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	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	validation_status	validation_method	validation_tumor_sample	validation_alt_allele
Unknown	0	broad.mit.edu	37	1	700532	700532	+	RNA	DEL	T	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:700532delT	uc001abo.2	-	7		c.1022delA								Homo sapiens cDNA clone IMAGE:4129277, partial cds.																														---	---	---	---
KIAA0562	9731	broad.mit.edu	37	1	3743486	3743490	+	Intron	DEL	GGTGG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3743486_3743490delGGTGG	uc001aky.2	-						KIAA0562_uc010nzm.1_Intron	NM_014704	NP_055519			glycine-, glutamate-,							centriole	binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8415164	8415166	+	In_Frame_Del	DEL	CTT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8415164_8415166delCTT	uc001ape.2	-	24	5492_5494	c.4682_4684delAAG	c.(4681-4686)GAAGGT>GGT	p.E1561del	RERE_uc001apf.2_In_Frame_Del_p.E1561del|RERE_uc001apd.2_In_Frame_Del_p.E1007del	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	1561					multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)														---	---	---	---
FBXO42	54455	broad.mit.edu	37	1	16621570	16621577	+	Intron	DEL	AATATATT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16621570_16621577delAATATATT	uc001ayg.2	-						FBXO42_uc001ayf.2_Intron|FBXO42_uc001ayh.2_Intron	NM_018994	NP_061867			F-box protein 42											upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)														---	---	---	---
MAP3K6	9064	broad.mit.edu	37	1	27683543	27683544	+	In_Frame_Ins	INS	-	AGT	AGT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27683543_27683544insAGT	uc001bny.1	-	24	3569_3570	c.3320_3321insACT	c.(3319-3321)CTG>CTACTG	p.1107_1107L>LL	MAP3K6_uc009vsw.1_In_Frame_Ins_p.1099_1099L>LL	NM_004672	NP_004663	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase	1107					activation of JUN kinase activity		ATP binding|magnesium ion binding|MAP kinase kinase kinase activity			breast(4)|lung(3)|ovary(1)|central_nervous_system(1)	9		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29338518	29338518	+	Intron	DEL	G	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29338518delG	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
PUM1	9698	broad.mit.edu	37	1	31531828	31531829	+	Intron	INS	-	AATG	AATG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31531828_31531829insAATG	uc001bsi.1	-						PUM1_uc001bsh.1_Intron|PUM1_uc001bsj.1_Intron|PUM1_uc010oga.1_Intron|PUM1_uc001bsk.1_Intron|PUM1_uc010ogb.1_Intron	NM_014676	NP_055491			pumilio 1 isoform 2						cellular membrane organization|post-Golgi vesicle-mediated transport|regulation of translation	cytosol	RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)														---	---	---	---
HDAC1	3065	broad.mit.edu	37	1	32797916	32797917	+	Intron	INS	-	GA	GA			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32797916_32797917insGA	uc001bvb.1	+						HDAC1_uc010ohf.1_Intron|HDAC1_uc001bvc.1_Intron	NM_004964	NP_004955			histone deacetylase 1						anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytosol|NuRD complex|Sin3 complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)	3		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)													---	---	---	---
ZNF362	149076	broad.mit.edu	37	1	33764495	33764496	+	Intron	INS	-	TGGT	TGGT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33764495_33764496insTGGT	uc001bxc.1	+							NM_152493	NP_689706			zinc finger protein 362						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)														OREG0013343	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GPBP1L1	60313	broad.mit.edu	37	1	46095140	46095140	+	Intron	DEL	A	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46095140delA	uc001coq.2	-						GPBP1L1_uc001coo.2_Intron	NM_021639	NP_067652			GC-rich promoter binding protein 1-like 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49119012	49119013	+	Frame_Shift_Ins	INS	-	AATG	AATG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49119012_49119013insAATG	uc001cru.2	-	8	993_994	c.835_836insCATT	c.(835-837)TACfs	p.Y279fs	AGBL4_uc010omw.1_Frame_Shift_Ins_p.Y12fs|AGBL4_uc010omx.1_Frame_Shift_Ins_p.Y291fs|AGBL4_uc001crv.1_Frame_Shift_Ins_p.Y132fs|AGBL4_uc010omy.1_Frame_Shift_Ins_p.Y102fs	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	279					C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
C1orf177	163747	broad.mit.edu	37	1	55307376	55307381	+	Intron	DEL	GTACCT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55307376_55307381delGTACCT	uc001cyb.3	+						C1orf177_uc001cya.3_Splice_Site	NM_001110533	NP_001104003			hypothetical protein LOC163747 isoform 2												0																		---	---	---	---
CLCC1	23155	broad.mit.edu	37	1	109492678	109492679	+	Intron	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109492678_109492679insA	uc001dwe.1	-						AKNAD1_uc010ovb.1_Intron|CLCC1_uc001dwf.1_Intron|CLCC1_uc001dwg.1_Intron|CLCC1_uc009wes.1_Intron|CLCC1_uc009wet.1_Intron|CLCC1_uc001dwh.1_Intron	NM_001048210	NP_001041675			Mid-1-related chloride channel 1 isoform 1							endoplasmic reticulum|Golgi apparatus|integral to membrane|nucleus				liver(1)	1		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)														---	---	---	---
TTF2	8458	broad.mit.edu	37	1	117640055	117640061	+	Splice_Site	DEL	GGTAATG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117640055_117640061delGGTAATG	uc001egy.2	+	21	3289	c.3269_splice	c.e21+1	p.W1090_splice		NM_003594	NP_003585			transcription termination factor, RNA polymerase						mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|termination of RNA polymerase II transcription	cytoplasm|spliceosomal complex|transcription elongation factor complex	ATP binding|ATP-dependent helicase activity|DNA binding|DNA-dependent ATPase activity|protein binding|zinc ion binding			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)														---	---	---	---
MRPS21	54460	broad.mit.edu	37	1	150266866	150266875	+	Splice_Site	DEL	ACAGGTAACT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150266866_150266875delACAGGTAACT	uc001euk.2	+	2	165	c.83_splice	c.e2+1	p.R28_splice	MRPS21_uc001eul.2_Splice_Site_p.R28_splice	NM_031901	NP_114107			mitochondrial ribosomal protein S21						translation	mitochondrial small ribosomal subunit	structural constituent of ribosome				0	Lung NSC(24;5.57e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
PRPF3	9129	broad.mit.edu	37	1	150307717	150307718	+	Intron	INS	-	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150307717_150307718insT	uc001eum.3	+						PRPF3_uc009wlp.2_Intron|PRPF3_uc010pca.1_Intron|PRPF3_uc010pcb.1_Intron|PRPF3_uc009wlq.1_Intron	NM_004698	NP_004689			PRP3 pre-mRNA processing factor 3 homolog						nuclear mRNA splicing, via spliceosome	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding			ovary(1)	1	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)														---	---	---	---
PRUNE	58497	broad.mit.edu	37	1	150981160	150981161	+	Intron	INS	-	AGGG	AGGG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150981160_150981161insAGGG	uc001ewh.1	+						PRUNE_uc001ewi.1_Intron|PRUNE_uc010pco.1_Intron|PRUNE_uc001ewj.1_Intron|FAM63A_uc001ewc.2_5'Flank|FAM63A_uc010pcm.1_5'Flank|FAM63A_uc001ewd.2_5'Flank|FAM63A_uc001ewe.2_5'Flank|FAM63A_uc001ewf.2_5'Flank|FAM63A_uc010pcn.1_5'Flank|FAM63A_uc001ewg.2_5'Flank	NM_021222	NP_067045			prune							cytoplasm|focal adhesion|nucleus	inorganic diphosphatase activity|manganese ion binding|protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
ARHGEF2	9181	broad.mit.edu	37	1	155931767	155931768	+	Intron	DEL	TC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155931767_155931768delTC	uc001fmt.2	-						ARHGEF2_uc001fmr.2_Intron|ARHGEF2_uc001fms.2_Intron|ARHGEF2_uc001fmu.2_Intron|ARHGEF2_uc010pgt.1_Intron|ARHGEF2_uc010pgu.1_Intron	NM_001162383	NP_001155855			Rho/Rac guanine nucleotide exchange factor 2						actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
DUSP27	92235	broad.mit.edu	37	1	167086627	167086628	+	Frame_Shift_Ins	INS	-	AGCT	AGCT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167086627_167086628insAGCT	uc001geb.1	+	3	268_269	c.268_269insAGCT	c.(268-270)CAGfs	p.Q90fs		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27	90					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3																		---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174340152	174340153	+	Frame_Shift_Ins	INS	-	TGTC	TGTC			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174340152_174340153insTGTC	uc001gjx.2	+	12	1696_1697	c.1501_1502insTGTC	c.(1501-1503)GTGfs	p.V501fs	RABGAP1L_uc009wwq.1_Frame_Shift_Ins_p.V513fs|RABGAP1L_uc001gjw.2_Frame_Shift_Ins_p.V464fs|RABGAP1L_uc001gjy.2_Frame_Shift_Ins_p.V169fs|RABGAP1L_uc001gjz.2_Frame_Shift_Ins_p.V148fs	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A	501					regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
MTR	4548	broad.mit.edu	37	1	237060180	237060183	+	Intron	DEL	CTAC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237060180_237060183delCTAC	uc001hyi.3	+						MTR_uc010pxw.1_Intron|MTR_uc010pxx.1_Intron|MTR_uc010pxy.1_Intron	NM_000254	NP_000245			5-methyltetrahydrofolate-homocysteine						nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)													---	---	---	---
C2orf48	348738	broad.mit.edu	37	2	10295167	10295168	+	Intron	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10295167_10295168insA	uc002rai.1	+							NM_182626	NP_872432			hypothetical protein LOC348738												0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.188)														---	---	---	---
AHSA2	130872	broad.mit.edu	37	2	61413433	61413434	+	Intron	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61413433_61413434insA	uc002sbc.1	+						AHSA2_uc002sbb.1_Intron	NM_152392	NP_689605			AHA1, activator of heat shock 90kDa protein						response to stress	cytoplasm	ATPase activator activity|chaperone binding			breast(1)	1			Epithelial(17;0.0994)															---	---	---	---
REG1P	5969	broad.mit.edu	37	2	79363175	79363176	+	RNA	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79363175_79363176insC	uc002soa.1	-	4		c.1138_1139insG			REG1P_uc002sob.1_RNA|REG1P_uc002soc.1_RNA					Homo sapiens mRNA for Reg-related sequence derived peptide-1, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	95613889	95613890	+	5'Flank	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95613889_95613890insA	uc002stv.1	-											Homo sapiens cDNA FLJ44118 fis, clone TESTI4047069.																														---	---	---	---
RGPD5	84220	broad.mit.edu	37	2	113147931	113147933	+	Intron	DEL	ATG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113147931_113147933delATG	uc002ths.1	-						RGPD8_uc010fkk.1_Intron|RGPD5_uc002tht.1_Intron	NM_005054	NP_005045			RANBP2-like and GRIP domain containing 5 isoform						intracellular transport	cytoplasm	binding				0																		---	---	---	---
SLC35F5	80255	broad.mit.edu	37	2	114480664	114480665	+	Intron	DEL	AT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114480664_114480665delAT	uc002tku.1	-						SLC35F5_uc002tkt.2_Intron	NM_025181	NP_079457			solute carrier family 35, member F5						transport	integral to membrane					0																		---	---	---	---
YSK4	80122	broad.mit.edu	37	2	135763132	135763133	+	Intron	INS	-	TTAG	TTAG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135763132_135763133insTTAG	uc002tue.1	-						YSK4_uc010fne.1_Intron|YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Intron|YSK4_uc010zbg.1_Intron|YSK4_uc002tui.3_Intron	NM_025052	NP_079328			Yeast Sps1/Ste20-related kinase 4 isoform 1								ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
IFIH1	64135	broad.mit.edu	37	2	163133243	163133249	+	Frame_Shift_Del	DEL	TGGTGGG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163133243_163133249delTGGTGGG	uc002uce.2	-	11	2474_2480	c.2252_2258delCCCACCA	c.(2251-2259)GCCCACCATfs	p.A751fs		NM_022168	NP_071451	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	751_753	Helicase C-terminal.				detection of virus|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|regulation of apoptosis	cytosol|nucleus	ATP binding|DNA binding|double-stranded RNA binding|helicase activity|protein binding|ribonucleoprotein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
SCN7A	6332	broad.mit.edu	37	2	167269169	167269170	+	Frame_Shift_Del	DEL	TA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167269169_167269170delTA	uc002udu.1	-	22	3603_3604	c.3476_3477delTA	c.(3475-3477)ATAfs	p.I1159fs	SCN7A_uc010fpm.1_RNA	NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	1159					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1																		---	---	---	---
FASTKD2	22868	broad.mit.edu	37	2	207651490	207651492	+	In_Frame_Del	DEL	TGG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207651490_207651492delTGG	uc002vbu.2	+	8	1871_1873	c.1461_1463delTGG	c.(1459-1464)ACTGGT>ACT	p.G488del	FASTKD2_uc002vbv.2_In_Frame_Del_p.G488del|FASTKD2_uc002vbx.2_In_Frame_Del_p.G488del|FASTKD2_uc002vbw.1_In_Frame_Del_p.G488del	NM_001136193	NP_001129665	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	488					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)|skin(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)														---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215843526	215843528	+	Splice_Site	DEL	ACC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215843526_215843528delACC	uc002vew.2	-	32	5197	c.4977_splice	c.e32+1	p.E1659_splice	ABCA12_uc002vev.2_Splice_Site_p.E1341_splice|ABCA12_uc010zjn.1_Splice_Site_p.E586_splice	NM_173076	NP_775099			ATP-binding cassette, sub-family A, member 12						cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
XRCC5	7520	broad.mit.edu	37	2	217012635	217012636	+	Intron	INS	-	AATA	AATA			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217012635_217012636insAATA	uc002vfy.2	+						XRCC5_uc002vfz.2_Intron	NM_021141	NP_066964			ATP-dependent DNA helicase II						double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|provirus integration|telomere maintenance|transcription, DNA-dependent	Ku70:Ku80 complex|nonhomologous end joining complex|nuclear telomere cap complex|nucleoplasm	ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|telomeric DNA binding|transcription regulatory region DNA binding			lung(1)|kidney(1)	2		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)									Direct_reversal_of_damage|NHEJ					---	---	---	---
GMPPA	29926	broad.mit.edu	37	2	220368627	220368627	+	Intron	DEL	G	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220368627delG	uc002vlr.2	+						GMPPA_uc002vls.2_Intron|GMPPA_uc002vlt.2_Intron|GMPPA_uc002vlu.2_Intron|GMPPA_uc002vlv.2_Intron|GMPPA_uc002vlw.2_Intron|GMPPA_uc002vlx.2_Intron	NM_013335	NP_037467			GDP-mannose pyrophosphorylase A						dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine		GTP binding|mannose-1-phosphate guanylyltransferase activity				0		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)														---	---	---	---
