Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
CHD5	26038	broad.mit.edu	37	1	6170533	6170533	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6170533A>T	uc001amb.1	-	37	5403	c.5303T>A	c.(5302-5304)CTC>CAC	p.L1768H	CHD5_uc001alz.1_Missense_Mutation_p.L625H|CHD5_uc001ama.1_RNA	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	1768					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GGGCTCGTTGAGGATCATGTA	0.572													22	85	---	---	---	---	PASS
ENO1	2023	broad.mit.edu	37	1	8926510	8926510	+	Missense_Mutation	SNP	C	A	A	rs11544509		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8926510C>A	uc001apj.1	-	7	646	c.495G>T	c.(493-495)ATG>ATT	p.M165I	ENO1_uc001api.1_Missense_Mutation_p.M69I|ENO1_uc001apk.1_Missense_Mutation_p.M110I|ENO1_uc001apl.1_Missense_Mutation_p.M165I|ENO1_uc009vmi.1_Missense_Mutation_p.M122I|ENO1_uc009vmj.1_Missense_Mutation_p.M165I|ENO1_uc009vmk.1_Missense_Mutation_p.M39I|ENO1_uc009vml.1_Missense_Mutation_p.M165I	NM_001428	NP_001419	P06733	ENOA_HUMAN	enolase 1	165	Required for repression of c-myc promoter activity.				gluconeogenesis|glycolysis|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|response to virus	phosphopyruvate hydratase complex|plasma membrane|sarcomere	DNA binding|magnesium ion binding|phosphopyruvate hydratase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|kidney(1)|central_nervous_system(1)	4	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.42e-07)|COAD - Colon adenocarcinoma(227;2.78e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		TGAACTCCTGCATGGCCAGCT	0.547													51	172	---	---	---	---	PASS
AADACL3	126767	broad.mit.edu	37	1	12785730	12785730	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12785730G>C	uc009vnn.1	+	4	1053	c.820G>C	c.(820-822)GAC>CAC	p.D274H	AADACL3_uc001aug.1_Missense_Mutation_p.D204H	NM_001103170	NP_001096640	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3 isoform 1	274							hydrolase activity				0	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TGCAGAAGATGACATAGTGTC	0.507													51	179	---	---	---	---	PASS
PRAMEF10	343071	broad.mit.edu	37	1	12954436	12954436	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12954436G>A	uc001auo.2	-	3	920	c.847C>T	c.(847-849)CAC>TAC	p.H283Y		NM_001039361	NP_001034450	O60809	PRA10_HUMAN	PRAME family member 10	283											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGCTCCAGGTGCTCTTTGATA	0.403													66	76	---	---	---	---	PASS
WDTC1	23038	broad.mit.edu	37	1	27621085	27621085	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27621085G>C	uc009vst.2	+	9	1373	c.838G>C	c.(838-840)GGC>CGC	p.G280R	WDTC1_uc001bno.2_Missense_Mutation_p.G280R|WDTC1_uc001bnp.1_RNA|WDTC1_uc001bnq.2_5'Flank	NM_015023	NP_055838	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	280	WD 5.						protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		CAGCCCCAATGGCACAGAGCT	0.552													18	45	---	---	---	---	PASS
RBBP4	5928	broad.mit.edu	37	1	33147502	33147502	+	3'UTR	SNP	G	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33147502G>C	uc001bvr.2	+	12					SYNC_uc001bvt.2_Intron|SYNC_uc010ohl.1_Intron|RBBP4_uc001bvs.2_3'UTR|RBBP4_uc010ohj.1_3'UTR|RBBP4_uc010ohk.1_3'UTR	NM_005610	NP_005601	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4 isoform a						cell cycle|CenH3-containing nucleosome assembly at centromere|DNA replication|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|ESC/E(Z) complex|NuRD complex|NURF complex|Sin3 complex	histone binding|histone deacetylase binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				GTGAACTTCTGAGGTTTAGTT	0.383													40	43	---	---	---	---	PASS
C1orf94	84970	broad.mit.edu	37	1	34666597	34666597	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34666597C>T	uc001bxs.3	+	3	1063	c.664C>T	c.(664-666)CGA>TGA	p.R222*	C1orf94_uc001bxt.2_Nonsense_Mutation_p.R412*	NM_032884	NP_116273	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform b	222							protein binding				0		Myeloproliferative disorder(586;0.0393)				GCCGAGACTTCGAAACAAAGT	0.577													3	23	---	---	---	---	PASS
