ5	ZN587_HUMAN	zinc finger protein 587						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		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;0.0264)		TGTGTCTCCCTTTCAGTGTGG	0.493													6	35	---	---	---	---	PASS
C20orf3	57136	broad.mit.edu	37	20	24944491	24944491	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24944491G>C	uc002wty.2	-	9	1310	c.1209C>G	c.(1207-1209)TTC>TTG	p.F403L	C20orf3_uc002wtz.2_Missense_Mutation_p.F411L|C20orf3_uc010zsw.1_3'UTR	NM_020531	NP_065392	Q9HDC9	APMAP_HUMAN	chromosome 20 open reading frame 3	403	Extracellular (Potential).				biosynthetic process	cell surface|integral to membrane	arylesterase activity|strictosidine synthase activity			ovary(1)	1						AGGGGGACCTGAAAGAGCCCA	0.627													8	119	---	---	---	---	PASS
EYA2	2139	broad.mit.edu	37	20	45717938	45717938	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45717938C>T	uc002xsm.2	+	8	1096	c.722C>T	c.(721-723)CCG>CTG	p.P241L	EYA2_uc010ghp.2_Missense_Mutation_p.P241L|EYA2_uc002xsn.2_Missense_Mutation_p.P246L|EYA2_uc002xso.2_Missense_Mutation_p.P241L|EYA2_uc002xsp.2_Missense_Mutation_p.P241L|EYA2_uc002xsq.2_Missense_Mutation_p.P241L	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a	241					DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				ACAGACAGGCCGCACCGGGCC	0.567													8	93	---	---	---	---	PASS
CBR1	873	broad.mit.edu	37	21	37444758	37444758	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37444758G>A	uc002yvb.1	+	3	541	c.412G>A	c.(412-414)GTA>ATA	p.V138I	uc011aea.1_Intron|SETD4_uc002yva.2_Intron|CBR1_uc010gmy.1_3'UTR	NM_001757	NP_001748	P16152	CBR1_HUMAN	carbonyl reductase 1	138					drug metabolic process|vitamin K metabolic process	cytoplasm	15-hydroxyprostaglandin dehydrogenase (NADP+) activity|carbonyl reductase (NADPH) activity|prostaglandin-E2 9-reductase activity|protein binding				0					Acetohexamide(DB00414)|Lubiprostone(DB01046)	AGTGGTGAACGTATCTAGCAT	0.507													20	87	---	---	---	---	PASS
ZMYM3	9203	broad.mit.edu	37	X	70472956	70472956	+	Silent	SNP	A	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70472956A>G	uc004dzh.1	-	2	237	c.150T>C	c.(148-150)CCT>CCC	p.P50P	BCYRN1_uc011mpt.1_Intron|ZMYM3_uc004dzi.1_Silent_p.P50P|ZMYM3_uc004dzj.1_Silent_p.P50P|ZMYM3_uc011mpu.1_5'Flank|ZMYM3_uc004dzk.3_Silent_p.P50P|ZMYM3_uc004dzl.3_Silent_p.P50P|ZMYM3_uc004dzm.3_Silent_p.P50P	NM_201599	NP_963893	Q14202	ZMYM3_HUMAN	zinc finger protein 261	50					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Renal(35;0.156)					AGGATGGAGAAGGGCCAGGGG	0.612											OREG0019858	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	11	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	18895161	18895164	+	IGR	DEL	AAGA	-	-	rs12746398		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18895161_18895164delAAGA								KLHDC7A (82622 upstream) : PAX7 (62336 downstream)																							ggaaggaaggaagaaagaaagaaa	0.098													4	2	---	---	---	---	
IPP	3652	broad.mit.edu	37	1	46193146	46193147	+	Intron	INS	-	TCCC	TCCC	rs117647066	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46193146_46193147insTCCC	uc001cou.2	-						IPP_uc001cos.3_Intron	NM_005897	NP_005888	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide							actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					TTTCTcttccttccctccctcc	0.277													5	4	---	---	---	---	
ST6GALNAC3	256435	broad.mit.edu	37	1	76592110	76592113	+	Intron	DEL	TTCC	-	-	rs67346097		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76592110_76592113delTTCC	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_Intron|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541	Q8NDV1	SIA7C_HUMAN	sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5						cctcctgcctttccttccttcctt	0.216													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	151742420	151742420	+	IGR	DEL	C	-	-	rs35221320		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151742420delC								OAZ3 (-1385 upstream) : OAZ3 (-6975 downstream)																							tggcggcacgcgcctgcaatc	0.000													5	5	---	---	---	---	