DGKD	8527	broad.mit.edu	37	2	234359866	234359873	+	Intron	DEL	TAAAAACA	-	-	rs13389393	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234359866_234359873delTAAAAACA	uc002vui.1	+						DGKD_uc002vuj.1_Intron|DGKD_uc010fyh.1_Intron|DGKD_uc010fyi.1_Intron	NM_152879	NP_690618			diacylglycerol kinase, delta 130kDa isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)													---	---	---	---
GBX2	2637	broad.mit.edu	37	2	237076315	237076316	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237076315_237076316delGA	uc002vvw.1	-	1	337_338	c.299_300delTC	c.(298-300)CTCfs	p.L100fs	GBX2_uc010zng.1_Frame_Shift_Del_p.L90fs	NM_001485	NP_001476	P52951	GBX2_HUMAN	gastrulation brain homeo box 2	100				LPPAHPHHQIPSLPTGFCSSLAQGMALTSTLMATLPGGFSA SPQHQEAAAARKFAPQPLPGGGNFDKAEALQADAEDGKGFL AKEGSLLAFSAAETVQASLVGAVRGQGKDESKVEDDPKG -> CRPHTLTTRSPACPQASAPAWRRAWRSPLRSWPRSPAA SPRRPSTRRRQRPASSRRSRCPAAVTSTRRRRCRLTRRTAK ASWPKRARCSPSPRPRRCRLRSSGLSEGKGKTSQRWKTTRS (in Ref. 1; AAC03241).		nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		Breast(86;0.00235)|Renal(207;0.00339)|all_hematologic(139;0.00357)|all_lung(227;0.0616)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|Lung NSC(271;0.179)		Epithelial(121;4.5e-25)|OV - Ovarian serous cystadenocarcinoma(60;5.16e-11)|BRCA - Breast invasive adenocarcinoma(100;3.4e-05)|Lung(119;0.00195)|LUSC - Lung squamous cell carcinoma(224;0.00471)														---	---	---	---
TRAF3IP1	26146	broad.mit.edu	37	2	239253057	239253058	+	Intron	INS	-	A	A	rs147538341	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239253057_239253058insA	uc002vye.2	+						TRAF3IP1_uc002vyf.2_Intron	NM_015650	NP_056465			TNF receptor-associated factor 3 interacting							cytoplasm|cytoskeleton	protein binding			ovary(1)	1		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)														---	---	---	---
HDAC4	9759	broad.mit.edu	37	2	240078399	240078408	+	Frame_Shift_Del	DEL	GGTGGTTATA	-	-	rs148880349	byFrequency;by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240078399_240078408delGGTGGTTATA	uc002vyk.3	-	7	1465_1474	c.673_682delTATAACCACC	c.(673-684)TATAACCACCCGfs	p.Y225fs	HDAC4_uc010fyz.1_Frame_Shift_Del_p.Y220fs|HDAC4_uc010zoa.1_Frame_Shift_Del_p.Y220fs|HDAC4_uc010fza.2_Frame_Shift_Del_p.Y225fs|HDAC4_uc010fyy.2_Frame_Shift_Del_p.Y177fs|HDAC4_uc010znz.1_Frame_Shift_Del_p.Y108fs|HDAC4_uc010fzb.1_5'Flank	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4	225_228	Interaction with MEF2A.				B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)														---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241713674	241713676	+	In_Frame_Del	DEL	ACC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241713674_241713676delACC	uc002vzy.2	-	12	1107_1109	c.961_963delGGT	c.(961-963)GGTdel	p.G321del	KIF1A_uc010fzk.2_In_Frame_Del_p.G321del|KIF1A_uc002vzz.1_In_Frame_Del_p.G321del	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	321	Kinesin-motor.				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)														---	---	---	---
OGG1	4968	broad.mit.edu	37	3	9792006	9792007	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9792006_9792007insC	uc003bsi.2	+	1	379_380	c.36_37insC	c.(34-39)GGGCATfs	p.G12fs	OGG1_uc003bsh.2_Frame_Shift_Ins_p.G12fs|OGG1_uc003bsj.2_Frame_Shift_Ins_p.G12fs|OGG1_uc003bsk.2_Frame_Shift_Ins_p.G12fs|OGG1_uc003bsl.2_Frame_Shift_Ins_p.G12fs|OGG1_uc003bsm.2_Frame_Shift_Ins_p.G12fs|OGG1_uc003bsn.2_Frame_Shift_Ins_p.G12fs|OGG1_uc003bso.2_Frame_Shift_Ins_p.G12fs|OGG1_uc003bsp.1_5'Flank|OGG1_uc010hcm.1_5'Flank|OGG1_uc003bsq.1_5'Flank|OGG1_uc003bsr.1_5'Flank	NM_002542	NP_002533	O15527	OGG1_HUMAN	8-oxoguanine DNA-glycosylase 1 isoform 1a	12_13					depurination|nucleotide-excision repair|regulation of protein import into nucleus, translocation|regulation of transcription, DNA-dependent|response to oxidative stress|response to radiation	mitochondrion|nuclear matrix|nuclear speck	damaged DNA binding|endonuclease activity|oxidized purine base lesion DNA N-glycosylase activity|protein binding				0	Medulloblastoma(99;0.227)												BER_DNA_glycosylases					---	---	---	---
SGOL1	151648	broad.mit.edu	37	3	20202702	20202703	+	Frame_Shift_Ins	INS	-	GA	GA			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20202702_20202703insGA	uc003cbs.2	-	9	1767_1768	c.1580_1581insTC	c.(1579-1581)TCAfs	p.S527fs	SGOL1_uc003cbr.2_Frame_Shift_Ins_p.S258fs|SGOL1_uc010hfa.2_Frame_Shift_Ins_p.S181fs|SGOL1_uc003cbt.2_Frame_Shift_Ins_p.S275fs|SGOL1_uc003cbu.2_Frame_Shift_Ins_p.S527fs|SGOL1_uc003cbv.2_Frame_Shift_Ins_p.S275fs|SGOL1_uc003cbw.2_Frame_Shift_Ins_p.S258fs	NM_001012410	NP_001012410	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 isoform A2	527					attachment of spindle microtubules to kinetochore|cell division|centriole-centriole cohesion|meiotic chromosome segregation|mitotic prometaphase	centrosome|condensed chromosome kinetochore|cytosol|mitotic cohesin complex|spindle pole	protein binding				0																		---	---	---	---
ARPP21	10777	broad.mit.edu	37	3	35723279	35723279	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35723279delA	uc003cgb.2	+	3	300	c.36delA	c.(34-36)GCAfs	p.A12fs	ARPP21_uc003cga.2_Frame_Shift_Del_p.A12fs|ARPP21_uc011axy.1_Frame_Shift_Del_p.A12fs|ARPP21_uc003cfz.2_RNA|ARPP21_uc003cgc.2_Frame_Shift_Del_p.A12fs|ARPP21_uc003cgd.2_Frame_Shift_Del_p.A12fs|ARPP21_uc011axx.1_RNA|ARPP21_uc003cge.2_Frame_Shift_Del_p.A12fs	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD	12						cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3																		---	---	---	---
RRP9	9136	broad.mit.edu	37	3	51975555	51975555	+	Intron	DEL	G	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51975555delG	uc003dbw.1	-						PARP3_uc003dby.2_5'Flank|PARP3_uc003dbz.2_5'Flank	NM_004704	NP_004695			RNA, U3 small nucleolar interacting protein 2						rRNA processing	nucleolus|small nuclear ribonucleoprotein complex|small nucleolar ribonucleoprotein complex	RNA binding			breast(2)|ovary(1)	3				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)														---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53836195	53836209	+	Splice_Site	DEL	CATTAGGTATGTGCT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53836195_53836209delCATTAGGTATGTGCT	uc003dgv.3	+	43	5598	c.5435_splice	c.e43+1	p.R1812_splice	CACNA1D_uc003dgu.3_Splice_Site_p.R1832_splice|CACNA1D_uc003dgy.3_Intron|CACNA1D_uc003dgw.3_Splice_Site_p.R1479_splice|CACNA1D_uc011bes.1_Splice_Site	NM_001128840	NP_001122312			calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108139758	108139759	+	Intron	INS	-	AAC	AAC			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108139758_108139759insAAC	uc003dxa.1	-							NM_014981	NP_055796			myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
DIRC2	84925	broad.mit.edu	37	3	122564454	122564455	+	Intron	INS	-	T	T	rs35604258		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122564454_122564455insT	uc003efw.3	+						DIRC2_uc010hrl.2_Intron|DIRC2_uc010hrm.2_Intron	NM_032839	NP_116228			disrupted in renal carcinoma 2						transport	integral to membrane					0				GBM - Glioblastoma multiforme(114;0.0614)														---	---	---	---
TF	7018	broad.mit.edu	37	3	133485263	133485264	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133485263_133485264insC	uc003epu.1	+	17	3200_3201	c.1472_1473insC	c.(1471-1473)AACfs	p.N491fs	TF_uc011blt.1_Frame_Shift_Ins_p.N364fs|TF_uc003epw.1_Intron|TF_uc003epv.1_Frame_Shift_Ins_p.N491fs	NM_001063	NP_001054	P02787	TRFE_HUMAN	transferrin precursor	491	Transferrin-like 2.				cellular iron ion homeostasis|platelet activation|platelet degranulation|transferrin transport|transmembrane transport	apical plasma membrane|basal plasma membrane|coated pit|early endosome|endocytic vesicle|endosome membrane|extracellular region|late endosome|perinuclear region of cytoplasm|recycling endosome|stored secretory granule	ferric iron binding			ovary(1)|skin(1)	2					Aluminium(DB01370)|Bismuth(DB01402)|Iron Dextran(DB00893)													---	---	---	---
SI	6476	broad.mit.edu	37	3	164786938	164786941	+	Frame_Shift_Del	DEL	AGTC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164786938_164786941delAGTC	uc003fei.2	-	4	360_363	c.298_301delGACT	c.(298-303)GACTCTfs	p.D100fs		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	100_101	Lumenal.|P-type 1.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)										HNSCC(35;0.089)			---	---	---	---
TM4SF19	116211	broad.mit.edu	37	3	196051187	196051188	+	Frame_Shift_Ins	INS	-	TC	TC			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196051187_196051188insTC	uc003fwl.1	-	4	528_529	c.403_404insGA	c.(403-405)ACAfs	p.T135fs	TM4SF19_uc003fwj.2_RNA|uc003fwk.1_3'UTR|TM4SF19_uc010iad.1_Frame_Shift_Ins_p.T135fs|TM4SF19_uc011btv.1_Frame_Shift_Ins_p.T109fs	NM_138461	NP_612470	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19	135	Extracellular (Potential).					integral to membrane					0	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)														---	---	---	---
NCAPG	64151	broad.mit.edu	37	4	17814404	17814411	+	Intron	DEL	TAGCATTA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17814404_17814411delTAGCATTA	uc003gpp.2	+						NCAPG_uc011bxj.1_Intron|DCAF16_uc003gpn.2_5'Flank	NM_022346	NP_071741			chromosome condensation protein G						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	protein binding			large_intestine(1)	1				STAD - Stomach adenocarcinoma(129;0.18)														---	---	---	---
DHX15	1665	broad.mit.edu	37	4	24529563	24529564	+	Frame_Shift_Ins	INS	-	CC	CC			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24529563_24529564insCC	uc003gqx.2	-	14	2539_2540	c.2371_2372insGG	c.(2371-2373)GAAfs	p.E791fs	DHX15_uc003gqv.2_Frame_Shift_Ins_p.E197fs|DHX15_uc003gqw.2_Frame_Shift_Ins_p.E214fs	NM_001358	NP_001349	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 15	791				KLQSKEYSQY -> QTSIQGIFTVLNSVLRTEVIERTALKD E (in Ref. 1; BAA23987).	mRNA processing	U12-type spliceosomal complex	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(1)	1		Breast(46;0.0503)																---	---	---	---
YIPF7	285525	broad.mit.edu	37	4	44651969	44651969	+	Intron	DEL	A	-	-	rs35447406		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44651969delA	uc010ifx.1	-						YIPF7_uc010ify.1_Intron	NM_182592	NP_872398			Yip1 domain family, member 7							endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	46726361	46726362	+	IGR	INS	-	TTGT	TTGT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46726361_46726362insTTGT								GABRA2 (333940 upstream) : COX7B2 (10487 downstream)																																			---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62363233	62363233	+	Intron	DEL	C	-	-	rs114845759		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62363233delC	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc010ihg.1_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
CXCL1	2919	broad.mit.edu	37	4	74736276	74736282	+	3'UTR	DEL	CTGGTGG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74736276_74736282delCTGGTGG	uc003hhh.1	+	4						NM_001511	NP_001502			chemokine (C-X-C motif) ligand 1						actin cytoskeleton organization|cell proliferation|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response|intracellular signal transduction|negative regulation of cell proliferation|nervous system development	extracellular space|intracellular	chemokine activity|enzyme activator activity|growth factor activity				0	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)															---	---	---	---
AFF1	4299	broad.mit.edu	37	4	87928679	87928689	+	Intron	DEL	GCTTTGTCATT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87928679_87928689delGCTTTGTCATT	uc003hqj.3	+						AFF1_uc011ccx.1_Intron|AFF1_uc003hqh.1_Intron|AFF1_uc011ccy.1_Intron|AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926			myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)														---	---	---	---
LRBA	987	broad.mit.edu	37	4	151935847	151935848	+	5'UTR	INS	-	CACT	CACT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151935847_151935848insCACT	uc010ipj.2	-	2					LRBA_uc003ilu.3_5'UTR|LRBA_uc003ilx.1_5'UTR	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
FAM198B	51313	broad.mit.edu	37	4	159076709	159076710	+	Intron	INS	-	AT	AT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159076709_159076710insAT	uc003ipp.3	-						FAM198B_uc003ipq.3_Intron|FAM198B_uc003ipr.3_Intron	NM_016613	NP_057697			hypothetical protein LOC51313 isoform 2							Golgi membrane|integral to membrane					0																		---	---	---	---
NDUFS6	4726	broad.mit.edu	37	5	1801427	1801428	+	5'Flank	INS	-	G	G	rs150444980	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1801427_1801428insG	uc003jcy.2	+						MRPL36_uc003jcx.3_5'Flank	NM_004553	NP_004544			NADH dehydrogenase (ubiquinone) Fe-S protein 6,						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	electron carrier activity|NADH dehydrogenase (ubiquinone) activity			central_nervous_system(1)	1					NADH(DB00157)													---	---	---	---
PAPD4	167153	broad.mit.edu	37	5	78981056	78981065	+	Frame_Shift_Del	DEL	ACAGTATACT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78981056_78981065delACAGTATACT	uc010jae.1	+	16	1833_1842	c.1415_1424delACAGTATACT	c.(1414-1425)AACAGTATACTAfs	p.N472fs	PAPD4_uc003kgb.2_Frame_Shift_Del_p.N472fs|PAPD4_uc010jaf.1_Frame_Shift_Del_p.N472fs|PAPD4_uc003kga.2_Frame_Shift_Del_p.N468fs|PAPD4_uc003kfz.2_Frame_Shift_Del_p.N429fs	NM_001114393	NP_001107865	Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	472_475					histone mRNA catabolic process|mRNA processing|RNA polyadenylation	cytoplasm	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity			ovary(1)	1		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)														---	---	---	---
DIAPH1	1729	broad.mit.edu	37	5	140951490	140951492	+	Splice_Site	DEL	CAC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140951490_140951492delCAC	uc003llb.3	-	17	2614	c.2473_splice	c.e17+1	p.T825_splice	DIAPH1_uc003llc.3_Splice_Site_p.T816_splice|DIAPH1_uc010jgc.1_Splice_Site_p.T264_splice	NM_005219	NP_005210			diaphanous 1 isoform 1						regulation of microtubule-based process|sensory perception of sound	cytoplasm|cytoskeleton|ruffle membrane	actin binding|receptor binding|Rho GTPase binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
MXD3	83463	broad.mit.edu	37	5	176733399	176733415	+	3'UTR	DEL	GCAGCCACCTGCCGTTC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176733399_176733415delGCAGCCACCTGCCGTTC	uc010jkk.2	-	6					RAB24_uc003mfu.2_5'Flank|RAB24_uc003mfv.2_5'Flank|RAB24_uc003mfw.2_5'Flank|PRELID1_uc003mfx.2_Intron|PRELID1_uc003mfy.2_Intron	NM_001142935	NP_001136407			MAX dimerization protein 3 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
F12	2161	broad.mit.edu	37	5	176836391	176836392	+	Intron	INS	-	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176836391_176836392insG	uc003mgo.3	-						F12_uc010jkl.2_Intron	NM_000505	NP_000496			coagulation factor XII precursor						Factor XII activation|fibrinolysis|innate immune response|positive regulation of blood coagulation|positive regulation of fibrinolysis|positive regulation of plasminogen activation|protein autoprocessing|response to misfolded protein|zymogen activation	extracellular space|plasma membrane	serine-type endopeptidase activity				0	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)											Hereditary_Angioedema				---	---	---	---