DNAJB4	11080	broad.mit.edu	37	1	78478852	78478852	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78478852T>C	uc001dij.2	+	2	488	c.329T>C	c.(328-330)ATT>ACT	p.I110T	DNAJB4_uc010orn.1_5'UTR	NM_007034	NP_008965	Q9UDY4	DNJB4_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 4	110					protein folding|response to heat|response to unfolded protein	cytoplasm|plasma membrane	heat shock protein binding|unfolded protein binding				0						CCCTTTGAAATTTTCTTTGGA	0.448													59	170	---	---	---	---	PASS
HFM1	164045	broad.mit.edu	37	1	91818686	91818686	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91818686A>G	uc001doa.3	-	15	1853	c.1753T>C	c.(1753-1755)TAT>CAT	p.Y585H	HFM1_uc009wdb.2_5'Flank|HFM1_uc010osu.1_Missense_Mutation_p.Y264H|HFM1_uc010osv.1_Missense_Mutation_p.Y269H	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	585	Helicase C-terminal.						ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		GCATGATGATAAGCAGCACCA	0.328													30	120	---	---	---	---	PASS
PHTF1	10745	broad.mit.edu	37	1	114252891	114252891	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114252891C>A	uc009wgp.1	-	10	1706	c.1254G>T	c.(1252-1254)GAG>GAT	p.E418D	PHTF1_uc001edn.2_Missense_Mutation_p.E418D|PHTF1_uc001edm.2_Missense_Mutation_p.E175D|PHTF1_uc001edo.1_Missense_Mutation_p.E175D	NM_006608	NP_006599	Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	418						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAAAAACATCCTCTTTGGGGT	0.358													44	49	---	---	---	---	PASS
ATP1A1	476	broad.mit.edu	37	1	116932982	116932982	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116932982A>G	uc001ege.2	+	9	1510	c.1171A>G	c.(1171-1173)ATG>GTG	p.M391V	ATP1A1_uc010owv.1_Missense_Mutation_p.M360V|ATP1A1_uc010oww.1_Missense_Mutation_p.M391V|ATP1A1_uc010owx.1_Missense_Mutation_p.M360V	NM_000701	NP_000692	P05023	AT1A1_HUMAN	Na+/K+ -ATPase alpha 1 subunit isoform a	391	Cytoplasmic (Potential).				ATP biosynthetic process	melanosome|sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Captopril(DB01197)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Esomeprazole(DB00736)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Ouabain(DB01092)|Pantoprazole(DB00213)|Trichlormethiazide(DB01021)	AGTGGCCCACATGTGGTTTGA	0.428													17	38	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144857634	144857634	+	Silent	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144857634C>T	uc001elw.3	-	39	6711	c.6420G>A	c.(6418-6420)ACG>ACA	p.T2140T	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Silent_p.T2034T|PDE4DIP_uc001elv.3_Silent_p.T1147T	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	2140					cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGATTATGGGCGTTTCTGAGC	0.483			T	PDGFRB	MPD								96	427	---	---	---	---	PASS
TARS2	80222	broad.mit.edu	37	1	150476838	150476838	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150476838G>A	uc001euq.2	+	14	1652	c.1645G>A	c.(1645-1647)GGC>AGC	p.G549S	TARS2_uc001eur.2_Missense_Mutation_p.G467S|TARS2_uc009wlt.2_Missense_Mutation_p.G175S|TARS2_uc009wls.2_Missense_Mutation_p.G419S	NM_025150	NP_079426	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial	549					threonyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|threonine-tRNA ligase activity			ovary(1)	1	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	CGATGCCCTGGGCCGGCCACA	0.438													16	76	---	---	---	---	PASS
FCRL4	83417	broad.mit.edu	37	1	157545298	157545298	+	3'UTR	SNP	G	A	A	rs61023553	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157545298G>A	uc001fqw.2	-	12					FCRL4_uc010phy.1_RNA	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor							integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)|skin(1)	4	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				GGACGTTCTCGTAACTTTTCA	0.453													8	74	---	---	---	---	PASS