RASAL2	9462	broad.mit.edu	37	1	178408858	178408858	+	Intron	DEL	T	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178408858delT	uc001glr.2	+						RASAL2_uc001glq.2_Intron	NM_004841	NP_004832	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 1						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5						AGAGAAAAAGTTAGAAATCTT	0.294													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	22328543	22328543	+	IGR	DEL	A	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22328543delA								None (None upstream) : None (None downstream)																							ggaaggaaggaaggaaggaag	0.139													4	3	---	---	---	---	
CAPN13	92291	broad.mit.edu	37	2	30999024	30999024	+	Intron	DEL	T	-	-	rs11318503		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30999024delT	uc002rnn.2	-						CAPN13_uc002rnp.1_Intron	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					AAATAATGCATTTTTTTTTCC	0.473													1	5	---	---	---	---	
GGCX	2677	broad.mit.edu	37	2	85781577	85781578	+	Intron	INS	-	TTGTTGTTG	TTGTTGTTG	rs145024834	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85781577_85781578insTTGTTGTTG	uc002sps.2	-						GGCX_uc010yss.1_Intron|GGCX_uc010yst.1_Intron	NM_000821	NP_000812	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase isoform 1						blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification	endoplasmic reticulum membrane|integral to membrane|membrane fraction	gamma-glutamyl carboxylase activity			ovary(1)	1					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|L-Glutamic Acid(DB00142)|Menadione(DB00170)|Phytonadione(DB01022)	CTCTAGgttgtttgttgttgtt	0.233													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89868040	89868040	+	IGR	DEL	G	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89868040delG								FLJ40330 (761915 upstream) : None (None downstream)																							attccaatcaggttgattcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	127992953	127992956	+	IGR	DEL	AAGA	-	-	rs62157501		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127992953_127992956delAAGA								CYP27C1 (29610 upstream) : ERCC3 (21910 downstream)																							aaggaaggagaagaaagaaagaaa	0.015													4	2	---	---	---	---	
TFDP2	7029	broad.mit.edu	37	3	141697191	141697192	+	Intron	DEL	AC	-	-	rs147134052	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141697191_141697192delAC	uc003eun.3	-						TFDP2_uc003euk.3_Intron|TFDP2_uc010hur.2_Intron|TFDP2_uc003eul.3_Intron|TFDP2_uc011bnf.1_Intron|TFDP2_uc011bng.1_Intron|TFDP2_uc003eum.3_Intron	NM_006286	NP_006277	Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1						cgcctaaaaaacaaaaaaaaaG	0.158													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194712076	194712081	+	IGR	DEL	CTCCTA	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194712076_194712081delCTCCTA								FAM43A (302312 upstream) : C3orf21 (76934 downstream)																							cctcttcctcctcctactcctcttcc	0.087													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	609854	609854	+	IGR	DEL	T	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:609854delT								PIGG (76535 upstream) : PDE6B (9509 downstream)																							tgttcttttattttttttttt	0.000													5	4	---	---	---	---	
MCCC2	64087	broad.mit.edu	37	5	70900409	70900410	+	Intron	INS	-	T	T	rs35873168		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70900409_70900410insT	uc003kbs.3	+						MCCC2_uc010iyv.1_Intron|MCCC2_uc003kbt.3_Intron|MCCC2_uc003kbu.1_Intron	NM_022132	NP_071415	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)						leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)	1		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	AAAATCTAAtcttttttttttt	0.153													4	2	---	---	---	---	