WRNIP1	56897	broad.mit.edu	37	6	2783745	2783746	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2783745_2783746insC	uc003mtz.2	+	5	1783_1784	c.1592_1593insC	c.(1591-1593)GACfs	p.D531fs	WRNIP1_uc003mua.2_Frame_Shift_Ins_p.D506fs	NM_020135	NP_064520	Q96S55	WRIP1_HUMAN	Werner helicase interacting protein isoform 1	531					DNA replication|DNA synthesis involved in DNA repair|regulation of DNA-dependent DNA replication initiation	mitochondrion|nucleus|perinuclear region of cytoplasm	ATP binding|ATPase activity|DNA binding|metal ion binding|protein binding			ovary(1)|pancreas(1)	2	Ovarian(93;0.0412)	all_hematologic(90;0.0895)																---	---	---	---
BTN2A3	54718	broad.mit.edu	37	6	26430816	26430817	+	Intron	INS	-	A	A	rs34293101		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26430816_26430817insA	uc011dkl.1	+						BTN2A3_uc011dkm.1_Intron					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0																		---	---	---	---
HLA-E	3133	broad.mit.edu	37	6	30460197	30460198	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30460197_30460198insT	uc003nqg.2	+	6	1058_1059	c.1020_1021insT	c.(1018-1023)AGCTACfs	p.S340fs	HLA-E_uc011dmg.1_RNA|HLA-E_uc011dmh.1_Frame_Shift_Ins_p.S381fs	NM_005516	NP_005507	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	340_341	Cytoplasmic (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			central_nervous_system(4)|ovary(1)	5																		---	---	---	---
HLA-DRB5	3127	broad.mit.edu	37	6	32497712	32497713	+	Intron	INS	-	A	A	rs146725750	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32497712_32497713insA	uc003obj.2	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB5_uc003obk.3_Intron	NM_002125	NP_002116			major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0																		---	---	---	---
MED20	9477	broad.mit.edu	37	6	41888526	41888527	+	Intron	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41888526_41888527insA	uc003ork.2	-						MED20_uc003orj.2_Intron|MED20_uc011duh.1_Intron|MED20_uc011dui.1_Intron|MED20_uc011duj.1_Intron|BYSL_uc003orl.2_5'Flank	NM_004275	NP_004266			Trf (TATA binding protein-related						regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	mediator complex	DNA-directed RNA polymerase activity|protein binding				0	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000367)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
MAD2L1BP	9587	broad.mit.edu	37	6	43603954	43603955	+	Intron	INS	-	TC	TC			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43603954_43603955insTC	uc003ovv.2	+						MAD2L1BP_uc003ovu.2_Intron	NM_014628	NP_055443			MAD2L1 binding protein isoform 2						mitotic cell cycle checkpoint|regulation of exit from mitosis	cytoplasm|nucleus|spindle	protein binding				0	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000351)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	86137454	86137455	+	IGR	INS	-	TGA	TGA			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86137454_86137455insTGA								TBX18 (663555 upstream) : NT5E (21847 downstream)																																			---	---	---	---
GABRR2	2570	broad.mit.edu	37	6	89977396	89977397	+	Splice_Site	DEL	AC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89977396_89977397delAC	uc003pnb.2	-	6	819	c.811_splice	c.e6+1	p.G271_splice	GABRR2_uc011dzx.1_Splice_Site_p.G147_splice	NM_002043	NP_002034			gamma-aminobutyric acid (GABA) receptor, rho 2						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				0		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)														---	---	---	---
AIM1	202	broad.mit.edu	37	6	106973114	106973115	+	Intron	INS	-	GT	GT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106973114_106973115insGT	uc003prh.2	+							NM_001624	NP_001615			absent in melanoma 1								sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)														---	---	---	---
PLEKHA8	84725	broad.mit.edu	37	7	30089000	30089001	+	Splice_Site	INS	-	AA	AA			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30089000_30089001insAA	uc003tam.1	+	5	688	c.597_splice	c.e5+2	p.K199_splice	PLEKHA8_uc003tao.2_Splice_Site_p.K83_splice|PLEKHA8_uc003tap.1_Splice_Site_p.K199_splice|PLEKHA8_uc003tan.2_Splice_Site_p.K199_splice	NM_032639	NP_116028			pleckstrin homology domain containing, family A						protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4																		---	---	---	---
CAMK2B	816	broad.mit.edu	37	7	44268438	44268439	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44268438_44268439insG	uc003tkq.2	-	19	1634_1635	c.1424_1425insC	c.(1423-1425)CCGfs	p.P475fs	CAMK2B_uc003tkp.2_Intron|CAMK2B_uc003tkx.2_Intron|CAMK2B_uc010kyd.2_Intron|CAMK2B_uc003tkr.2_Intron|CAMK2B_uc003tks.2_Intron|CAMK2B_uc003tku.2_Intron|CAMK2B_uc003tkv.2_Intron|CAMK2B_uc003tkt.2_Intron|CAMK2B_uc003tkw.2_Intron|CAMK2B_uc010kyc.2_Intron|CAMK2B_uc003tkn.2_Frame_Shift_Ins_p.P108fs	NM_001220	NP_001211	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II	475					interferon-gamma-mediated signaling pathway|synaptic transmission	cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
COPS6	10980	broad.mit.edu	37	7	99688578	99688578	+	Intron	DEL	A	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99688578delA	uc003usu.2	+							NM_006833	NP_006824			COP9 signalosome subunit 6						cullin deneddylation|interspecies interaction between organisms	cytoplasm|signalosome	protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
ACHE	43	broad.mit.edu	37	7	100490777	100490783	+	Intron	DEL	ACTAGTT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100490777_100490783delACTAGTT	uc003uxd.2	-						ACHE_uc003uxe.2_Intron|ACHE_uc003uxf.2_Intron|ACHE_uc003uxg.2_Intron|ACHE_uc003uxh.2_Intron|ACHE_uc003uxi.2_Intron	NM_000665	NP_000656			acetylcholinesterase isoform E4-E6 precursor						acetylcholine catabolic process in synaptic cleft|amyloid precursor protein metabolic process|cell adhesion|cell proliferation|choline metabolic process|DNA replication|muscle organ development|neurotransmitter biosynthetic process|osteoblast development|positive regulation of protein secretion|regulation of axonogenesis|regulation of dendrite morphogenesis|response to wounding|synapse assembly	anchored to membrane|axon|basal lamina|cell junction|cell surface|dendrite|endoplasmic reticulum lumen|extracellular space|Golgi apparatus|neuromuscular junction|nucleus|perinuclear region of cytoplasm|postsynaptic membrane|presynaptic membrane|synaptic cleft	acetylcholine binding|acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|collagen binding|laminin-1 binding|protein homodimerization activity|serine hydrolase activity			skin(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Atropine(DB00572)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium bromide(DB00944)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tacrine(DB00382)|Tubocurarine(DB01199)													---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138555817	138555817	+	Intron	DEL	C	-	-	rs35334186		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138555817delC	uc011kql.1	-						KIAA1549_uc011kqi.1_Intron|KIAA1549_uc003vuk.3_Intron|KIAA1549_uc011kqj.1_Intron|KIAA1549_uc011kqk.1_Intron	NM_020910	NP_065961			hypothetical protein LOC57670 isoform 1							integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230								O	BRAF	pilocytic astrocytoma								---	---	---	---
EZH2	2146	broad.mit.edu	37	7	148526680	148526681	+	Intron	INS	-	CC	CC			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148526680_148526681insCC	uc003wfd.1	-						EZH2_uc011kug.1_Intron|EZH2_uc003wfb.1_Intron|EZH2_uc003wfc.1_Intron|EZH2_uc011kuh.1_Intron|EZH2_uc011kui.1_Intron|EZH2_uc011kuj.1_Intron	NM_004456	NP_004447			enhancer of zeste 2 isoform a						negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding			haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1)	183	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)					Mis		DLBCL								---	---	---	---
PCM1	5108	broad.mit.edu	37	8	17882706	17882707	+	Intron	INS	-	A	A	rs146647405	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17882706_17882707insA	uc003wyi.3	+						PCM1_uc011kyh.1_Intron|PCM1_uc003wyj.3_Intron|PCM1_uc011kyi.1_Intron|PCM1_uc011kyj.1_Intron|PCM1_uc003wyk.3_Intron|PCM1_uc011kyk.1_Intron	NM_006197	NP_006188			pericentriolar material 1						centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome	centriolar satellite|cytosol|nuclear membrane|pericentriolar material	identical protein binding		PCM1/JAK2(30)	haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2)	36				Colorectal(111;0.0789)				T	RET|JAK2	papillary thyroid|CML|MPD								---	---	---	---
RBPMS	11030	broad.mit.edu	37	8	30336681	30336686	+	Intron	DEL	TCATGA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30336681_30336686delTCATGA	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc003xif.1_Intron|RBPMS_uc011lba.1_Intron|RBPMS_uc003xib.2_Intron|RBPMS_uc010lvh.1_Intron	NM_006867	NP_006858			RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)														---	---	---	---
MAK16	84549	broad.mit.edu	37	8	33353187	33353192	+	Intron	DEL	CTAAGA	-	-	rs71541850		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33353187_33353192delCTAAGA	uc003xjj.2	+						C8orf41_uc010lvu.1_Intron	NM_032509	NP_115898			MAK16 homolog							nucleolus				ovary(1)	1																		---	---	---	---
GDAP1	54332	broad.mit.edu	37	8	75275019	75275020	+	Intron	INS	-	TTTTTTT	TTTTTTT	rs6150661		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75275019_75275020insTTTTTTT	uc003yah.2	+						GDAP1_uc011lfj.1_Intron|GDAP1_uc003yai.2_Intron	NM_018972	NP_061845			ganglioside-induced differentiation-associated							cytoplasm					0	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	125132062	125132063	+	3'UTR	INS	-	TACT	TACT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125132062_125132063insTACT	uc003yqw.2	+	41					uc003yqy.1_Intron	NM_001039112	NP_001034201			fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)															---	---	---	---
PLEC	5339	broad.mit.edu	37	8	145049608	145049609	+	Intron	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145049608_145049609insC	uc003zaj.2	-						PLEC_uc003zah.2_5'Flank	NM_000445	NP_000436			plectin isoform 1c						cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9																OREG0019050	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FBXL6	26233	broad.mit.edu	37	8	145581995	145581996	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145581995_145581996insG	uc003zcb.2	-	1	137_138	c.112_113insC	c.(112-114)CACfs	p.H38fs	C8ORFK29_uc003zby.3_5'Flank|FBXL6_uc003zbz.2_5'Flank|FBXL6_uc003zca.2_Frame_Shift_Ins_p.H38fs|FBXL6_uc010mfx.2_5'UTR|GPR172A_uc003zcc.1_5'Flank|GPR172A_uc003zcd.1_5'Flank|GPR172A_uc003zce.1_5'Flank|GPR172A_uc010mfy.1_5'Flank|GPR172A_uc003zcf.1_5'Flank|GPR172A_uc011llc.1_5'Flank	NM_012162	NP_036294	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6 isoform	38	F-box.				proteolysis		ubiquitin-protein ligase activity			ovary(1)|lung(1)	2	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)															---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145781086	145781087	+	Intron	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145781086_145781087insC	uc003zdt.1	-						ARHGAP39_uc011llk.1_Intron|ARHGAP39_uc003zds.1_Intron	NM_025251	NP_079527			KIAA1688 protein						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0																		---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97730194	97730195	+	Intron	INS	-	CTC	CTC			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97730194_97730195insCTC	uc004ava.2	+						C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron|C9orf3_uc004avc.2_Intron	NM_032823	NP_116212			aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
CDC14B	8555	broad.mit.edu	37	9	99327506	99327506	+	Intron	DEL	T	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99327506delT	uc004awj.2	-						CDC14B_uc004awk.2_Intron|CDC14B_uc004awl.2_Intron|CDC14B_uc004awi.2_Intron	NM_033331	NP_201588			CDC14 homolog B isoform 2						activation of anaphase-promoting complex activity|DNA repair|G2/M transition DNA damage checkpoint	nucleolus|nucleoplasm	protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
C9orf78	51759	broad.mit.edu	37	9	132597307	132597308	+	Intron	INS	-	CCAC	CCAC			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132597307_132597308insCCAC	uc004byp.2	-						C9orf78_uc004byo.2_5'Flank|C9orf78_uc004byq.1_5'Flank|USP20_uc004bys.2_5'Flank|USP20_uc004byr.2_5'Flank|USP20_uc004byt.1_5'Flank	NM_016520	NP_057604			chromosome 9 open reading frame 78												0		Ovarian(14;0.00556)																---	---	---	---
CUBN	8029	broad.mit.edu	37	10	17109903	17109903	+	Intron	DEL	A	-	-	rs63451761		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17109903delA	uc001ioo.2	-							NM_001081	NP_001072			cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
PTF1A	256297	broad.mit.edu	37	10	23482392	23482393	+	Intron	INS	-	TT	TT	rs72117811		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23482392_23482393insTT	uc001irp.2	+							NM_178161	NP_835455			pancreas specific transcription factor, 1a						endocrine pancreas development|exocrine pancreas development|regulation of transcription, DNA-dependent|tissue development|transcription, DNA-dependent	cytoplasm|transcription factor complex				pancreas(1)|skin(1)	2																		---	---	---	---
PRTFDC1	56952	broad.mit.edu	37	10	25140566	25140571	+	Intron	DEL	AGGACT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25140566_25140571delAGGACT	uc001ise.1	-						PRTFDC1_uc010qdd.1_Intron|PRTFDC1_uc001isf.1_Intron	NM_020200	NP_064585			phosphoribosyl transferase domain containing 1						adenine salvage|central nervous system neuron development|cerebral cortex neuron differentiation|cytolysis|dendrite morphogenesis|GMP salvage|grooming behavior|hypoxanthine metabolic process|IMP salvage|lymphocyte proliferation|positive regulation of dopamine metabolic process|purine ribonucleoside salvage|response to amphetamine|striatum development	cytosol	hypoxanthine phosphoribosyltransferase activity|magnesium ion binding|nucleotide binding|protein homodimerization activity			ovary(1)	1																		---	---	---	---
ACBD5	91452	broad.mit.edu	37	10	27529251	27529252	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27529251_27529252insC	uc010qdp.1	-	2	368_369	c.177_178insG	c.(175-180)AAGAATfs	p.K59fs	ACBD5_uc010qdm.1_Frame_Shift_Ins_p.K57fs|ACBD5_uc010qdn.1_5'UTR|ACBD5_uc010qdo.1_5'UTR|ACBD5_uc001ito.2_Frame_Shift_Ins_p.K24fs|ACBD5_uc001itp.2_5'UTR|ACBD5_uc001itq.2_5'UTR|ACBD5_uc001itr.1_5'UTR	NM_145698	NP_663736	Q5T8D3	ACBD5_HUMAN	acyl-Coenzyme A binding domain containing 5	57_58	ACB.				transport	integral to membrane|peroxisomal membrane	fatty-acyl-CoA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	38368812	38368813	+	IGR	INS	-	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38368812_38368813insT								ZNF33A (14786 upstream) : ZNF37A (14462 downstream)																																			---	---	---	---