METTL13	51603	broad.mit.edu	37	1	171765592	171765592	+	Intron	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171765592G>A	uc001ghz.2	+						METTL13_uc001gia.2_Intron|METTL13_uc001gib.2_Intron|METTL13_uc010pml.1_Intron|METTL13_uc001gic.1_RNA	NM_015935	NP_057019	Q8N6R0	MTL13_HUMAN	CGI-01 protein isoform 1								methyltransferase activity|protein binding			kidney(1)	1						CTGATGTGAGGTCATTCTGAC	0.473													154	194	---	---	---	---	PASS
CTSE	1510	broad.mit.edu	37	1	206325277	206325277	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206325277A>T	uc001hdu.2	+	5	620	c.502A>T	c.(502-504)AGT>TGT	p.S168C	CTSE_uc001hdv.2_Missense_Mutation_p.S168C|CTSE_uc010prs.1_Missense_Mutation_p.S93C	NM_001910	NP_001901	P14091	CATE_HUMAN	cathepsin E isoform a preproprotein	173					antigen processing and presentation of exogenous peptide antigen via MHC class II|digestion|proteolysis	endosome	aspartic-type endopeptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.0754)			GTTTGGAGAAAGTGTCACAGA	0.547													20	185	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216380760	216380760	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216380760T>G	uc001hku.1	-	16	3558	c.3171A>C	c.(3169-3171)CAA>CAC	p.Q1057H	USH2A_uc001hkv.2_Missense_Mutation_p.Q1057H	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1057	Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TGGGCGGAGGTTGCTGGAATG	0.413										HNSCC(13;0.011)			54	151	---	---	---	---	PASS
OR2L8	391190	broad.mit.edu	37	1	248112339	248112339	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248112339C>G	uc001idt.1	+	1	180	c.180C>G	c.(178-180)TTC>TTG	p.F60L	OR2L13_uc001ids.2_Intron	NM_001001963	NP_001001963	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L,	60	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			CCATGTATTTCCTACTGAGTC	0.413													236	612	---	---	---	---	PASS
OR2T27	403239	broad.mit.edu	37	1	248813490	248813490	+	Silent	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248813490C>T	uc010pzo.1	-	1	696	c.696G>A	c.(694-696)GAG>GAA	p.E232E		NM_001001824	NP_001001824	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T,	232	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTCCCCTCCCCTCTGCCTCGC	0.502													18	35	---	---	---	---	PASS
OTOF	9381	broad.mit.edu	37	2	26703722	26703722	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26703722C>G	uc002rhk.2	-	15	1862	c.1735G>C	c.(1735-1737)GAC>CAC	p.D579H	OTOF_uc002rhh.2_5'Flank|OTOF_uc002rhi.2_5'Flank|OTOF_uc002rhj.2_5'Flank	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	579	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGGAGGTGTCTACGATCTCC	0.662													56	86	---	---	---	---	PASS
EHD3	30845	broad.mit.edu	37	2	31484438	31484438	+	Silent	SNP	T	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31484438T>C	uc002rnu.2	+	5	1547	c.939T>C	c.(937-939)TCT>TCC	p.S313S	EHD3_uc010ymt.1_Intron	NM_014600	NP_055415	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	313					blood coagulation|endocytic recycling|protein homooligomerization	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding			skin(2)	2	Acute lymphoblastic leukemia(172;0.155)					TCATCAGCTCTCTGAAGAAGG	0.562													113	177	---	---	---	---	PASS
ANKRD20B	729171	broad.mit.edu	37	2	95497757	95497757	+	RNA	SNP	C	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95497757C>G	uc010fhp.2	-	7		c.791G>C				NR_003366				Homo sapiens ankyrin repeat domain 20B (ANKRD20B), non-coding RNA.												0						CTCACCTTCTCCTTGTCCATT	0.279													47	215	---	---	---	---	PASS
STARD7	56910	broad.mit.edu	37	2	96861119	96861119	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96861119C>T	uc002svm.3	-	2	860	c.459G>A	c.(457-459)TGG>TGA	p.W153*	STARD7_uc002svl.2_5'UTR	NM_020151	NP_064536	Q9NQZ5	STAR7_HUMAN	START domain containing 7 precursor	153	START.					mitochondrion					0						TTGGGCGCCGCCACAGCTTAA	0.498													5	19	---	---	---	---	PASS