HMGCR	3156	broad.mit.edu	37	5	74639545	74639549	+	Intron	DEL	TTGTA	-	-	rs3064191		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74639545_74639549delTTGTA	uc003kdp.2	+						HMGCR_uc011cst.1_Intron|HMGCR_uc003kdq.2_Intron|HMGCR_uc010izn.1_5'Flank	NM_000859	NP_000850	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-Coenzyme A reductase						cholesterol biosynthetic process|coenzyme A metabolic process|germ cell migration|gonad development|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal membrane	hydroxymethylglutaryl-CoA reductase (NADPH) activity|NADP binding			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Cerivastatin(DB00439)|Fluvastatin(DB01095)|Lovastatin(DB00227)|NADH(DB00157)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	TTTATTGGACTTGTATTGTGCTTAC	0.244													5	3	---	---	---	---	
MATR3	9782	broad.mit.edu	37	5	138662111	138662112	+	Intron	INS	-	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138662111_138662112insT	uc003ldu.2	+						MATR3_uc003ldt.2_Intron|MATR3_uc003ldw.2_Intron|MATR3_uc003ldx.2_Intron|MATR3_uc010jfc.2_Intron|MATR3_uc011czb.1_Intron|MATR3_uc003ldz.2_Intron|MATR3_uc003lea.2_Intron|MATR3_uc003leb.2_Intron|MATR3_uc003lec.2_Intron	NM_199189	NP_954659	P43243	MATR3_HUMAN	matrin 3							nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			tttttatttacttttttttttt	0.158													9	4	---	---	---	---	
IK	3550	broad.mit.edu	37	5	140028327	140028327	+	Intron	DEL	T	-	-	rs113938710		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140028327delT	uc003lgq.2	+						NDUFA2_uc003lgp.2_5'Flank|IK_uc011czk.1_Intron	NM_006083	NP_006074	Q13123	RED_HUMAN	RED protein						cell-cell signaling|immune response	extracellular space|nucleus|soluble fraction				large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGTGTTAAGTTTTTTTTTTT	0.338													3	3	---	---	---	---	
RNF145	153830	broad.mit.edu	37	5	158608809	158608809	+	Intron	DEL	A	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158608809delA	uc003lxp.2	-						RNF145_uc011ddy.1_Intron|RNF145_uc003lxo.1_Intron|RNF145_uc011ddz.1_Intron|RNF145_uc010jiq.1_Intron|RNF145_uc011dea.1_Intron	NM_144726	NP_653327	Q96MT1	RN145_HUMAN	ring finger protein 145							integral to membrane	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AAGAAGACTTAAAAAAAAAAA	0.294													7	5	---	---	---	---	
MYLK4	340156	broad.mit.edu	37	6	2692890	2692890	+	Intron	DEL	A	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2692890delA	uc003mty.3	-							NM_001012418	NP_001012418	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4								ATP binding|protein serine/threonine kinase activity			breast(3)|ovary(1)	4	Ovarian(93;0.0412)	all_hematologic(90;0.0897)				GGGGGGGGGCATTTTTTTATA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14383214	14383221	+	IGR	DEL	TCCTTCCT	-	-	rs58552935		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14383214_14383221delTCCTTCCT								CD83 (246068 upstream) : JARID2 (862513 downstream)																							ccttccttcctccttccttccttccttc	0.159													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27410560	27410561	+	IGR	INS	-	GAAAGGAA	GAAAGGAA			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27410560_27410561insGAAAGGAA								ZNF391 (41333 upstream) : ZNF184 (7961 downstream)																							aaggaaggaaggaaaggaagaa	0.000													5	3	---	---	---	---	
PCMT1	5110	broad.mit.edu	37	6	150094487	150094501	+	Intron	DEL	GTTTTGTTTTGTTTT	-	-	rs71672010		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150094487_150094501delGTTTTGTTTTGTTTT	uc003qne.2	+						PCMT1_uc003qna.2_Intron|PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		TGTAGAAGGAgttttgttttgttttgttttgtttt	0.130													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160133182	160133183	+	IGR	INS	-	C	C			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160133182_160133183insC								SOD2 (18829 upstream) : WTAP (14946 downstream)																							accaccACTCAGCTGCTCTGac	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1228521	1228526	+	IGR	DEL	GAGGAG	-	-	rs111919793		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1228521_1228526delGAGGAG								ZFAND2A (28666 upstream) : UNCX (44128 downstream)																							agaagaggaagaggaggaagaggaag	0.000													7	4	---	---	---	---	