PTEN	5728	broad.mit.edu	37	10	89711879	89711880	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89711879_89711880insA	uc001kfb.2	+	7	1528_1529	c.497_498insA	c.(496-498)GTAfs	p.V166fs		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	166	Phosphatase tensin-type.				activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R55fs*1(4)|p.V166fs*17(3)|p.?(3)|p.G165fs*9(3)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.V166fs*10(1)|p.G165_K342del(1)|p.G165_*404del(1)|p.K163_V166>NKGE(1)|p.V166L(1)|p.V166I(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)			31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93695274	93695275	+	Intron	INS	-	CA	CA			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93695274_93695275insCA	uc001khr.2	+						BTAF1_uc009xua.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
BLNK	29760	broad.mit.edu	37	10	98031175	98031184	+	5'UTR	DEL	AGACACGAAT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98031175_98031184delAGACACGAAT	uc001kls.3	-	1					BLNK_uc001kme.3_5'UTR|BLNK_uc001klt.3_5'UTR|BLNK_uc009xvc.2_RNA|BLNK_uc001klu.3_5'UTR|BLNK_uc001klv.3_5'UTR|BLNK_uc001klw.3_RNA|BLNK_uc001klx.3_5'UTR|BLNK_uc001kly.3_5'UTR|BLNK_uc001klz.3_RNA|BLNK_uc001kma.3_5'UTR|BLNK_uc001kmb.3_5'UTR|BLNK_uc001kmc.3_RNA|BLNK_uc001kmd.3_5'UTR|BLNK_uc009xvd.2_RNA	NM_013314	NP_037446			B-cell linker isoform 1						B cell differentiation|humoral immune response|inflammatory response|intracellular signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(2)	2		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)														---	---	---	---
TRIM8	81603	broad.mit.edu	37	10	104416942	104416943	+	Frame_Shift_Ins	INS	-	AGTG	AGTG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104416942_104416943insAGTG	uc001kvz.2	+	6	1610_1611	c.1487_1488insAGTG	c.(1486-1488)ACAfs	p.T496fs		NM_030912	NP_112174	Q9BZR9	TRIM8_HUMAN	tripartite motif-containing 8	496						cytoplasm|PML body	ligase activity|protein homodimerization activity|zinc ion binding			ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
C10orf119	79892	broad.mit.edu	37	10	121597962	121597965	+	Intron	DEL	ATAG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121597962_121597965delATAG	uc001ler.2	-						C10orf119_uc001leq.1_Intron|C10orf119_uc001les.1_Intron	NM_024834	NP_079110			chromosome 10 open reading frame 119						cell division|DNA-dependent DNA replication|mitosis|S phase of mitotic cell cycle|sister chromatid cohesion	nucleus	chromatin binding				0		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.0044)														---	---	---	---
BTBD16	118663	broad.mit.edu	37	10	124094588	124094593	+	Intron	DEL	AATTAC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124094588_124094593delAATTAC	uc001lgc.1	+						BTBD16_uc001lgd.1_Intron	NM_144587	NP_653188			BTB (POZ) domain containing 16											skin(1)	1		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)																---	---	---	---
PRMT3	10196	broad.mit.edu	37	11	20409823	20409824	+	Intron	INS	-	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20409823_20409824insT	uc001mqb.2	+						PRMT3_uc001mqc.2_Intron|PRMT3_uc010rdn.1_Intron	NM_005788	NP_005779			protein arginine methyltransferase 3 isoform 1								zinc ion binding				0																		---	---	---	---
CELF1	10658	broad.mit.edu	37	11	47510448	47510451	+	Frame_Shift_Del	DEL	CCAT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47510448_47510451delCCAT	uc001nfl.2	-	1	126_129	c.116_119delATGG	c.(115-120)TATGGTfs	p.Y39fs	CELF1_uc001nfm.2_Frame_Shift_Del_p.Y39fs|CELF1_uc001nfn.2_Frame_Shift_Del_p.Y39fs|CELF1_uc001nfo.1_Frame_Shift_Del_p.Y66fs|CELF1_uc010rhm.1_Frame_Shift_Del_p.Y39fs|CELF1_uc001nfp.2_Frame_Shift_Del_p.Y66fs|CELF1_uc001nfq.1_Frame_Shift_Del_p.Y39fs|CELF1_uc001nfr.1_Frame_Shift_Del_p.Y39fs	NM_001025596	NP_001020767	Q92879	CELF1_HUMAN	CUG triplet repeat, RNA-binding protein 1	39_40	RRM 1.				embryo development|mRNA splice site selection|regulation of RNA splicing|RNA interference	cytoplasm|nucleus|ribonucleoprotein complex	BRE binding|mRNA binding|nucleotide binding|translation repressor activity, nucleic acid binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
TNKS1BP1	85456	broad.mit.edu	37	11	57075654	57075655	+	Intron	INS	-	TAG	TAG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57075654_57075655insTAG	uc001njr.2	-						TNKS1BP1_uc001njs.2_Intron	NM_033396	NP_203754			tankyrase 1-binding protein 1						nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)																---	---	---	---
MS4A5	64232	broad.mit.edu	37	11	60201421	60201422	+	Intron	INS	-	AAAG	AAAG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60201421_60201422insAAAG	uc001npo.2	+							NM_023945	NP_076434			membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
FTH1	2495	broad.mit.edu	37	11	61732384	61732385	+	Intron	INS	-	AACT	AACT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61732384_61732385insAACT	uc001nsu.2	-							NM_002032	NP_002023			ferritin, heavy polypeptide 1						cell proliferation|cellular membrane organization|immune response|intracellular sequestering of iron ion|iron ion transport|negative regulation of cell proliferation|post-Golgi vesicle-mediated transport	cytosol|intracellular ferritin complex	ferric iron binding|ferroxidase activity|protein binding			ovary(1)	1					Iron Dextran(DB00893)													---	---	---	---
UBXN1	51035	broad.mit.edu	37	11	62446163	62446165	+	In_Frame_Del	DEL	AGT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62446163_62446165delAGT	uc001nul.1	-	2	242_244	c.110_112delACT	c.(109-114)GACTGG>GGG	p.37_38DW>G	UBXN1_uc001nuj.2_In_Frame_Del_p.37_38DW>G|UBXN1_uc001num.1_In_Frame_Del_p.37_38DW>G|UBXN1_uc001nuk.2_In_Frame_Del_p.2_3DW>G|UBXN1_uc010rme.1_In_Frame_Del_p.37_38DW>G|UBXN1_uc010rmf.1_In_Frame_Del_p.37_38DW>G	NM_015853	NP_056937	Q04323	UBXN1_HUMAN	UBX domain protein 1	37_38	UBA.				negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process	cytoplasm	ATPase binding|K6-linked polyubiquitin binding				0																		---	---	---	---
PYGM	5837	broad.mit.edu	37	11	64514700	64514704	+	Frame_Shift_Del	DEL	CATGG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64514700_64514704delCATGG	uc001oax.3	-	18	3121_3125	c.2304_2308delCCATG	c.(2302-2310)CACCATGACfs	p.H768fs	RASGRP2_uc009ypv.2_5'Flank|RASGRP2_uc009ypw.2_5'Flank|RASGRP2_uc001oaw.1_5'Flank|PYGM_uc001oay.3_Frame_Shift_Del_p.H680fs	NM_005609	NP_005600	P11217	PYGM_HUMAN	muscle glycogen phosphorylase isoform 1	768_770					glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)													---	---	---	---
MALAT1	378938	broad.mit.edu	37	11	65268390	65268402	+	RNA	DEL	TTTTTCAGGCTTA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65268390_65268402delTTTTTCAGGCTTA	uc010roh.1	+	1		c.3158_3170delTTTTTCAGGCTTA			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0																		---	---	---	---
KAT5	10524	broad.mit.edu	37	11	65480413	65480414	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65480413_65480414insG	uc001ofi.2	+	4	419_420	c.169_170insG	c.(169-171)TGGfs	p.W57fs	KAT5_uc001ofj.2_Frame_Shift_Ins_p.W57fs|KAT5_uc001ofk.2_Frame_Shift_Ins_p.W90fs|KAT5_uc010roo.1_Frame_Shift_Ins_p.W90fs|KAT5_uc001ofl.2_Translation_Start_Site	NM_006388	NP_006379	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5 isoform 2	57					androgen receptor signaling pathway|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|double-strand break repair|interspecies interaction between organisms|negative regulation of interleukin-2 production|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nucleolus|perinuclear region of cytoplasm|Piccolo NuA4 histone acetyltransferase complex	androgen receptor binding|histone acetyltransferase activity|metal ion binding|repressing transcription factor binding|transcription coactivator activity				0																		---	---	---	---
UCP3	7352	broad.mit.edu	37	11	73712708	73712709	+	Intron	INS	-	TC	TC	rs150967250	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73712708_73712709insTC	uc001our.2	-							NM_003356	NP_003347			uncoupling protein 3 isoform UCP3L						mitochondrial transport|respiratory electron transport chain|respiratory gaseous exchange	integral to membrane|mitochondrial inner membrane	binding			pancreas(1)	1	Breast(11;2.08e-05)																	---	---	---	---
CCDC90B	60492	broad.mit.edu	37	11	82984574	82984575	+	Intron	INS	-	AG	AG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82984574_82984575insAG	uc001pae.2	-						CCDC90B_uc001pac.2_Intron|CCDC90B_uc001pad.2_Intron|CCDC90B_uc001paf.2_Intron	NM_021825	NP_068597			coiled-coil domain containing 90B precursor							integral to membrane|mitochondrion|mitochondrion					0		Acute lymphoblastic leukemia(157;0.103)																---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6679931	6679938	+	Intron	DEL	ATAGGCCA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6679931_6679938delATAGGCCA	uc001qpo.2	-						CHD4_uc001qpn.2_Intron|CHD4_uc001qpp.2_Intron|NOP2_uc001qph.1_5'Flank|NOP2_uc001qpi.1_5'Flank|NOP2_uc001qpj.1_5'Flank|NOP2_uc001qpk.1_5'Flank|NOP2_uc001qpl.1_5'Flank|NOP2_uc001qpm.1_5'Flank	NM_001273	NP_001264			chromodomain helicase DNA binding protein 4						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13724556	13724557	+	Intron	INS	-	CG	CG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13724556_13724557insCG	uc001rbt.2	-							NM_000834	NP_000825			N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	31297957	31297957	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31297957delA	uc010sjy.1	-	13	1673	c.1673delT	c.(1672-1674)TTAfs	p.L558fs						RecName: Full=Ovostatin homolog 1; Flags: Precursor;																														---	---	---	---
AGAP2	116986	broad.mit.edu	37	12	58129302	58129303	+	Intron	INS	-	C	C	rs149789274	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58129302_58129303insC	uc001spq.2	-						AGAP2_uc001spp.2_Intron|AGAP2_uc001spr.2_Intron	NM_001122772	NP_001116244			centaurin, gamma 1 isoform PIKE-L						axon guidance|negative regulation of neuron apoptosis|negative regulation of protein catabolic process|protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	mitochondrion|nucleolus	ARF GTPase activator activity|GTP binding|zinc ion binding			central_nervous_system(3)|breast(2)	5																		---	---	---	---
POC1B	282809	broad.mit.edu	37	12	89894874	89894876	+	Intron	DEL	ATA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89894874_89894876delATA	uc001tbc.2	-						POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc010sun.1_Intron	NM_172240	NP_758440			WD repeat domain 51B						cell projection organization	centriole|microtubule basal body				ovary(1)	1																		---	---	---	---
ACACB	32	broad.mit.edu	37	12	109637263	109637267	+	Frame_Shift_Del	DEL	CAGTC	-	-	rs138636393		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109637263_109637267delCAGTC	uc001tob.2	+	18	2803_2807	c.2684_2688delCAGTC	c.(2683-2688)ACAGTCfs	p.T895fs	ACACB_uc001toc.2_Frame_Shift_Del_p.T895fs	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	895_896	Biotinyl-binding.				acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
ARPC3	10094	broad.mit.edu	37	12	110878359	110878360	+	Intron	INS	-	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110878359_110878360insT	uc001tqq.2	-							NM_005719	NP_005710			actin related protein 2/3 complex subunit 3						cellular component movement|regulation of actin filament polymerization	Arp2/3 protein complex|cytoplasm	actin binding|structural constituent of cytoskeleton			ovary(1)	1																		---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124950550	124950556	+	Intron	DEL	CACCGGT	-	-	rs144484097	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124950550_124950556delCACCGGT	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
POLE	5426	broad.mit.edu	37	12	133235765	133235766	+	Intron	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133235765_133235766insA	uc001uks.1	-						POLE_uc001ukr.1_5'Flank|POLE_uc010tbq.1_Intron|POLE_uc009zyu.1_Intron	NM_006231	NP_006222			DNA-directed DNA polymerase epsilon						base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
HSPH1	10808	broad.mit.edu	37	13	31735543	31735544	+	Intron	INS	-	CGCG	CGCG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31735543_31735544insCGCG	uc001utj.2	-						HSPH1_uc001utk.2_Intron|HSPH1_uc010aaw.2_Intron|HSPH1_uc001utl.2_Intron|HSPH1_uc010tds.1_Intron|HSPH1_uc010tdt.1_Intron|HSPH1_uc010aax.1_Intron|HSPH1_uc010aay.1_Intron	NM_006644	NP_006635			heat shock 105kD						positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein	cytoplasm|extracellular region	ATP binding				0		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32831939	32831940	+	Intron	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32831939_32831940insA	uc001utx.2	+						FRY_uc010tdw.1_Intron|FRY_uc001uty.2_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	20444821	20444828	+	IGR	DEL	TCAGTTGA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20444821_20444828delTCAGTTGA								OR4K15 (99 upstream) : OR4K14 (37593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	22180369	22180372	+	Intron	DEL	CATT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22180369_22180372delCATT	uc010tme.1	+						uc001wbm.2_5'Flank					Homo sapiens mRNA for T cell receptor alpha variable 2, partial cds, clone: SEB 280.																														---	---	---	---
PSME2	5721	broad.mit.edu	37	14	24613493	24613494	+	Intron	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24613493_24613494insA	uc001wmj.2	-						FAM158A_uc001wmi.2_5'Flank|PSME2_uc001wmk.2_Intron|RNF31_uc001wml.1_5'Flank	NM_002818	NP_002809			proteasome activator subunit 2						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|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	proteasome activator complex					0				GBM - Glioblastoma multiforme(265;0.00839)														---	---	---	---
ENTPD5	957	broad.mit.edu	37	14	74443720	74443721	+	Intron	INS	-	TATT	TATT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74443720_74443721insTATT	uc010tuo.1	-						ENTPD5_uc001xpi.2_Intron	NM_001249	NP_001240			ectonucleoside triphosphate diphosphohydrolase 5						'de novo' posttranslational protein folding|ATP metabolic process|cell growth|cell proliferation|glycolysis|protein N-linked glycosylation|regulation of phosphatidylinositol 3-kinase cascade	endoplasmic reticulum lumen	guanosine-diphosphatase activity|uridine-diphosphatase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00394)														---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81259511	81259514	+	Intron	DEL	AGCA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81259511_81259514delAGCA	uc001xux.2	-						C14orf145_uc010asz.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106773997	106774002	+	Intron	DEL	CTGTCA	-	-	rs144451395		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106773997_106774002delCTGTCA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