GALNT3	2591	broad.mit.edu	37	2	166611170	166611170	+	Silent	SNP	A	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166611170A>T	uc010fph.1	-	9	1980	c.1593T>A	c.(1591-1593)ATT>ATA	p.I531I		NM_004482	NP_004473	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	531	Ricin B-type lectin.|Lumenal (Potential).				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	Golgi cisterna membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	calcium ion binding|manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(2)|ovary(1)	3						ATGTATACATAATTAATGGTT	0.368													39	67	---	---	---	---	PASS
LASS6	253782	broad.mit.edu	37	2	169622847	169622847	+	Intron	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169622847C>T	uc002ueb.1	+						LASS6_uc002uec.1_Missense_Mutation_p.P340S	NM_203463	NP_982288	Q6ZMG9	CERS6_HUMAN	longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1						GAAGTGGAACCCTTTACATGT	0.468													49	101	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179600277	179600277	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179600277C>T	uc010zfg.1	-	47	11388	c.11164G>A	c.(11164-11166)GCT>ACT	p.A3722T	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.A383T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	4649							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGCTTCCAGCCTCATTTGAA	0.408													12	35	---	---	---	---	PASS
GULP1	51454	broad.mit.edu	37	2	189458666	189458666	+	Splice_Site	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189458666G>A	uc010fru.2	+	12	1305	c.844_splice	c.e12-1	p.E282_splice	GULP1_uc002uqd.2_Splice_Site_p.W285_splice|GULP1_uc010zfw.1_Splice_Site_p.E179_splice|GULP1_uc002uqf.2_Splice_Site_p.E282_splice|GULP1_uc002uqg.2_Splice_Site_p.E282_splice|GULP1_uc002uqh.1_3'UTR	NM_016315	NP_057399	Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			CTGTTTTACAGGAGGGGTTCA	0.338													52	92	---	---	---	---	PASS
MFSD6	54842	broad.mit.edu	37	2	191301590	191301590	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191301590T>C	uc002urz.2	+	3	1159	c.835T>C	c.(835-837)TAT>CAT	p.Y279H		NM_017694	NP_060164	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing	279					transmembrane transport	integral to membrane				ovary(2)	2						CATGCTTGTTTATGATCAACA	0.428													137	223	---	---	---	---	PASS
CASP10	843	broad.mit.edu	37	2	202060612	202060612	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202060612C>A	uc002uxl.1	+	5	1043	c.625C>A	c.(625-627)CAA>AAA	p.Q209K	CASP10_uc002uxi.1_Missense_Mutation_p.Q209K|CASP10_uc010zhn.1_RNA|CASP10_uc002uxj.1_Missense_Mutation_p.Q209K|CASP10_uc002uxk.1_Missense_Mutation_p.Q209K|CASP10_uc010fta.1_Missense_Mutation_p.Q209K|CASP10_uc002uxm.1_Missense_Mutation_p.Q209K|CASP10_uc010ftb.1_RNA	NM_032974	NP_116756	Q92851	CASPA_HUMAN	caspase 10 isoform b preproprotein	209					apoptosis|induction of apoptosis by extracellular signals|proteolysis	cytosol|plasma membrane	cysteine-type endopeptidase activity|identical protein binding|protein binding			skin(3)|ovary(1)|pancreas(1)|breast(1)	6						CGAGTCGTATCAAGGAGAGGA	0.333													97	191	---	---	---	---	PASS
ABCA12	26154	broad.mit.edu	37	2	215868936	215868936	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215868936G>T	uc002vew.2	-	20	2900	c.2680C>A	c.(2680-2682)CTC>ATC	p.L894I	ABCA12_uc002vev.2_Missense_Mutation_p.L576I|ABCA12_uc010zjn.1_5'UTR	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	894					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)		GACTCACCGAGTTCATCTATC	0.363													25	59	---	---	---	---	PASS
SNED1	25992	broad.mit.edu	37	2	241974046	241974046	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241974046A>G	uc002wah.1	+	4	704	c.704A>G	c.(703-705)GAC>GGC	p.D235G		NM_001080437	NP_001073906	Q8TER0	SNED1_HUMAN	6720455I24Rik homolog precursor	235	NIDO.				cell-matrix adhesion	extracellular region	calcium ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		CGCACAGCAGACATGGCCGAG	0.672													4	13	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188200	10188200	+	Missense_Mutation	SNP	C	A	A	rs5030811		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188200C>A	uc003bvc.2	+	2	556	c.343C>A	c.(343-345)CAC>AAC	p.H115N	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	115	Involved in binding to CCT complex.		H -> Q (in VHLD; type II).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.H115N(5)|p.?(3)|p.H115Y(3)|p.H115fs*44(3)|p.H115D(1)|p.H115fs*41(1)|p.H115fs*42(1)|p.H115P(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CCCGATAGGTCACCTTTGGCT	0.333		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				106	71	---	---	---	---	PASS