TBXAS1	6916	broad.mit.edu	37	7	139578987	139578988	+	Intron	INS	-	CCA	CCA			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139578987_139578988insCCA	uc011kqv.1	+						TBXAS1_uc003vvh.2_Intron|TBXAS1_uc010lne.2_Intron|TBXAS1_uc011kqu.1_Intron|TBXAS1_uc003vvi.2_Intron|TBXAS1_uc003vvj.2_Intron|TBXAS1_uc011kqw.1_Intron|TBXAS1_uc011kqx.1_Intron	NM_001130966	NP_001124438	P24557	THAS_HUMAN	thromboxane A synthase 1, platelet isoform						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)					caccaacactgccaccaccacc	0.342													4	2	---	---	---	---	
MYOM2	9172	broad.mit.edu	37	8	2047838	2047844	+	Intron	DEL	CTTCCTT	-	-	rs143470094	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2047838_2047844delCTTCCTT	uc003wpx.3	+						MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		tccttccttccttccttctttctttcc	0.130													4	3	---	---	---	---	
CYP7A1	1581	broad.mit.edu	37	8	59412826	59412826	+	5'Flank	DEL	A	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59412826delA	uc003xtm.3	-							NM_000780	NP_000771	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A,						bile acid biosynthetic process|cellular lipid metabolic process|cellular response to cholesterol|cellular response to glucose stimulus|cholesterol catabolic process|cholesterol homeostasis|regulation of bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	cholesterol 7-alpha-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				ATTCTATTAGAAAAAAAAAAG	0.368									Neonatal_Giant_Cell_Hepatitis				4	2	---	---	---	---	
TRAM1	23471	broad.mit.edu	37	8	71520608	71520609	+	5'Flank	INS	-	A	A	rs112550133		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71520608_71520609insA	uc003xyo.1	-						TRAM1_uc011lfc.1_5'UTR	NM_014294	NP_055109	Q15629	TRAM1_HUMAN	translocation associated membrane protein 1						cotranslational protein targeting to membrane|transmembrane transport	endoplasmic reticulum membrane|integral to membrane	protein binding|receptor activity			ovary(1)	1			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)			CCGCCCGGGGGAAAAAAAAAAA	0.723													4	5	---	---	---	---	
CNTNAP3	79937	broad.mit.edu	37	9	39107309	39107310	+	Intron	INS	-	GGAA	GGAA			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39107309_39107310insGGAA	uc004abi.2	-						CNTNAP3_uc004abj.2_Intron|CNTNAP3_uc011lqr.1_Intron|CNTNAP3_uc004abk.1_Intron	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3 precursor						cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		ggagggagtggggaaggaagga	0.035													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44084401	44084402	+	IGR	INS	-	ATCTT	ATCTT			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44084401_44084402insATCTT								FAM75A6 (453671 upstream) : FAM27C (905834 downstream)																							TAAAGACTATATATAAAAATAA	0.277													10	6	---	---	---	---	
CERCAM	51148	broad.mit.edu	37	9	131187045	131187045	+	Intron	DEL	T	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131187045delT	uc004buz.3	+						CERCAM_uc004buy.1_Intron|CERCAM_uc010mxz.2_Intron|CERCAM_uc010mya.1_Intron	NM_016174	NP_057258	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule 1						cellular component movement|leukocyte cell-cell adhesion|lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen|plasma membrane				pancreas(1)	1						TTTCTCTCTCTTTTTTTTTTT	0.075													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8555337	8555338	+	IGR	INS	-	C	C	rs138737388	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8555337_8555338insC								GATA3 (438175 upstream) : None (None downstream)																							TTttctttttttccttccttcc	0.173													3	4	---	---	---	---	
TCTN3	26123	broad.mit.edu	37	10	97442250	97442251	+	Intron	INS	-	A	A			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97442250_97442251insA	uc001klb.3	-						TCTN3_uc001kla.3_Intron|TCTN3_uc010qoi.1_Intron	NM_015631	NP_056446	Q6NUS6	TECT3_HUMAN	tectonic 3 isoform a precursor						apoptosis	integral to membrane					0		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		gactccatctcaaaaaaaaaaa	0.168													4	2	---	---	---	---	