POTEB	339010	broad.mit.edu	37	15	22077310	22077310	+	Intron	DEL	A	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22077310delA	uc010tzr.1	-						POTEB_uc010tzq.1_Intron	NM_207355	NP_997238			protein expressed in prostate, ovary, testis,												0																		---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28491744	28491745	+	Intron	INS	-	A	A	rs139539730		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28491744_28491745insA	uc001zbj.2	-							NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
INO80	54617	broad.mit.edu	37	15	41340538	41340539	+	Intron	INS	-	AG	AG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41340538_41340539insAG	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023			INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
MGA	23269	broad.mit.edu	37	15	41961590	41961590	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41961590delT	uc001zog.1	+	2	589	c.498delT	c.(496-498)GGTfs	p.G166fs	MGA_uc010ucy.1_Frame_Shift_Del_p.G166fs|MGA_uc010ucz.1_Frame_Shift_Del_p.G166fs	NM_001080541	NP_001074010	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 2	166	T-box.					MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
ELL3	80237	broad.mit.edu	37	15	44088752	44088753	+	Intron	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44088752_44088753insC	uc001zsx.1	-						C15orf63_uc001ztb.2_Intron|MIR1282_hsa-mir-1282|MI0006429_5'Flank|SERINC4_uc001ztc.1_Intron|SERINC4_uc001ztd.1_Intron|SERINC4_uc010bds.1_Intron|SERINC4_uc001zte.1_Intron	NM_025165	NP_079441			elongation factor RNA polymerase II-like 3						positive regulation of transcription elongation, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				ovary(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)														---	---	---	---
SLC30A4	7782	broad.mit.edu	37	15	45777428	45777429	+	Frame_Shift_Del	DEL	AT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45777428_45777429delAT	uc001zvj.2	-	8	1534_1535	c.1222_1223delAT	c.(1222-1224)ATTfs	p.I408fs		NM_013309	NP_037441	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter),	408	Cytoplasmic (Potential).				regulation of sequestering of zinc ion|response to toxin	endosome membrane|integral to membrane|late endosome	zinc ion transmembrane transporter activity				0		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)														---	---	---	---
CYP1A2	1544	broad.mit.edu	37	15	75041941	75041942	+	Intron	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75041941_75041942insA	uc002ayr.1	+							NM_000761	NP_000752			cytochrome P450, family 1, subfamily A,						alkaloid metabolic process|exogenous drug catabolic process|methylation|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative deethylation|oxidative demethylation|steroid catabolic process|toxin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|caffeine oxidase activity|demethylase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding			ovary(3)|breast(1)	4					Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Aciclovir(DB00787)|Alosetron(DB00969)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Anagrelide(DB00261)|Azelastine(DB00972)|Bortezomib(DB00188)|Caffeine(DB00201)|Carmustine(DB00262)|Chlordiazepoxide(DB00475)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Clomipramine(DB01242)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Desloratadine(DB00967)|Diazepam(DB00829)|Dibucaine(DB00527)|Diclofenac(DB00586)|Duloxetine(DB00476)|Enoxacin(DB00467)|Esomeprazole(DB00736)|Estradiol(DB00783)|Estrone(DB00655)|Fluorouracil(DB00544)|Flutamide(DB00499)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Grepafloxacin(DB00365)|Haloperidol(DB00502)|Hesperetin(DB01094)|Imipramine(DB00458)|Ketoconazole(DB01026)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Melatonin(DB01065)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mirtazapine(DB00370)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pefloxacin(DB00487)|Pimozide(DB01100)|Propafenone(DB01182)|Propranolol(DB00571)|Quinidine(DB00908)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifampin(DB01045)|Riluzole(DB00740)|Rofecoxib(DB00533)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Tacrine(DB00382)|Telithromycin(DB00976)|Terfenadine(DB00342)|Theophylline(DB00277)|Thiabendazole(DB00730)|Tizanidine(DB00697)|Tolbutamide(DB01124)|Verapamil(DB00661)|Warfarin(DB00682)|Zileuton(DB00744)|Zolmitriptan(DB00315)													---	---	---	---
UBE2Q2	92912	broad.mit.edu	37	15	76168391	76168392	+	Intron	INS	-	CT	CT			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76168391_76168392insCT	uc002bbg.2	+						UBE2Q2_uc002bbh.2_Intron|UBE2Q2_uc010umn.1_Intron|UBE2Q2_uc002bbi.2_Intron	NM_173469	NP_775740			ubiquitin-conjugating enzyme E2Q 2 isoform 1						protein K48-linked ubiquitination	cytoplasm	ATP binding|ubiquitin-protein ligase activity			ovary(2)	2																		---	---	---	---
NRG4	145957	broad.mit.edu	37	15	76242694	76242695	+	Intron	DEL	TC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76242694_76242695delTC	uc002bbo.2	-						NRG4_uc010bkm.1_Intron|NRG4_uc002bbn.2_Intron|NRG4_uc010bkn.2_Intron|NRG4_uc010bko.2_Intron	NM_138573	NP_612640			neuregulin 4							extracellular region|integral to membrane|plasma membrane	growth factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	80236839	80236840	+	IGR	INS	-	AG	AG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80236839_80236840insAG								C15orf37 (19643 upstream) : BCL2A1 (16393 downstream)																																			---	---	---	---
MCTP2	55784	broad.mit.edu	37	15	94883506	94883507	+	Splice_Site	INS	-	ACCG	ACCG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94883506_94883507insACCG	uc002btj.2	+	5	922	c.857_splice	c.e5+2	p.R286_splice	MCTP2_uc010urg.1_Splice_Site_p.R286_splice|MCTP2_uc002bti.2_Splice_Site_p.R286_splice|MCTP2_uc010boj.2_Splice_Site_p.R15_splice|MCTP2_uc010bok.2_Splice_Site_p.R286_splice|MCTP2_uc002btg.3_Splice_Site_p.R286_splice|MCTP2_uc002bth.3_Splice_Site_p.R286_splice	NM_018349	NP_060819			multiple C2 domains, transmembrane 2 isoform 1						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)															---	---	---	---
FAHD1	81889	broad.mit.edu	37	16	1889459	1889461	+	3'UTR	DEL	ATG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1889459_1889461delATG	uc002cnd.2	+	3					FAHD1_uc010brz.2_3'UTR|C16orf73_uc010uvq.1_Intron|C16orf73_uc010uvr.1_Intron|C16orf73_uc002cne.2_Intron	NM_001018104	NP_001018114			fumarylacetoacetate hydrolase domain containing							mitochondrion	hydrolase activity|metal ion binding|protein binding				0																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14700252	14700252	+	Intron	DEL	G	-	-	rs62037478		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14700252delG	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573			poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
SEZ6L2	26470	broad.mit.edu	37	16	29883844	29883845	+	Frame_Shift_Ins	INS	-	TCAC	TCAC			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29883844_29883845insTCAC	uc002duq.3	-	15	2731_2732	c.2491_2492insGTGA	c.(2491-2493)ACCfs	p.T831fs	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Frame_Shift_Ins_p.T774fs|SEZ6L2_uc002dur.3_Frame_Shift_Ins_p.T761fs|SEZ6L2_uc002dus.3_Frame_Shift_Ins_p.T730fs|SEZ6L2_uc010vec.1_Frame_Shift_Ins_p.T844fs|SEZ6L2_uc010ved.1_Frame_Shift_Ins_p.T800fs	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform	831	Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
PAPD5	64282	broad.mit.edu	37	16	50258847	50258848	+	Frame_Shift_Ins	INS	-	AG	AG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50258847_50258848insAG	uc010vgo.1	+	10	1544_1545	c.1509_1510insAG	c.(1507-1512)TATAGAfs	p.Y503fs	PAPD5_uc010cbi.2_RNA|PAPD5_uc002efz.2_Frame_Shift_Ins_p.Y294fs|PAPD5_uc002ega.2_Frame_Shift_Ins_p.Y294fs	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a	424_425					cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)														---	---	---	---
PER1	5187	broad.mit.edu	37	17	8045401	8045402	+	Intron	INS	-	GG	GG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8045401_8045402insGG	uc002gkd.2	-						PER1_uc010cns.2_5'UTR|PER1_uc010vuq.1_Intron	NM_002616	NP_002607			period 1						circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9								T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					---	---	---	---
WDR16	146845	broad.mit.edu	37	17	9490044	9490045	+	Frame_Shift_Ins	INS	-	AG	AG			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9490044_9490045insAG	uc002gly.2	+	3	369_370	c.300_301insAG	c.(298-303)AACAGAfs	p.N100fs	WDR16_uc002glz.2_Frame_Shift_Ins_p.N32fs|WDR16_uc010coc.2_Frame_Shift_Ins_p.N110fs	NM_145054	NP_659491	Q8N1V2	WDR16_HUMAN	WD40-repeat protein upregulated in HCC isoform	100_101	WD 1.					cytoplasm|intracellular membrane-bounded organelle	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10440404	10440410	+	Intron	DEL	AATTACA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10440404_10440410delAATTACA	uc010coi.2	-						uc002gml.1_Intron|MYH2_uc002gmp.3_Intron|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582			myosin heavy chain IIa						muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14																		---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11607900	11607900	+	Intron	DEL	T	-	-	rs11364560		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11607900delT	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363			dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
TEKT3	64518	broad.mit.edu	37	17	15215904	15215904	+	Intron	DEL	T	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15215904delT	uc002gon.2	-							NM_031898	NP_114104			tektin 3						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)														---	---	---	---
ULK2	9706	broad.mit.edu	37	17	19705364	19705365	+	Intron	INS	-	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19705364_19705365insT	uc002gwm.3	-						ULK2_uc002gwn.2_Intron	NM_001142610	NP_001136082			unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)																	---	---	---	---
NLK	51701	broad.mit.edu	37	17	26518374	26518375	+	Intron	INS	-	AA	AA			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26518374_26518375insAA	uc010crj.2	+						NLK_uc010cri.1_Intron	NM_016231	NP_057315			nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
ATAD5	79915	broad.mit.edu	37	17	29163198	29163199	+	Intron	INS	-	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29163198_29163199insT	uc002hfs.1	+						ATAD5_uc002hft.1_Intron	NM_024857	NP_079133			ATPase family, AAA domain containing 5						response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)																---	---	---	---
SYNRG	11276	broad.mit.edu	37	17	35930790	35930791	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35930790_35930791insC	uc002hoa.2	-	10	1375_1376	c.1292_1293insG	c.(1291-1293)GGTfs	p.G431fs	SYNRG_uc010wde.1_Frame_Shift_Ins_p.G353fs|SYNRG_uc010wdf.1_Frame_Shift_Ins_p.G353fs|SYNRG_uc002hoc.2_Frame_Shift_Ins_p.G352fs|SYNRG_uc002hoe.2_Frame_Shift_Ins_p.G353fs|SYNRG_uc002hod.2_Frame_Shift_Ins_p.G353fs|SYNRG_uc010wdg.1_Intron|SYNRG_uc002hob.2_Frame_Shift_Ins_p.G431fs|SYNRG_uc002hof.2_Frame_Shift_Ins_p.G143fs|SYNRG_uc010cvd.1_Frame_Shift_Ins_p.G231fs|SYNRG_uc002hog.1_Frame_Shift_Ins_p.G565fs	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1	431					endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2																		---	---	---	---
MBTD1	54799	broad.mit.edu	37	17	49284184	49284185	+	Intron	INS	-	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49284184_49284185insT	uc002itr.3	-						MBTD1_uc002itp.3_Intron|MBTD1_uc002itq.3_Intron	NM_017643	NP_060113			mbt domain containing 1						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)															---	---	---	---
ITGB4	3691	broad.mit.edu	37	17	73737234	73737234	+	Intron	DEL	C	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73737234delC	uc002jpg.2	+						ITGB4_uc002jph.2_Intron|ITGB4_uc002jpi.3_Intron|ITGB4_uc010dgp.1_Intron|ITGB4_uc002jpj.2_Intron	NM_000213	NP_000204			integrin beta 4 isoform 1 precursor						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)															---	---	---	---
SLC38A10	124565	broad.mit.edu	37	17	79263586	79263587	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79263586_79263587insC	uc002jzz.1	-	2	496_497	c.121_122insG	c.(121-123)CTGfs	p.L41fs	SLC38A10_uc002kab.2_Frame_Shift_Ins_p.L41fs	NM_001037984	NP_001033073	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10 isoform a	41	Helical; (Potential).				amino acid transport|sodium ion transport	integral to membrane				pancreas(1)|skin(1)	2	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)															---	---	---	---
DSG4	147409	broad.mit.edu	37	18	28979734	28979735	+	Intron	INS	-	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28979734_28979735insA	uc002kwq.2	+						DSG4_uc002kwr.2_Intron	NM_177986	NP_817123			desmoglein 4 isoform 2 preproprotein						homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8			OV - Ovarian serous cystadenocarcinoma(10;0.00504)															---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59920037	59920039	+	Intron	DEL	AAG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59920037_59920039delAAG	uc002lil.2	+						KIAA1468_uc002lik.1_Intron|KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905			hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)																---	---	---	---
JSRP1	126306	broad.mit.edu	37	19	2255353	2255368	+	5'Flank	DEL	GTGGGGAACAAGGTCT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2255353_2255368delGTGGGGAACAAGGTCT	uc002lvi.1	-						JSRP1_uc002lvj.1_Intron	NM_144616	NP_653217			junctional sarcoplasmic reticulum protein 1							sarcoplasmic reticulum membrane				pancreas(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
VAV1	7409	broad.mit.edu	37	19	6829798	6829799	+	Frame_Shift_Ins	INS	-	ATGC	ATGC			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6829798_6829799insATGC	uc002mfu.1	+	14	1364_1365	c.1267_1268insATGC	c.(1267-1269)TATfs	p.Y423fs	VAV1_uc010xjh.1_Frame_Shift_Ins_p.Y391fs|VAV1_uc010dva.1_Frame_Shift_Ins_p.Y423fs|VAV1_uc002mfv.1_Frame_Shift_Ins_p.Y368fs	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	423	PH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16																		---	---	---	---
ZNF562	54811	broad.mit.edu	37	19	9764669	9764669	+	Intron	DEL	T	-	-	rs145922849		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9764669delT	uc010xks.1	-						ZNF562_uc002mly.2_Intron|ZNF562_uc002mlx.2_Intron|ZNF562_uc010xkt.1_Intron|ZNF562_uc010xku.1_Intron|ZNF562_uc010xkv.1_Intron|ZNF562_uc010xkw.1_Intron	NM_001130032	NP_001123504			zinc finger protein 562 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