ATP2B2	491	broad.mit.edu	37	3	10401807	10401807	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10401807G>T	uc003bvt.2	-	13	2099	c.1660C>A	c.(1660-1662)CCC>ACC	p.P554T	ATP2B2_uc003bvv.2_Missense_Mutation_p.P509T|ATP2B2_uc003bvw.2_Missense_Mutation_p.P509T|ATP2B2_uc010hdo.2_Missense_Mutation_p.P259T	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	554	Cytoplasmic (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6						TTCTCTGGGGGCTGCAGAGAG	0.677													6	44	---	---	---	---	PASS
SLC6A1	6529	broad.mit.edu	37	3	11078671	11078671	+	3'UTR	SNP	A	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11078671A>C	uc010hdq.2	+	16						NM_003042	NP_003033	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)|skin(1)	2		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Cocaine(DB00907)|Tiagabine(DB00906)	CCACTCACCGACCCGACACTC	0.622													4	11	---	---	---	---	PASS
SCN10A	6336	broad.mit.edu	37	3	38797338	38797338	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38797338C>A	uc003ciq.2	-	10	1402	c.1402G>T	c.(1402-1404)GAG>TAG	p.E468*		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	468					sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	GTGGAGCCCTCTGACACTCTT	0.353													70	152	---	---	---	---	PASS
MAP4	4134	broad.mit.edu	37	3	48019414	48019414	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48019414G>A	uc003csb.2	-	3	759	c.233C>T	c.(232-234)TCT>TTT	p.S78F	MAP4_uc003csc.3_Missense_Mutation_p.S78F|MAP4_uc011bbf.1_Intron|MAP4_uc003csf.3_Missense_Mutation_p.S95F|MAP4_uc003csg.2_Missense_Mutation_p.S78F	NM_002375	NP_002366	P27816	MAP4_HUMAN	microtubule-associated protein 4 isoform 1	78					negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)		TGGTTTAGAAGATGGAGTATC	0.408													110	52	---	---	---	---	PASS
UBA7	7318	broad.mit.edu	37	3	49847308	49847308	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49847308G>T	uc003cxr.2	-	15	2015	c.1844C>A	c.(1843-1845)GCC>GAC	p.A615D		NM_003335	NP_003326	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	615					ISG15-protein conjugation|negative regulation of type I interferon production	cytosol	ATP binding|ISG15 activating enzyme activity|ligase activity			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CTCATGCCGGGCCCACTGTGG	0.587													74	45	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52662912	52662912	+	Nonsense_Mutation	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52662912G>A	uc003des.2	-	12	1453	c.1441C>T	c.(1441-1443)CAG>TAG	p.Q481*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.Q481*|PBRM1_uc003der.2_Nonsense_Mutation_p.Q449*|PBRM1_uc003det.2_Nonsense_Mutation_p.Q481*|PBRM1_uc003deu.2_Nonsense_Mutation_p.Q481*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.Q481*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.Q481*|PBRM1_uc003dey.2_Nonsense_Mutation_p.Q481*|PBRM1_uc003dez.1_Nonsense_Mutation_p.Q481*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.Q379*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	481					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AATCACACCTGCATAACTTGC	0.358			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								51	30	---	---	---	---	PASS
GOLIM4	27333	broad.mit.edu	37	3	167750471	167750471	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167750471T>G	uc003ffe.2	-	9	1357	c.1013A>C	c.(1012-1014)GAG>GCG	p.E338A	GOLIM4_uc011bpe.1_Missense_Mutation_p.E338A|GOLIM4_uc011bpf.1_Missense_Mutation_p.E310A|GOLIM4_uc011bpg.1_Missense_Mutation_p.E310A	NM_014498	NP_055313	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	338	Glu-rich.|Lumenal (Potential).				transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5						CTTTCTGTGCTCCTCTTCCAC	0.552													73	68	---	---	---	---	PASS