GRK5	2869	broad.mit.edu	37	10	121051696	121051696	+	Intron	DEL	C	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121051696delC	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		tcttcctcctcctcctcttcc	0.000													4	2	---	---	---	---	
TUBGCP2	10844	broad.mit.edu	37	10	135097178	135097195	+	Intron	DEL	TCCCTGCCTCTCCCGCAT	-	-	rs66529543	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135097178_135097195delTCCCTGCCTCTCCCGCAT	uc001lmg.1	-						TUBGCP2_uc001lmf.1_Intron|TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650	Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		ctccctgcactccctgcctctcccgcattccctgcctc	0.193													9	4	---	---	---	---	
C11orf48	79081	broad.mit.edu	37	11	62436869	62436869	+	Intron	DEL	A	-	-	rs75785265		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62436869delA	uc001nue.2	-						C11orf48_uc001nuf.2_Intron|C11orf48_uc010rmd.1_Intron|C11orf83_uc001nui.3_5'Flank	NM_024099	NP_077004	Q9BQE6	CK048_HUMAN	hypothetical protein LOC79081												0						actcagtctcaaaaaaaaaaa	0.159													4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2656822	2656823	+	Intron	DEL	TG	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2656822_2656823delTG	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron|CACNA1C_uc009zdy.1_Intron|CACNA1C_uc001qkv.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	gtatatatgttgtgtgtgtgtg	0.366													6	3	---	---	---	---	
SLCO1B3	28234	broad.mit.edu	37	12	21014281	21014282	+	Intron	INS	-	T	T	rs144976030	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21014281_21014282insT	uc001rek.2	+						SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron|SLCO1B3_uc001reo.2_5'Flank	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					ttatatgcagcttttgtccaac	0.267													2	5	---	---	---	---	
BRAP	8315	broad.mit.edu	37	12	112116757	112116757	+	Intron	DEL	A	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112116757delA	uc001tsn.3	-						BRAP_uc010syh.1_Intron|BRAP_uc009zvv.2_Intron	NM_006768	NP_006759	Q7Z569	BRAP_HUMAN	BRCA1 associated protein						MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1						atctctaccgaaaaaaaaaaa	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20255410	20255411	+	IGR	INS	-	CTTCTTTCCTTTTCTTT	CTTCTTTCCTTTTCTTT	rs151235154	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20255410_20255411insCTTCTTTCCTTTTCTTT								OR4M1 (5988 upstream) : OR4N2 (40197 downstream)																							ttccttccttccttcTTGTTTT	0.114													4	2	---	---	---	---	
CTAGE5	4253	broad.mit.edu	37	14	39748365	39748365	+	Intron	DEL	A	-	-	rs11357175		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39748365delA	uc001wvg.3	+						CTAGE5_uc010tqe.1_Intron|CTAGE5_uc001wuz.3_Intron|CTAGE5_uc001wuy.3_Intron|CTAGE5_uc001wvb.3_Intron|CTAGE5_uc001wvc.3_Intron|CTAGE5_uc001wva.3_Intron|CTAGE5_uc001wve.1_Intron|CTAGE5_uc001wvh.3_Intron|CTAGE5_uc001wvf.3_Intron|CTAGE5_uc001wvi.3_Intron|CTAGE5_uc010amz.2_Intron|CTAGE5_uc001wvj.3_Intron	NM_005930	NP_005921	O15320	CTGE5_HUMAN	CTAGE family, member 5 isoform 1								enzyme activator activity|protein binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		actctgtctcaaaaaaaaaaa	0.129													5	3	---	---	---	---	
SOS2	6655	broad.mit.edu	37	14	50670810	50670810	+	Intron	DEL	T	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50670810delT	uc001wxs.3	-						SOS2_uc010tql.1_Intron	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)					ttgttctaagttttttttttt	0.030													4	2	---	---	---	---	
INF2	64423	broad.mit.edu	37	14	105173451	105173452	+	Intron	INS	-	G	G			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105173451_105173452insG	uc001ypb.2	+						INF2_uc010tyi.1_Intron|INF2_uc001ypc.2_Intron|INF2_uc010awz.1_5'Flank	NM_022489	NP_071934	Q27J81	INF2_HUMAN	inverted formin 2 isoform 1						actin cytoskeleton organization	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm	actin binding|Rho GTPase binding				0		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		TCTTAGACCATGGGGGGGGGAG	0.693													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	40604470	40604470	+	IGR	DEL	T	-	-	rs35116724		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40604470delT								PLCB2 (4296 upstream) : C15orf52 (19184 downstream)																							TGGTCCAACCTTTTTTTTTTT	0.378													5	3	---	---	---	---	