AKAP8	10270	broad.mit.edu	37	19	15469962	15469963	+	Intron	DEL	AT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15469962_15469963delAT	uc002nav.2	-						AKAP8_uc010dzy.2_Intron	NM_005858	NP_005849			A-kinase anchor protein 8						signal transduction	nuclear matrix				ovary(1)|breast(1)	2																		---	---	---	---
CGB	1082	broad.mit.edu	37	19	49532322	49532322	+	Intron	DEL	T	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49532322delT	uc010yad.1	-						CGB2_uc002plw.2_5'Flank|CGB2_uc010yaf.1_5'Flank	NM_033183	NP_149439			chorionic gonadotropin, beta polypeptide 8						apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)													---	---	---	---
CACNG7	59284	broad.mit.edu	37	19	54418575	54418577	+	Intron	DEL	GGA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54418575_54418577delGGA	uc002qcr.1	+						CACNG7_uc010era.1_Intron	NM_031896	NP_114102			voltage-dependent calcium channel gamma-7						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(1)	1	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)														---	---	---	---
ACSS1	84532	broad.mit.edu	37	20	24995855	24995856	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24995855_24995856insG	uc002wub.2	-	8	2135_2136	c.1257_1258insC	c.(1255-1260)CCCATCfs	p.P419fs	ACSS1_uc002wuc.2_Frame_Shift_Ins_p.P419fs|ACSS1_uc010gdc.2_Frame_Shift_Ins_p.P214fs|ACSS1_uc002wud.1_RNA|ACSS1_uc002wua.2_Frame_Shift_Ins_p.P336fs	NM_032501	NP_115890	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	419_420					acetyl-CoA biosynthetic process|ethanol oxidation|xenobiotic metabolic process	mitochondrial matrix	acetate-CoA ligase activity|AMP binding|ATP binding|protein binding			ovary(1)|skin(1)	2					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
SFRS6	6431	broad.mit.edu	37	20	42087877	42087878	+	Intron	INS	-	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42087877_42087878insC	uc010zwg.1	+						SFRS6_uc002xki.2_5'UTR|SFRS6_uc002xkk.2_Intron	NM_006275	NP_006266			arginine/serine-rich splicing factor 6						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
PTK6	5753	broad.mit.edu	37	20	62161438	62161439	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62161438_62161439delGG	uc002yfg.2	-	7	1200_1201	c.1160_1161delCC	c.(1159-1161)CCCfs	p.P387fs	PTK6_uc011aay.1_Frame_Shift_Del_p.P286fs|PTK6_uc011aaz.1_Frame_Shift_Del_p.P149fs	NM_005975	NP_005966	Q13882	PTK6_HUMAN	PTK6 protein tyrosine kinase 6	387	Protein kinase.					cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			stomach(1)|kidney(1)	2	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)															---	---	---	---
ARFRP1	10139	broad.mit.edu	37	20	62338528	62338529	+	5'UTR	INS	-	C	C	rs143886078	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62338528_62338529insC	uc002yga.2	-	1					ARFRP1_uc002ygc.2_Intron|ARFRP1_uc002ygh.3_Intron|ARFRP1_uc011abf.1_Intron|ARFRP1_uc011abg.1_Intron|ARFRP1_uc002yge.2_Intron|ARFRP1_uc002ygd.2_Intron|ARFRP1_uc002ygf.2_Intron|ARFRP1_uc002ygg.2_Intron|ARFRP1_uc011abh.1_Intron|ZGPAT_uc002ygi.2_5'Flank|ZGPAT_uc002ygj.2_5'Flank|ZGPAT_uc002ygk.2_5'Flank|ZGPAT_uc010gkk.1_5'Flank|ZGPAT_uc010gkl.1_5'Flank|ZGPAT_uc002ygm.2_5'Flank|ZGPAT_uc002ygn.3_5'Flank	NM_003224	NP_003215			ADP-ribosylation factor related protein 1						small GTPase mediated signal transduction	Golgi apparatus|membrane fraction	GTP binding|GTPase activity			breast(1)|skin(1)	2	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)															---	---	---	---
CBS	875	broad.mit.edu	37	21	44477002	44477002	+	Intron	DEL	A	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44477002delA	uc002zcu.2	-						CBS_uc002zcs.1_Intron|CBS_uc002zct.2_Intron|CBS_uc002zcw.3_Intron|CBS_uc002zcv.2_Intron|CBS_uc002zcx.2_Intron	NM_000071	NP_000062			cystathionine-beta-synthase						cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process	cytosol|nucleolus	cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding				0					L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118)													---	---	---	---
TCF20	6942	broad.mit.edu	37	22	42607130	42607161	+	Frame_Shift_Del	DEL	TTCAGGAGGACCACTCTTCAAAGACAGTATAT	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42607130_42607161delTTCAGGAGGACCACTCTTCAAAGACAGTATAT	uc003bcj.1	-	1	4285_4316	c.4151_4182delATATACTGTCTTTGAAGAGTGGTCCTCCTGAA	c.(4150-4182)GATATACTGTCTTTGAAGAGTGGTCCTCCTGAAfs	p.D1384fs	TCF20_uc003bck.1_Frame_Shift_Del_p.D1384fs|TCF20_uc003bnt.2_Frame_Shift_Del_p.D1384fs	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1	1384_1394					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5																		---	---	---	---
PARVG	64098	broad.mit.edu	37	22	44584803	44584804	+	Intron	INS	-	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44584803_44584804insG	uc011aqe.1	+						PARVG_uc003bep.2_Intron|PARVG_uc011aqf.1_Intron|PARVG_uc003beq.2_Intron|PARVG_uc003ber.2_Intron	NM_001137605	NP_001131077			parvin, gamma						cell-matrix adhesion	cytoplasm|cytoskeleton|focal adhesion	actin binding				0		Ovarian(80;0.024)|all_neural(38;0.0299)																---	---	---	---
ARHGAP6	395	broad.mit.edu	37	X	11316153	11316158	+	Intron	DEL	TGGATG	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11316153_11316158delTGGATG	uc004cup.1	-						ARHGAP6_uc004cuo.1_Intron|ARHGAP6_uc004cur.1_Intron|ARHGAP6_uc004cun.1_Intron|ARHGAP6_uc011mif.1_Intron|AMELX_uc004cus.2_Intron|AMELX_uc004cut.2_Intron|AMELX_uc004cuu.2_Intron	NM_013427	NP_038286			Rho GTPase activating protein 6 isoform 1						actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2																		---	---	---	---
PHKA2	5256	broad.mit.edu	37	X	18959435	18959436	+	Intron	INS	-	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18959435_18959436insT	uc004cyv.3	-							NM_000292	NP_000283			phosphorylase kinase, alpha 2 (liver)						glucose metabolic process|glycogen catabolic process	cytosol|phosphorylase kinase complex|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(1)|central_nervous_system(1)	2	Hepatocellular(33;0.183)																	---	---	---	---
APOO	79135	broad.mit.edu	37	X	23896839	23896846	+	Intron	DEL	CTTGCTAT	-	-	rs56274557		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23896839_23896846delCTTGCTAT	uc004dax.2	-						APOO_uc004daw.2_Intron|APOO_uc004day.3_Intron	NM_024122	NP_077027			apolipoprotein O precursor						lipid transport	high-density lipoprotein particle|integral to membrane|low-density lipoprotein particle|very-low-density lipoprotein particle					0																		---	---	---	---
IL13RA1	3597	broad.mit.edu	37	X	117907950	117907957	+	Intron	DEL	GCCCAGGC	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117907950_117907957delGCCCAGGC	uc004eqs.2	+						IL13RA1_uc004eqt.1_Intron	NM_001560	NP_001551			interleukin 13 receptor, alpha 1 precursor							interleukin-13 receptor complex	cytokine receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	122695641	122695645	+	IGR	DEL	TACTA	-	-			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122695641_122695645delTACTA								GRIA3 (70881 upstream) : MIR220A (301 downstream)																																			---	---	---	---
NPHP4	261734	broad.mit.edu	37	1	5935110	5935110	+	Silent	SNP	G	A	A	rs138025088	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5935110G>A	uc001alq.1	-	21	3134	c.2868C>T	c.(2866-2868)GCC>GCT	p.A956A		NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	956					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
NBPF3	84224	broad.mit.edu	37	1	21806573	21806573	+	Missense_Mutation	SNP	A	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21806573A>G	uc001ber.2	+	11	1588	c.1238A>G	c.(1237-1239)GAG>GGG	p.E413G	NBPF3_uc001bes.2_Missense_Mutation_p.E357G|NBPF3_uc009vqb.2_Missense_Mutation_p.E401G|NBPF3_uc010odm.1_Missense_Mutation_p.E343G	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	413	NBPF 3.					cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
KDM4A	9682	broad.mit.edu	37	1	44159762	44159762	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44159762C>T	uc001cjx.2	+	17	2639	c.2473C>T	c.(2473-2475)CGC>TGC	p.R825C	KDM4A_uc010oki.1_Intron	NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A	825					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1																		---	---	---	---
LPPR4	9890	broad.mit.edu	37	1	99762420	99762420	+	Missense_Mutation	SNP	G	A	A	rs150483469	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99762420G>A	uc001dse.2	+	3	641	c.535G>A	c.(535-537)GTT>ATT	p.V179I	LPPR4_uc010oue.1_Missense_Mutation_p.V179I	NM_014839	NP_055654	Q7Z2D5	LPPR4_HUMAN	plasticity related gene 1	179	Helical; (Potential).						phosphatidate phosphatase activity			ovary(3)	3		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)														---	---	---	---
PI4KB	5298	broad.mit.edu	37	1	151288250	151288250	+	Silent	SNP	T	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151288250T>C	uc001ext.2	-	2	1123	c.708A>G	c.(706-708)CTA>CTG	p.L236L	PI4KB_uc001exr.2_Silent_p.L248L|PI4KB_uc001exs.2_Silent_p.L236L|PI4KB_uc001exu.2_Silent_p.L236L|PI4KB_uc010pcw.1_Intron|PI4KB_uc009wmq.1_Silent_p.L248L	NM_002651	NP_002642	Q9UBF8	PI4KB_HUMAN	catalytic phosphatidylinositol 4-kinase beta	236					phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|receptor-mediated endocytosis	endosome|Golgi apparatus|mitochondrial outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum membrane	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			ovary(2)|skin(2)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
SHC1	6464	broad.mit.edu	37	1	154938525	154938525	+	Silent	SNP	A	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154938525A>G	uc001ffv.2	-	10	1502	c.1281T>C	c.(1279-1281)TAT>TAC	p.Y427Y	SHC1_uc001ffu.2_5'Flank|SHC1_uc001ffz.1_Silent_p.Y198Y|SHC1_uc001ffw.2_Silent_p.Y428Y|SHC1_uc001ffx.2_Silent_p.Y318Y|SHC1_uc001ffy.2_Silent_p.Y317Y	NM_183001	NP_892113	P29353	SHC1_HUMAN	SHC-transforming protein 1 isoform 1	427	Pro-rich.|CH1.				activation of MAPK activity|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|positive regulation of DNA replication|Ras protein signal transduction|regulation of epidermal growth factor receptor activity|regulation of growth	cytosol|mitochondrial matrix|Shc-EGFR complex	epidermal growth factor receptor binding|insulin receptor binding|insulin-like growth factor receptor binding|phospholipid binding|protein binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(1)|skin(1)	2	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)															---	---	---	---
VANGL2	57216	broad.mit.edu	37	1	160389028	160389028	+	Silent	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160389028G>A	uc001fwb.1	+	5	728	c.429G>A	c.(427-429)ACG>ACA	p.T143T	VANGL2_uc001fwc.1_Silent_p.T143T	NM_020335	NP_065068	Q9ULK5	VANG2_HUMAN	vang-like 2	143	Extracellular (Potential).				apical protein localization|heart looping|nonmotile primary cilium assembly	apical plasma membrane|integral to membrane				ovary(1)	1	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
ALDH9A1	223	broad.mit.edu	37	1	165652343	165652343	+	Missense_Mutation	SNP	C	T	T	rs118096304	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165652343C>T	uc001gdh.1	-	3	437	c.332G>A	c.(331-333)CGG>CAG	p.R111Q	ALDH9A1_uc010pky.1_Missense_Mutation_p.R17Q|ALDH9A1_uc010pkz.1_Missense_Mutation_p.R101Q|ALDH9A1_uc010pla.1_Missense_Mutation_p.R17Q	NM_000696	NP_000687	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9A1	87					carnitine biosynthetic process|cellular aldehyde metabolic process|hormone metabolic process|neurotransmitter biosynthetic process	cytosol|plasma membrane	3-chloroallyl aldehyde dehydrogenase activity|4-trimethylammoniobutyraldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aminobutyraldehyde dehydrogenase activity				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				NADH(DB00157)													---	---	---	---
HIST3H2A	92815	broad.mit.edu	37	1	228645463	228645463	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228645463G>A	uc001hsy.2	-	1	98	c.56C>T	c.(55-57)TCG>TTG	p.S19L	HIST3H2BB_uc001hsz.2_5'Flank	NM_033445	NP_254280	Q7L7L0	H2A3_HUMAN	histone cluster 3, H2a	19					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)	1		Prostate(94;0.183)																---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236894617	236894617	+	Intron	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236894617G>A	uc001hyf.2	+						ACTN2_uc001hyg.2_Intron|ACTN2_uc009xgi.1_Intron|ACTN2_uc010pxu.1_Intron	NM_001103	NP_001094			actinin, alpha 2						focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)															---	---	---	---
AHCTF1	25909	broad.mit.edu	37	1	247079612	247079612	+	Missense_Mutation	SNP	T	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247079612T>A	uc001ibu.1	-	2	214	c.207A>T	c.(205-207)AGA>AGT	p.R69S	AHCTF1_uc001ibv.1_Missense_Mutation_p.R78S	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	69	Necessary for cytoplasmic localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)															---	---	---	---
MDH1	4190	broad.mit.edu	37	2	63824528	63824528	+	Intron	SNP	C	A	A	rs78810459	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63824528C>A	uc002scj.1	+						MDH1_uc010ypv.1_Intron|MDH1_uc010ypw.1_Intron	NM_005917	NP_005908			cytosolic malate dehydrogenase						gluconeogenesis|tricarboxylic acid cycle	centrosome|cytosol	L-malate dehydrogenase activity|malic enzyme activity			kidney(2)	2					NADH(DB00157)													---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109087107	109087107	+	Missense_Mutation	SNP	A	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109087107A>G	uc002tec.2	+	6	1476	c.1322A>G	c.(1321-1323)AAT>AGT	p.N441S	GCC2_uc002ted.2_Missense_Mutation_p.N340S	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	441	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1																		---	---	---	---
ITGA6	3655	broad.mit.edu	37	2	173337570	173337570	+	Intron	SNP	C	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173337570C>T	uc002uhp.1	+						ITGA6_uc010fqk.1_Intron|ITGA6_uc010zdy.1_Missense_Mutation_p.R124W|ITGA6_uc002uho.1_Intron|ITGA6_uc010fql.2_RNA|ITGA6_uc010fqm.1_5'Flank	NM_001079818	NP_001073286			integrin alpha chain, alpha 6 isoform a						blood coagulation|cell adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|positive regulation of apoptosis|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter	integrin complex	protein binding|receptor activity			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0979)															---	---	---	---
COQ10B	80219	broad.mit.edu	37	2	198324810	198324810	+	Intron	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198324810G>A	uc002uuh.1	+						COQ10B_uc010fsl.1_Intron	NM_025147	NP_079423			coenzyme Q10 homolog B precursor							mitochondrial inner membrane					0			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62535796	62535796	+	Intron	SNP	A	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62535796A>G	uc003dll.2	-						CADPS_uc003dlk.1_Intron|CADPS_uc003dlm.2_Intron|CADPS_uc003dln.2_Intron	NM_003716	NP_003707			Ca2+-dependent secretion activator isoform 1						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)														---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113655147	113655147	+	Missense_Mutation	SNP	T	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113655147T>G	uc003eaq.3	+	14	1567	c.1491T>G	c.(1489-1491)AAT>AAG	p.N497K	GRAMD1C_uc011bil.1_RNA|GRAMD1C_uc003ear.2_Missense_Mutation_p.N330K|GRAMD1C_uc003eas.2_Missense_Mutation_p.N292K|GRAMD1C_uc003eat.2_Missense_Mutation_p.N156K	NM_017577	NP_060047	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	497						integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