NOP14	8602	broad.mit.edu	37	4	2955192	2955192	+	Intron	SNP	C	G	G	rs1475976	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2955192C>G	uc003ggj.1	-						C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_Intron|NOP14_uc003ggk.3_Intron|NOP14_uc003ggl.2_Intron|NOP14_uc010icq.1_RNA	NM_003703	NP_003694	P78316	NOP14_HUMAN	probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1						AAGTCGGTCACCCAAGCTCAG	0.483													6	217	---	---	---	---	PASS
WDFY3	23001	broad.mit.edu	37	4	85731357	85731357	+	Silent	SNP	C	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85731357C>G	uc003hpd.2	-	14	2436	c.2028G>C	c.(2026-2028)GTG>GTC	p.V676V	WDFY3_uc003hpf.2_Silent_p.V676V	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	676						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		GATTCTGGTTCACTTTCTCCC	0.438													41	73	---	---	---	---	PASS
POLK	51426	broad.mit.edu	37	5	74889874	74889874	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74889874G>A	uc003kdw.2	+	12	1624	c.1528G>A	c.(1528-1530)GGT>AGT	p.G510S	POLK_uc003kdx.2_RNA|POLK_uc003kdy.2_RNA|POLK_uc010izq.2_Intron|POLK_uc003kec.2_Missense_Mutation_p.G420S|POLK_uc010izr.2_RNA|POLK_uc010izs.2_Intron|POLK_uc003ked.2_Intron|POLK_uc003kee.2_Intron|POLK_uc003kef.2_Missense_Mutation_p.G420S	NM_016218	NP_057302	Q9UBT6	POLK_HUMAN	DNA-directed DNA polymerase kappa	510					DNA replication|nucleotide-excision repair, DNA gap filling	nucleus	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			ovary(2)|kidney(2)	4		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		AAGGCTTATGGGTATGACTTT	0.274								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					124	159	---	---	---	---	PASS
PDLIM4	8572	broad.mit.edu	37	5	131598428	131598428	+	Missense_Mutation	SNP	G	T	T	rs138635559		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131598428G>T	uc003kwn.2	+	2	297	c.220G>T	c.(220-222)GAT>TAT	p.D74Y	uc003kwm.3_Intron|PDLIM4_uc003kwp.2_Missense_Mutation_p.D74Y|PDLIM4_uc003kwo.2_Missense_Mutation_p.D74Y	NM_003687	NP_003678	P50479	PDLI4_HUMAN	PDZ and LIM domain 4 isoform 1	74	PDZ.						protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGGCTGCCACGATCACCTCAC	0.597													5	61	---	---	---	---	PASS
LECT2	3950	broad.mit.edu	37	5	135286840	135286840	+	Intron	SNP	G	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135286840G>C	uc003lbe.1	-						FBXL21_uc003lbc.2_RNA	NM_002302	NP_002293	O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2 precursor						chemotaxis|skeletal system development	cytoplasm|extracellular space				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTCTACGTATGGAACCTGCAT	0.368													3	60	---	---	---	---	PASS
TRPC7	57113	broad.mit.edu	37	5	135692925	135692925	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135692925C>T	uc003lbn.1	-	1	151	c.148G>A	c.(148-150)GCT>ACT	p.A50T	TRPC7_uc010jef.1_Missense_Mutation_p.A42T|TRPC7_uc010jeg.1_RNA|TRPC7_uc010jeh.1_Missense_Mutation_p.A42T|TRPC7_uc010jei.1_Missense_Mutation_p.A42T|TRPC7_uc010jej.1_5'UTR	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,	51	Cytoplasmic (Potential).|ANK 1.				axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCATACTCAGCCGAGTCCAGG	0.607													182	212	---	---	---	---	PASS
TCOF1	6949	broad.mit.edu	37	5	149749096	149749096	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149749096G>T	uc003lry.2	+	6	678	c.570G>T	c.(568-570)ATG>ATT	p.M190I	TCOF1_uc003lrw.2_Missense_Mutation_p.M190I|TCOF1_uc011dch.1_Missense_Mutation_p.M190I|TCOF1_uc003lrz.2_Missense_Mutation_p.M190I|TCOF1_uc003lrx.2_Missense_Mutation_p.M190I|TCOF1_uc003lsa.2_Missense_Mutation_p.M190I	NM_001135243	NP_001128715	Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	190					skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTCAGGGATGGTGTCAGCGG	0.627													18	102	---	---	---	---	PASS