BOLA2	552900	broad.mit.edu	37	16	30027022	30027023	+	Intron	INS	-	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30027022_30027023insT	uc010bzb.1	-						uc002dtf.2_Intron|DOC2A_uc002dvq.2_5'Flank			Q9H3K6	BOLA2_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0						cttcctttttcttttttttttt	0.025													5	3	---	---	---	---	
STX1B	112755	broad.mit.edu	37	16	31004014	31004015	+	3'UTR	INS	-	GGGGTGGAGGA	GGGGTGGAGGA	rs143292802	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31004014_31004015insGGGGTGGAGGA	uc010cad.2	-	10						NM_052874	NP_443106	P61266	STX1B_HUMAN	syntaxin 1B						intracellular protein transport|neurotransmitter transport|synaptic transmission	integral to plasma membrane	extracellular-glutamate-gated ion channel activity|SNAP receptor activity				0						GGTCTGCCGTGGGGGTGGGGCT	0.653													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32471773	32471774	+	IGR	INS	-	A	A	rs149995933	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32471773_32471774insA								HERC2P4 (307899 upstream) : TP53TG3B (213067 downstream)																							TATCACTTGCTAAAAAAAAATC	0.252													4	2	---	---	---	---	
PSMB3	5691	broad.mit.edu	37	17	36909737	36909737	+	Intron	DEL	T	-	-	rs35484180		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36909737delT	uc002hqr.2	+							NM_002795	NP_002786	P49720	PSB3_HUMAN	proteasome beta 3 subunit						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	protein binding|threonine-type endopeptidase activity				0						CTTCCCtttcttttttttttt	0.264													4	2	---	---	---	---	
SLC4A1	6521	broad.mit.edu	37	17	42329088	42329089	+	Intron	INS	-	T	T	rs67064853		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42329088_42329089insT	uc002igf.3	-							NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member						bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		cttttcttttcttttttttttt	0.248													7	4	---	---	---	---	
NUP85	79902	broad.mit.edu	37	17	73204376	73204376	+	Intron	DEL	A	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73204376delA	uc002jng.1	+						NUP85_uc010dgd.1_Intron|NUP85_uc010wrv.1_Intron	NM_024844	NP_079120	Q9BW27	NUP85_HUMAN	nucleoporin 85						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|nuclear membrane|Nup107-160 complex|spindle	protein binding			ovary(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			actaaaaatgaaaaaaaaaaa	0.000													3	3	---	---	---	---	
TBCD	6904	broad.mit.edu	37	17	80878413	80878413	+	Intron	DEL	T	-	-	rs3214869		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80878413delT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|TBCD_uc002kgb.1_Intron	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			GCGTCTATCCTTTTTTTTTTT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15198505	15198508	+	IGR	DEL	TTTG	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15198505_15198508delTTTG								ANKRD30B (345768 upstream) : LOC644669 (115047 downstream)																							CACATTCTGATTTGTTTTTTGTAT	0.358													4	2	---	---	---	---	
C18orf45	85019	broad.mit.edu	37	18	20889479	20889480	+	Intron	INS	-	T	T			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20889479_20889480insT	uc002kuf.2	-						C18orf45_uc010xaq.1_Intron|C18orf45_uc010xar.1_Intron|C18orf45_uc002kug.2_Intron|C18orf45_uc002kuh.2_Intron|C18orf45_uc002kue.2_Intron	NM_032933	NP_116322	Q24JQ0	CR045_HUMAN	hypothetical protein LOC85019							integral to membrane					0	all_cancers(21;0.000238)|all_epithelial(16;5.29e-06)|Lung NSC(20;0.00925)|Colorectal(14;0.0202)|all_lung(20;0.0255)|Ovarian(20;0.127)					gtcaatacaagtttTTTTTTTT	0.178													4	2	---	---	---	---	