AGXT2	64902	broad.mit.edu	37	5	35033644	35033644	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35033644C>A	uc003jjf.2	-	6	675	c.596G>T	c.(595-597)GGA>GTA	p.G199V	AGXT2_uc011com.1_Missense_Mutation_p.G199V|AGXT2_uc011con.1_Missense_Mutation_p.G107V	NM_031900	NP_114106	Q9BYV1	AGT2_HUMAN	alanine-glyoxylate aminotransferase 2 precursor	199					glyoxylate metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity|alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(3)|skin(1)	4	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)													---	---	---	---
SLC38A9	153129	broad.mit.edu	37	5	54941640	54941640	+	Missense_Mutation	SNP	T	C	C	rs145248317		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54941640T>C	uc003jqf.2	-	12	1345	c.1144A>G	c.(1144-1146)AAC>GAC	p.N382D	SLC38A9_uc003jqd.2_Missense_Mutation_p.N319D|SLC38A9_uc010ivx.2_Missense_Mutation_p.N319D|SLC38A9_uc003jqe.2_RNA|SLC38A9_uc010ivy.2_Missense_Mutation_p.N253D	NM_173514	NP_775785	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	382					amino acid transport|sodium ion transport	integral to membrane					0		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)																---	---	---	---
PCDHGC5	56097	broad.mit.edu	37	5	140869709	140869709	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140869709C>A	uc003lla.1	+	1	902	c.902C>A	c.(901-903)GCA>GAA	p.A301E	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lkv.1_Intron|PCDHGC3_uc003lkw.1_Intron|PCDHGC4_uc003lky.1_Intron|PCDHGC5_uc011dbc.1_Missense_Mutation_p.A301E	NM_018929	NP_061752	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5 isoform 1	301	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150922741	150922741	+	Silent	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150922741C>A	uc003lue.3	-	9	7960	c.7947G>T	c.(7945-7947)CTG>CTT	p.L2649L	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	2649	Cadherin 23.|Extracellular (Potential).				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
MGAT1	4245	broad.mit.edu	37	5	180218745	180218745	+	Silent	SNP	C	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180218745C>T	uc003mmg.3	-	2	1722	c.1227G>A	c.(1225-1227)TCG>TCA	p.S409S	MGAT1_uc010jlf.2_Silent_p.S409S|MGAT1_uc010jlg.2_Silent_p.S409S|MGAT1_uc003mmh.3_Silent_p.S409S|MGAT1_uc010jlh.2_Silent_p.S409S|MGAT1_uc003mmi.3_Silent_p.S409S	NM_002406	NP_002397	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein	409	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(1)	1	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38877482	38877482	+	Missense_Mutation	SNP	T	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38877482T>A	uc003ooe.1	+	63	9651	c.9051T>A	c.(9049-9051)CAT>CAA	p.H3017Q	uc003oof.1_Intron	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
BAI3	577	broad.mit.edu	37	6	69349199	69349199	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69349199C>T	uc003pev.3	+	3	1080	c.632C>T	c.(631-633)TCG>TTG	p.S211L	BAI3_uc010kak.2_Missense_Mutation_p.S211L	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	211	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)																---	---	---	---
USP42	84132	broad.mit.edu	37	7	6189487	6189487	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6189487C>A	uc011jwo.1	+	13	1783	c.1660C>A	c.(1660-1662)CCC>ACC	p.P554T	USP42_uc010kth.1_Missense_Mutation_p.P487T|USP42_uc011jwp.1_Missense_Mutation_p.P554T|USP42_uc011jwq.1_Missense_Mutation_p.P361T|USP42_uc011jwr.1_Missense_Mutation_p.P399T	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	554					cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)														---	---	---	---
HOXA3	3200	broad.mit.edu	37	7	27147975	27147975	+	Silent	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27147975G>A	uc011jzl.1	-	3	1091	c.891C>T	c.(889-891)TTC>TTT	p.F297F	HOXA3_uc011jzk.1_Silent_p.F139F|HOXA3_uc003syk.2_Silent_p.F297F	NM_030661	NP_109377	O43365	HXA3_HUMAN	homeobox A3 isoform a	297					angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)	2																		---	---	---	---
ABCB1	5243	broad.mit.edu	37	7	87144608	87144608	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87144608C>A	uc003uiz.1	-	26	3639	c.3221G>T	c.(3220-3222)TGT>TTT	p.C1074F	ABCB1_uc011khc.1_Missense_Mutation_p.C1010F	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	1074	Cytoplasmic (Potential).|ABC transporter 2.|ATP 2 (By similarity).				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	142124567	142124567	+	Intron	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142124567G>A	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
ZNF395	55893	broad.mit.edu	37	8	28209312	28209312	+	Missense_Mutation	SNP	G	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28209312G>C	uc003xgq.2	-	7	1021	c.933C>G	c.(931-933)GAC>GAG	p.D311E	ZNF395_uc003xgt.2_Missense_Mutation_p.D311E|ZNF395_uc003xgr.2_Missense_Mutation_p.D311E|ZNF395_uc003xgs.2_Missense_Mutation_p.D311E	NM_018660	NP_061130	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	311					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)														---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110457585	110457585	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110457585C>A	uc003yne.2	+	38	5591	c.5487C>A	c.(5485-5487)AGC>AGA	p.S1829R		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	1829	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)												HNSCC(38;0.096)			---	---	---	---
WDR67	93594	broad.mit.edu	37	8	124094943	124094943	+	Missense_Mutation	SNP	T	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124094943T>G	uc003ypp.1	+	3	316	c.226T>G	c.(226-228)TTC>GTC	p.F76V	WDR67_uc011lig.1_Missense_Mutation_p.F76V|WDR67_uc011lih.1_Intron|WDR67_uc003ypq.1_Intron|WDR67_uc003ypo.1_Missense_Mutation_p.F76V	NM_145647	NP_663622	Q96DN5	WDR67_HUMAN	WD repeat domain 67 isoform 1	76	WD 1.					centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
OC90	729330	broad.mit.edu	37	8	133045361	133045361	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133045361C>A	uc003ytg.2	-	10	784	c.784G>T	c.(784-786)GTC>TTC	p.V262F	OC90_uc011lix.1_Missense_Mutation_p.V262F	NM_001080399	NP_001073868	Q02509	OC90_HUMAN	otoconin 90	278					lipid catabolic process|phospholipid metabolic process		calcium ion binding|phospholipase A2 activity			ovary(2)|skin(1)	3	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)															---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18721657	18721657	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18721657C>A	uc003zne.3	+	15	2127	c.2000C>A	c.(1999-2001)CCA>CAA	p.P667Q		NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	667	TSP type-1 6.					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
KIAA1529	57653	broad.mit.edu	37	9	100053767	100053767	+	Silent	SNP	G	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100053767G>C	uc011lut.1	+	10	857	c.84G>C	c.(82-84)GGG>GGC	p.G28G	KIAA1529_uc011lur.1_RNA|KIAA1529_uc004axe.1_Silent_p.G28G|KIAA1529_uc011lus.1_5'UTR|KIAA1529_uc011luu.1_Missense_Mutation_p.G173A|KIAA1529_uc010msm.1_RNA	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)|skin(1)	7		Acute lymphoblastic leukemia(62;0.154)																---	---	---	---
NR5A1	2516	broad.mit.edu	37	9	127262899	127262899	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127262899G>A	uc004boo.1	-	4	527	c.340C>T	c.(340-342)CGG>TGG	p.R114W		NM_004959	NP_004950	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	114					cell-cell signaling|male gonad development|positive regulation of transcription from RNA polymerase II promoter|primary sex determination|regulation of steroid biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|phospholipid binding|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0																		---	---	---	---
GLT6D1	360203	broad.mit.edu	37	9	138523289	138523289	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138523289C>A	uc010nbd.1	-	3	361	c.107G>T	c.(106-108)TGG>TTG	p.W36L		NM_182974	NP_892019	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	36	Lumenal (Potential).				carbohydrate metabolic process	integral to membrane	transferase activity, transferring hexosyl groups			ovary(1)	1		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)														---	---	---	---
BMS1	9790	broad.mit.edu	37	10	43294033	43294033	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43294033G>A	uc001jaj.2	+	12	2565	c.2207G>A	c.(2206-2208)AGA>AAA	p.R736K		NM_014753	NP_055568	Q14692	BMS1_HUMAN	BMS1-like, ribosome assembly protein	736					ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
IFIT3	3437	broad.mit.edu	37	10	91099105	91099105	+	Missense_Mutation	SNP	A	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91099105A>C	uc001kgf.2	+	2	922	c.693A>C	c.(691-693)GAA>GAC	p.E231D	LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|uc001kgd.2_Intron|IFIT3_uc001kgg.2_Missense_Mutation_p.E231D	NM_001549	NP_001540	O14879	IFIT3_HUMAN	interferon-induced protein with	231	TPR 5.				type I interferon-mediated signaling pathway		protein binding			central_nervous_system(1)	1																		---	---	---	---
ZNF195	7748	broad.mit.edu	37	11	3381028	3381028	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3381028C>A	uc001lxt.2	-	6	1388	c.1210G>T	c.(1210-1212)GAG>TAG	p.E404*	uc001lxr.2_5'Flank|ZNF195_uc001lxv.2_Nonsense_Mutation_p.E381*|ZNF195_uc001lxs.2_Nonsense_Mutation_p.E332*|ZNF195_uc010qxr.1_Nonsense_Mutation_p.E385*|ZNF195_uc009ydz.2_Nonsense_Mutation_p.E359*|ZNF195_uc001lxu.2_Nonsense_Mutation_p.E336*	NM_001130520	NP_001123992	O14628	ZN195_HUMAN	zinc finger protein 195 isoform 1	404				Missing (in Ref. 2; BAD18466).	regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)														---	---	---	---
HBG2	3048	broad.mit.edu	37	11	5274499	5274499	+	Intron	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5274499C>A	uc001mai.1	-						HBG2_uc001maj.1_3'UTR	NM_000559	NP_000550			A-gamma globin						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
C11orf49	79096	broad.mit.edu	37	11	47183053	47183053	+	Missense_Mutation	SNP	C	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47183053C>G	uc001ndp.2	+	9	966	c.860C>G	c.(859-861)GCC>GGC	p.A287G	C11orf49_uc001nds.2_Intron|C11orf49_uc001ndq.2_3'UTR|C11orf49_uc001ndr.2_Missense_Mutation_p.A293G|C11orf49_uc010rgx.1_Missense_Mutation_p.A190G|C11orf49_uc010rgy.1_Missense_Mutation_p.A278G|C11orf49_uc010rgz.1_Missense_Mutation_p.A203G	NM_024113	NP_077018	Q9H6J7	CK049_HUMAN	hypothetical protein LOC79096 isoform 3	287											0																OREG0020950	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C11orf49	79096	broad.mit.edu	37	11	47183076	47183076	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47183076C>T	uc001ndp.2	+	9	989	c.883C>T	c.(883-885)CCT>TCT	p.P295S	C11orf49_uc001nds.2_Intron|C11orf49_uc001ndq.2_3'UTR|C11orf49_uc001ndr.2_Missense_Mutation_p.P301S|C11orf49_uc010rgx.1_Missense_Mutation_p.P198S|C11orf49_uc010rgy.1_Missense_Mutation_p.P286S|C11orf49_uc010rgz.1_Missense_Mutation_p.P211S	NM_024113	NP_077018	Q9H6J7	CK049_HUMAN	hypothetical protein LOC79096 isoform 3	295											0																OREG0020950	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
OR4A5	81318	broad.mit.edu	37	11	51412276	51412276	+	Silent	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51412276G>A	uc001nhi.1	-	1	120	c.120C>T	c.(118-120)AAC>AAT	p.N40N		NM_001005272	NP_001005272	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A,	40	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(304;0.236)																---	---	---	---
OR5M3	219482	broad.mit.edu	37	11	56237947	56237947	+	Missense_Mutation	SNP	C	A	A	rs150255727	byFrequency;by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56237947C>A	uc010rjk.1	-	1	27	c.27G>T	c.(25-27)GAG>GAT	p.E9D		NM_001004742	NP_001004742	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M,	9	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)																	---	---	---	---
TULP3	7289	broad.mit.edu	37	12	3039437	3039437	+	Missense_Mutation	SNP	G	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3039437G>C	uc010seh.1	+	5	499	c.418G>C	c.(418-420)GAT>CAT	p.D140H	TULP3_uc010sef.1_RNA|TULP3_uc009zec.1_5'UTR|TULP3_uc010seg.1_RNA|TULP3_uc001qlj.2_Missense_Mutation_p.D140H|TULP3_uc010sei.1_Intron	NM_003324	NP_003315	O75386	TULP3_HUMAN	tubby like protein 3 isoform 1	140					G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
TAS2R9	50835	broad.mit.edu	37	12	10962472	10962472	+	Missense_Mutation	SNP	A	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10962472A>G	uc001qyx.2	-	1	296	c.203T>C	c.(202-204)TTT>TCT	p.F68S	TAS2R8_uc010shh.1_5'Flank	NM_023917	NP_076406	Q9NYW1	TA2R9_HUMAN	taste receptor, type 2, member 9	68	Helical; Name=2; (Potential).				sensory perception of taste	integral to membrane	taste receptor activity			skin(1)	1																		---	---	---	---
KIF5A	3798	broad.mit.edu	37	12	57970599	57970599	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57970599C>A	uc001sor.1	+	20	2462	c.2254C>A	c.(2254-2256)CTG>ATG	p.L752M	KIF5A_uc010srr.1_Missense_Mutation_p.L663M	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A	752					blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3																		---	---	---	---
STK24	8428	broad.mit.edu	37	13	99174029	99174029	+	Silent	SNP	C	T	T	rs140679513	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99174029C>T	uc001vnm.1	-	1	313	c.78G>A	c.(76-78)ACG>ACA	p.T26T	STK24_uc001vnn.1_Intron|STK24_uc010tim.1_Intron	NM_003576	NP_003567	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24 isoform a	26					cellular component disassembly involved in apoptosis|signal transduction	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)															---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92625468	92625468	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92625468G>A	uc001yah.1	+	14	2200	c.1963G>A	c.(1963-1965)GAT>AAT	p.D655N		NM_017437	NP_059133	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2	655					histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)														---	---	---	---
C14orf68	283600	broad.mit.edu	37	14	100793646	100793646	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100793646C>T	uc001yhc.2	+	4	339	c.266C>T	c.(265-267)CCT>CTT	p.P89L	C14orf68_uc001yhd.2_5'UTR	NM_207117	NP_997000	Q6Q0C1	S2547_HUMAN	chromosome 14 open reading frame 68	89					transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0		Melanoma(154;0.152)																---	---	---	---
C14orf73	91828	broad.mit.edu	37	14	103574722	103574722	+	Intron	SNP	C	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103574722C>G	uc001ymk.2	+							NM_001077594	NP_001071062			hypothetical protein LOC91828												0		Melanoma(154;0.155)	Epithelial(46;0.221)															---	---	---	---