CYFIP2	26999	broad.mit.edu	37	5	156746796	156746796	+	Silent	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156746796G>A	uc003lwq.2	+	16	1521	c.1383G>A	c.(1381-1383)CAG>CAA	p.Q461Q	CYFIP2_uc011ddn.1_Silent_p.Q435Q|CYFIP2_uc011ddo.1_Silent_p.Q265Q|CYFIP2_uc003lwr.2_Silent_p.Q461Q|CYFIP2_uc003lws.2_Silent_p.Q461Q|CYFIP2_uc003lwt.2_Silent_p.Q339Q|CYFIP2_uc011ddp.1_Silent_p.Q195Q	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2	461					apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AAGGCCTGCAGGTGCTCATGG	0.602													52	95	---	---	---	---	PASS
ERGIC1	57222	broad.mit.edu	37	5	172341926	172341926	+	Intron	SNP	T	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172341926T>A	uc003mbw.3	+						ERGIC1_uc003mby.3_Intron|ERGIC1_uc011dfa.1_Intron|ERGIC1_uc003mbz.3_Missense_Mutation_p.S109T	NM_001031711	NP_001026881	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate						ER to Golgi vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GTGGAGGCACTCACTCGACCT	0.612													16	7	---	---	---	---	PASS
CPLX2	10814	broad.mit.edu	37	5	175306865	175306865	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175306865G>T	uc003mde.1	+	5	568	c.222G>T	c.(220-222)AAG>AAT	p.K74N	CPLX2_uc003mdf.1_Missense_Mutation_p.K74N	NM_006650	NP_006641	Q6PUV4	CPLX2_HUMAN	complexin 2	74	Potential.|Interaction with the SNARE complex (By similarity).				mast cell degranulation|positive regulation of synaptic plasticity|vesicle docking involved in exocytosis	cytosol				ovary(1)	1	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGCTGAAGAAGAAGGAGGAGA	0.647													18	22	---	---	---	---	PASS
MUTED	63915	broad.mit.edu	37	6	8015841	8015841	+	3'UTR	SNP	A	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8015841A>C	uc003mxy.2	-	5					TXNDC5_uc003mxw.2_Intron|MUTED_uc010joc.2_3'UTR|MUTED_uc010job.2_RNA	NM_201280	NP_958437	Q8TDH9	MUTED_HUMAN	muted							BLOC-1 complex	protein binding				0	Ovarian(93;0.0398)					GAGAGAGGTGAACATCTTCTC	0.388													31	92	---	---	---	---	PASS
C6orf48	50854	broad.mit.edu	37	6	31804867	31804867	+	Intron	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31804867C>T	uc003rjx.1	+						C6orf48_uc003rjy.1_Intron|C6orf48_uc003rjz.1_Intron|SNORD52_uc003nxp.2_RNA	NM_001040437	NP_001035527	Q9UBA6	G8_HUMAN	G8 protein												0						ATGATGATTTCACAGACTAGA	0.443													21	48	---	---	---	---	PASS
HSP90AB1	3326	broad.mit.edu	37	6	44218220	44218220	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44218220G>A	uc003oxa.1	+	6	925	c.841G>A	c.(841-843)GAA>AAA	p.E281K	HSP90AB1_uc011dvr.1_Missense_Mutation_p.E271K|HSP90AB1_uc003oxb.1_Missense_Mutation_p.E281K|HSP90AB1_uc011dvs.1_Missense_Mutation_p.E101K|HSP90AB1_uc003oxc.1_5'UTR	NM_007355	NP_031381	P08238	HS90B_HUMAN	heat shock 90kDa protein 1, beta	281					axon guidance|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of nitric oxide biosynthetic process|protein folding|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to unfolded protein	cytosol|melanosome	ATP binding|nitric-oxide synthase regulator activity|TPR domain binding|unfolded protein binding			lung(3)|breast(1)	4	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGATCAGGAAGAACTAAACAA	0.249													24	46	---	---	---	---	PASS
ZNF451	26036	broad.mit.edu	37	6	57013213	57013213	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57013213A>C	uc003pdm.1	+	10	2554	c.2330A>C	c.(2329-2331)AAA>ACA	p.K777T	ZNF451_uc003pdl.2_Missense_Mutation_p.K777T|ZNF451_uc003pdn.1_Missense_Mutation_p.K777T|uc003pdq.1_Intron|ZNF451_uc003pdk.1_Missense_Mutation_p.K777T	NM_001031623	NP_001026794	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451 isoform 1	777					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			CAAGTGCACAAAGAAAAGAGT	0.438													14	34	---	---	---	---	PASS
ZNF292	23036	broad.mit.edu	37	6	87970890	87970890	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87970890C>T	uc003plm.3	+	8	7584	c.7543C>T	c.(7543-7545)CAG>TAG	p.Q2515*		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	2515					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TAATGATTTTCAGGAAGATAA	0.299													10	25	---	---	---	---	PASS