ATP9B	374868	broad.mit.edu	37	18	77119247	77119247	+	Intron	DEL	A	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77119247delA	uc002lmx.2	+						ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmz.1_Intron|ATP9B_uc002lna.2_Intron|ATP9B_uc002lnb.1_Intron|ATP9B_uc010drb.2_Intron	NM_198531	NP_940933	O43861	ATP9B_HUMAN	ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		GTTTTTGTGGAGTATTTTTTG	0.423													2	4	---	---	---	---	
PCSK4	54760	broad.mit.edu	37	19	1484152	1484152	+	Intron	DEL	G	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1484152delG	uc002ltb.1	-						PCSK4_uc002lsz.2_5'Flank|PCSK4_uc002lta.2_Intron	NM_017573	NP_060043	Q6UW60	PCSK4_HUMAN	proprotein convertase subtilisin/kexin type 4						proteolysis	integral to membrane	serine-type endopeptidase activity				0		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTGGGACTCGGGGGGCCGTG	0.498													4	2	---	---	---	---	
SMARCA4	6597	broad.mit.edu	37	19	11168783	11168783	+	Intron	DEL	A	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11168783delA	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc010dxq.2_Intron|SMARCA4_uc010dxr.2_Intron|SMARCA4_uc002mqj.3_Intron|SMARCA4_uc010dxs.2_Intron|SMARCA4_uc002mqh.3_Intron	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity			lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				actccgtctcaaaaaaaaaaa	0.229			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	11384264	11384265	+	IGR	INS	-	TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC	TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC	rs151202085	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11384264_11384265insTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC								DOCK6 (11107 upstream) : TSPAN16 (22559 downstream)																							TGGACCACATTttccttccttc	0.158													4	3	---	---	---	---	
APOC2	344	broad.mit.edu	37	19	45452269	45452270	+	Intron	INS	-	CCT	CCT	rs10622462		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45452269_45452270insCCT	uc002pah.2	+							NM_000483	NP_000474	P02655	APOC2_HUMAN	apolipoprotein C-II precursor						cholesterol efflux|chylomicron remnant clearance|high-density lipoprotein particle clearance|lipid catabolic process|lipoprotein metabolic process|negative regulation of cholesterol transport|negative regulation of lipid metabolic process|negative regulation of receptor-mediated endocytosis|negative regulation of very-low-density lipoprotein particle clearance|phospholipid efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of phospholipase activity|positive regulation of phospholipid catabolic process|positive regulation of triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	chylomicron|intermediate-density lipoprotein particle|low-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	lipase inhibitor activity|lipid binding|lipoprotein lipase activator activity|phospholipase activator activity|phospholipase binding|protein homodimerization activity			kidney(1)	1	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)		ggcccccagcccgtcctccctc	0.015													6	5	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26413089	26413090	+	Intron	INS	-	CCTT	CCTT	rs76444799		TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26413089_26413090insCCTT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron|MYO18B_uc010gva.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						cttccttccttctttcctccct	0.010													4	2	---	---	---	---	
EIF2S3	1968	broad.mit.edu	37	X	24095043	24095043	+	3'UTR	DEL	C	-	-	rs5949273	by1000genomes	TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24095043delC	uc004dbc.2	+	12						NM_001415	NP_001406	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2,							cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			lung(1)	1						AGGTTAttctctttttttttt	0.284													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	14359924	14359924	+	IGR	DEL	A	-	-			TCGA-BP-4988-01A-01D-1462-08	TCGA-BP-4988-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:14359924delA								None (None upstream) : TTTY15 (414374 downstream)																							cccgtctcagaaaaaaaaaaa	0.015													4	2	---	---	---	---	