C15orf2	23742	broad.mit.edu	37	15	24922006	24922006	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24922006C>T	uc001ywo.2	+	1	1466	c.992C>T	c.(991-993)TCG>TTG	p.S331L		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	331	Pro-rich.				cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	8		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)														---	---	---	---
THBS1	7057	broad.mit.edu	37	15	39885837	39885837	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39885837G>A	uc001zkh.2	+	19	3414	c.3235G>A	c.(3235-3237)GCC>ACC	p.A1079T	THBS1_uc010bbi.2_Missense_Mutation_p.A551T	NM_003246	NP_003237	P07996	TSP1_HUMAN	thrombospondin 1 precursor	1079	TSP C-terminal.				activation of MAPK activity|anti-apoptosis|apoptosis|cell adhesion|cell cycle arrest|cell migration|cellular response to heat|chronic inflammatory response|engulfment of apoptotic cell|immune response|induction of apoptosis|negative regulation of angiogenesis|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|negative regulation of blood vessel endothelial cell migration|negative regulation of caspase activity|negative regulation of cGMP-mediated signaling|negative regulation of dendritic cell antigen processing and presentation|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of focal adhesion assembly|negative regulation of interleukin-12 production|negative regulation of nitric oxide mediated signal transduction|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of plasminogen activation|peptide cross-linking|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of fibroblast migration|positive regulation of macrophage activation|positive regulation of macrophage chemotaxis|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transforming growth factor-beta1 production|positive regulation of translation|positive regulation of tumor necrosis factor biosynthetic process|response to calcium ion|response to drug|response to glucose stimulus|response to hypoxia|response to magnesium ion|response to progesterone stimulus|sprouting angiogenesis	external side of plasma membrane|extracellular matrix|fibrinogen complex|platelet alpha granule lumen	calcium ion binding|collagen V binding|eukaryotic cell surface binding|fibrinogen binding|fibroblast growth factor 2 binding|fibronectin binding|heparin binding|identical protein binding|integrin binding|laminin binding|low-density lipoprotein particle binding|phosphatidylserine binding|proteoglycan binding|structural molecule activity|transforming growth factor beta binding			ovary(3)|central_nervous_system(3)	6		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)	Becaplermin(DB00102)													---	---	---	---
HMG20A	10363	broad.mit.edu	37	15	77769900	77769900	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77769900G>A	uc002bcr.2	+	8	820	c.619G>A	c.(619-621)GAA>AAA	p.E207K	HMG20A_uc002bcs.2_Missense_Mutation_p.E207K	NM_018200	NP_060670	Q9NP66	HM20A_HUMAN	high-mobility group 20A	207					chromatin modification	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
VPS33B	26276	broad.mit.edu	37	15	91551141	91551141	+	Silent	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91551141G>A	uc002bqp.1	-	7	811	c.457C>T	c.(457-459)CTG>TTG	p.L153L	VPS33B_uc002bqq.1_Silent_p.L62L|VPS33B_uc010uqu.1_Silent_p.L126L	NM_018668	NP_061138	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33B (yeast homolog))	153					cellular membrane fusion|lysosome localization|melanosome localization|platelet alpha granule organization|protein transport|vesicle docking involved in exocytosis	late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm|platelet alpha granule	protein binding			ovary(2)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)																	---	---	---	---
PKD1	5310	broad.mit.edu	37	16	2156661	2156661	+	Silent	SNP	C	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2156661C>T	uc002cos.1	-	18	7436	c.7227G>A	c.(7225-7227)ACG>ACA	p.T2409T	PKD1_uc002cot.1_Silent_p.T2409T|PKD1_uc010bse.1_5'Flank	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	2409	Extracellular (Potential).|REJ.				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3																		---	---	---	---
USP31	57478	broad.mit.edu	37	16	23116813	23116813	+	Silent	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23116813G>A	uc002dll.2	-	5	1038	c.1038C>T	c.(1036-1038)GTC>GTT	p.V346V		NM_020718	NP_065769	Q70CQ4	UBP31_HUMAN	ubiquitin specific peptidase 31	346					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(3)|lung(3)|breast(2)|pancreas(1)|skin(1)	10				GBM - Glioblastoma multiforme(48;0.0187)														---	---	---	---
ERBB2	2064	broad.mit.edu	37	17	37868618	37868618	+	Silent	SNP	A	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37868618A>G	uc002hso.2	+	9	1303	c.1065A>G	c.(1063-1065)GCA>GCG	p.A355A	ERBB2_uc002hsm.2_Silent_p.A325A|ERBB2_uc010cwa.2_Silent_p.A340A|ERBB2_uc002hsp.2_Silent_p.A158A|ERBB2_uc010cwb.2_Silent_p.A355A|ERBB2_uc010wek.1_Silent_p.A79A|ERBB2_uc002hsl.2_Silent_p.A325A	NM_004448	NP_004439	P04626	ERBB2_HUMAN	erbB-2 isoform a	355	Extracellular (Potential).				cell proliferation|heart development|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell adhesion|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|protein autophosphorylation|regulation of angiogenesis|regulation of microtubule-based process|regulation of transcription, DNA-dependent|transcription, DNA-dependent|wound healing	integral to membrane|nucleus|perinuclear region of cytoplasm|receptor complex	ATP binding|DNA binding|epidermal growth factor receptor activity|ErbB-3 class receptor binding|identical protein binding|protein C-terminus binding|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(73)|central_nervous_system(16)|ovary(16)|stomach(14)|breast(9)|upper_aerodigestive_tract(5)|large_intestine(3)|liver(3)|endometrium(2)|skin(1)|pancreas(1)	143	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	Lapatinib(DB01259)|Letrozole(DB01006)|Trastuzumab(DB00072)		1	A|Mis|O		breast|ovarian|other tumour types|NSCLC|gastric					TCGA GBM(5;<1E-08)			---	---	---	---
TOP2A	7153	broad.mit.edu	37	17	38560458	38560458	+	Missense_Mutation	SNP	C	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38560458C>A	uc002huq.2	-	19	2355	c.2229G>T	c.(2227-2229)AAG>AAT	p.K743N		NM_001067	NP_001058	P11388	TOP2A_HUMAN	DNA topoisomerase II, alpha isozyme	743					apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding			ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)													---	---	---	---
CDK5RAP3	80279	broad.mit.edu	37	17	46052926	46052926	+	Missense_Mutation	SNP	C	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46052926C>G	uc002imr.2	+	7	644	c.560C>G	c.(559-561)CCG>CGG	p.P187R	CDK5RAP3_uc010wlc.1_Missense_Mutation_p.P207R|CDK5RAP3_uc002imq.1_5'UTR|CDK5RAP3_uc002imu.2_Missense_Mutation_p.P31R|CDK5RAP3_uc002ims.2_Missense_Mutation_p.P100R|CDK5RAP3_uc002imv.2_Missense_Mutation_p.P31R|CDK5RAP3_uc002imw.2_Missense_Mutation_p.P31R|CDK5RAP3_uc002imx.2_5'UTR	NM_176096	NP_788276	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	187					brain development|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation		neuronal Cdc2-like kinase binding				0																		---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61498904	61498904	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61498904G>A	uc002jal.3	+	25	5584	c.5561G>A	c.(5560-5562)CGG>CAG	p.R1854Q	TANC2_uc010wpe.1_3'UTR|TANC2_uc002jao.3_Missense_Mutation_p.R965Q	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1854							binding			ovary(2)	2																		---	---	---	---
TMEM104	54868	broad.mit.edu	37	17	72785005	72785005	+	Missense_Mutation	SNP	T	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72785005T>G	uc002jls.3	+	4	407	c.245T>G	c.(244-246)CTC>CGC	p.L82R	TMEM104_uc010wrf.1_Missense_Mutation_p.L82R|TMEM104_uc010wrg.1_Missense_Mutation_p.L95R|TMEM104_uc010dfx.2_Missense_Mutation_p.L82R	NM_017728	NP_060198	Q8NE00	TM104_HUMAN	transmembrane protein 104	82	Cytoplasmic (Potential).					integral to membrane					0	all_lung(278;0.23)																	---	---	---	---
CASKIN2	57513	broad.mit.edu	37	17	73498181	73498181	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73498181G>A	uc002joc.2	-	18	3524	c.2974C>T	c.(2974-2976)CGG>TGG	p.R992W	CASKIN2_uc010wsc.1_Missense_Mutation_p.R910W	NM_020753	NP_065804	Q8WXE0	CSKI2_HUMAN	cask-interacting protein 2 isoform a	992	Pro-rich.					cytoplasm				pancreas(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
QRICH2	84074	broad.mit.edu	37	17	74288853	74288853	+	Missense_Mutation	SNP	T	G	G	rs78570050	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74288853T>G	uc002jrd.1	-	4	1637	c.1457A>C	c.(1456-1458)CAA>CCA	p.Q486P	QRICH2_uc010wsz.1_Missense_Mutation_p.Q412P|QRICH2_uc010dgw.1_Intron	NM_032134	NP_115510	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	486	Gln-rich.						protein binding			ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
CYGB	114757	broad.mit.edu	37	17	74533626	74533626	+	5'UTR	SNP	A	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74533626A>T	uc002jru.1	-	1					CYGB_uc002jrv.1_Intron|PRCD_uc002jrw.1_Intron|PRCD_uc002jrx.2_5'Flank|PRCD_uc002jry.1_5'Flank	NM_134268	NP_599030			cytoglobin						response to oxidative stress	cytoplasm	heme binding|oxygen binding|oxygen transporter activity|peroxidase activity				0																		---	---	---	---
LONP1	9361	broad.mit.edu	37	19	5692159	5692159	+	Missense_Mutation	SNP	C	T	T	rs139476430		TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5692159C>T	uc002mcx.2	-	18	2797	c.2764G>A	c.(2764-2766)GAC>AAC	p.D922N	LONP1_uc002mcy.2_Missense_Mutation_p.D858N|LONP1_uc010duh.2_Missense_Mutation_p.D663N|LONP1_uc010dui.2_Missense_Mutation_p.D906N|LONP1_uc002mcz.2_Missense_Mutation_p.D726N	NM_004793	NP_004784	P36776	LONM_HUMAN	mitochondrial lon peptidase 1 precursor	922					cellular chaperone-mediated protein complex assembly|cellular response to oxidative stress|misfolded or incompletely synthesized protein catabolic process|mitochondrial DNA metabolic process|oxidation-dependent protein catabolic process|protein homooligomerization|response to hypoxia	mitochondrial nucleoid	ADP binding|ATP binding|ATP-dependent peptidase activity|DNA polymerase binding|G-quadruplex DNA binding|mitochondrial heavy strand promoter anti-sense binding|mitochondrial light strand promoter anti-sense binding|sequence-specific DNA binding|serine-type endopeptidase activity|single-stranded DNA binding|single-stranded RNA binding				0																		---	---	---	---
RANBP3	8498	broad.mit.edu	37	19	5925727	5925727	+	Missense_Mutation	SNP	C	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5925727C>T	uc002mdw.2	-	10	1062	c.835G>A	c.(835-837)GAA>AAA	p.E279K	RANBP3_uc002mdv.2_5'UTR|RANBP3_uc002mdx.2_Missense_Mutation_p.E274K|RANBP3_uc002mdy.2_Missense_Mutation_p.E211K|RANBP3_uc002mdz.2_Missense_Mutation_p.E206K|RANBP3_uc010duq.2_Missense_Mutation_p.E184K|RANBP3_uc002mea.2_Missense_Mutation_p.E146K|RANBP3_uc010xix.1_Missense_Mutation_p.E151K	NM_007322	NP_015561	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3 isoform RANBP3-d	279					intracellular transport|protein transport	cytoplasm|nucleus	Ran GTPase binding			breast(1)	1																		---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	31039824	31039824	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31039824G>A	uc002nsu.1	+	4	3436	c.3298G>A	c.(3298-3300)GTG>ATG	p.V1100M	ZNF536_uc010edd.1_Missense_Mutation_p.V1100M	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	1100					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)																	---	---	---	---
LIPE	3991	broad.mit.edu	37	19	42906851	42906851	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42906851G>A	uc002otr.2	-	9	3152	c.2875C>T	c.(2875-2877)CTC>TTC	p.L959F	uc010eif.1_Intron	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	959					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43585245	43585245	+	Missense_Mutation	SNP	C	G	G			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43585245C>G	uc002ovi.2	-	2	311	c.218G>C	c.(217-219)AGG>ACG	p.R73T	PSG6_uc010xwk.1_Intron|PSG2_uc002ovr.2_Missense_Mutation_p.R73T|PSG2_uc002ovq.3_Missense_Mutation_p.R73T|PSG2_uc010eiq.1_Missense_Mutation_p.R73T|PSG2_uc002ovs.3_Missense_Mutation_p.R73T|PSG2_uc002ovt.3_Missense_Mutation_p.R73T			Q00889	PSG6_HUMAN	SubName: Full=Putative uncharacterized protein PSG6;	73	Ig-like V-type.				female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
PSG4	5672	broad.mit.edu	37	19	43708100	43708100	+	Missense_Mutation	SNP	T	A	A	rs79787751	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43708100T>A	uc002ovy.2	-	2	470	c.368A>T	c.(367-369)CAC>CTC	p.H123L	PSG4_uc002owa.2_RNA|PSG4_uc002owb.2_Missense_Mutation_p.H123L|PSG4_uc002ovz.2_Missense_Mutation_p.H123L	NM_002780	NP_002771	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4 isoform	123	Ig-like V-type.				defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47266096	47266096	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47266096G>A	uc002xtw.1	-	25	3070	c.3047C>T	c.(3046-3048)TCG>TTG	p.S1016L	PREX1_uc002xtv.1_Missense_Mutation_p.S313L	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	1016					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
NCAM2	4685	broad.mit.edu	37	21	22849797	22849797	+	Intron	SNP	G	T	T			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22849797G>T	uc002yld.1	+						NCAM2_uc011acb.1_Intron	NM_004540	NP_004531			neural cell adhesion molecule 2 precursor						neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)														---	---	---	---
ZNF645	158506	broad.mit.edu	37	X	22291218	22291218	+	Missense_Mutation	SNP	G	A	A			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22291218G>A	uc004dai.1	+	1	159	c.110G>A	c.(109-111)CGT>CAT	p.R37H		NM_152577	NP_689790	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	37						intracellular	zinc ion binding			lung(1)|pancreas(1)	2																		---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53611157	53611157	+	Missense_Mutation	SNP	T	C	C			TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53611157T>C	uc004dsp.2	-	41	5552	c.5150A>G	c.(5149-5151)AAT>AGT	p.N1717S	HUWE1_uc004dsn.2_Missense_Mutation_p.N542S	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	1717					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17																		---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107457351	107457351	+	Silent	SNP	G	A	A	rs2295920	by1000genomes	TCGA-CG-5725-01	TCGA-CG-5725-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107457351G>A	uc004enw.3	-	6	538	c.435C>T	c.(433-435)CTC>CTT	p.L145L	COL4A6_uc004env.3_Silent_p.L144L|COL4A6_uc011msn.1_Silent_p.L144L|COL4A6_uc010npk.2_Silent_p.L144L	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	145	Triple-helical region.				cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