ZUFSP	221302	broad.mit.edu	37	6	116979974	116979974	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116979974T>C	uc003pxf.1	-	4	1030	c.784A>G	c.(784-786)AAG>GAG	p.K262E	ZUFSP_uc010kef.1_Missense_Mutation_p.K66E	NM_145062	NP_659499	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	262	Potential.					intracellular	zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		ACCTGCAGCTTCTGAAATTCT	0.323													7	23	---	---	---	---	PASS
UTRN	7402	broad.mit.edu	37	6	144780343	144780343	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144780343A>G	uc003qkt.2	+	20	2652	c.2560A>G	c.(2560-2562)AAA>GAA	p.K854E	UTRN_uc010khq.1_Missense_Mutation_p.K854E	NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	854	Interaction with SYNM.|Spectrin 6.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		CCTTCACCCCAAAATTGAAAT	0.502													18	47	---	---	---	---	PASS
FNDC1	84624	broad.mit.edu	37	6	159653887	159653887	+	Silent	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159653887G>T	uc010kjv.2	+	11	2543	c.2343G>T	c.(2341-2343)GCG>GCT	p.A781A	FNDC1_uc010kjw.1_Silent_p.A666A	NM_032532	NP_115921	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	781						extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CTGAGGGAGCGGAGGCTTCTG	0.662													3	33	---	---	---	---	PASS
FTSJ2	29960	broad.mit.edu	37	7	2274853	2274853	+	Silent	SNP	T	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2274853T>A	uc003slm.2	-	3	674	c.645A>T	c.(643-645)GTA>GTT	p.V215V	MAD1L1_uc003slh.1_5'Flank|MAD1L1_uc003slf.1_5'Flank|MAD1L1_uc003slg.1_5'Flank|MAD1L1_uc010ksh.1_5'Flank|MAD1L1_uc003sli.1_5'Flank|MAD1L1_uc010ksi.1_5'Flank|MAD1L1_uc010ksj.2_5'Flank|FTSJ2_uc003slk.2_Silent_p.V61V|FTSJ2_uc003sll.2_Silent_p.V61V|FTSJ2_uc003sln.2_RNA|FTSJ2_uc003slo.2_Silent_p.V61V	NM_013393	NP_037525	Q9UI43	RRMJ2_HUMAN	FtsJ homolog 2	215					cell proliferation	mitochondrion|nucleolus	nucleic acid binding|rRNA (uridine-2'-O-)-methyltransferase activity			ovary(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.7e-14)		TGATGATCCTTACATTCTGGA	0.502													96	166	---	---	---	---	PASS
FOXK1	221937	broad.mit.edu	37	7	4796681	4796681	+	Silent	SNP	C	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4796681C>G	uc003snc.1	+	5	1117	c.1107C>G	c.(1105-1107)TCC>TCG	p.S369S	FOXK1_uc003sna.1_Silent_p.S206S	NM_001037165	NP_001032242	P85037	FOXK1_HUMAN	forkhead box K1	369	Fork-head.				cell differentiation|embryo development|muscle organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			upper_aerodigestive_tract(1)|skin(1)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		TCCCACGTTCCCAGGAGGAGC	0.527													39	189	---	---	---	---	PASS
WIPI2	26100	broad.mit.edu	37	7	5270558	5270558	+	Missense_Mutation	SNP	A	G	G	rs144773383	byFrequency	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5270558A>G	uc003snv.2	+	13	1561	c.1345A>G	c.(1345-1347)ATG>GTG	p.M449V	WIPI2_uc003snw.2_Missense_Mutation_p.M438V|WIPI2_uc003snx.2_Missense_Mutation_p.M431V|WIPI2_uc003sny.2_Missense_Mutation_p.M420V|WIPI2_uc010ksv.2_Missense_Mutation_p.M305V|WIPI2_uc003soa.2_Missense_Mutation_p.M379V|WIPI2_uc003sob.2_Missense_Mutation_p.M192V	NM_015610	NP_056425	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2	449					autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)		GCACCCGCCCATGATTCTTCG	0.597													40	61	---	---	---	---	PASS
GLCCI1	113263	broad.mit.edu	37	7	8126006	8126006	+	Silent	SNP	T	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8126006T>G	uc003srk.2	+	8	2041	c.1482T>G	c.(1480-1482)GTT>GTG	p.V494V		NM_138426	NP_612435	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	494											0		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)		CTCTGACCGTTGAGCAGCTCT	0.557													260	482	---	---	---	---	PASS
SLC26A4	5172	broad.mit.edu	37	7	107329537	107329537	+	Silent	SNP	G	A	A	rs140778437		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107329537G>A	uc003vep.2	+	9	1265	c.1041G>A	c.(1039-1041)TCG>TCA	p.S347S	SLC26A4_uc011kmb.1_5'Flank|SLC26A4_uc011kmc.1_5'Flank	NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin	347	Helical; (Potential).				regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7						GCTTGTTCTCGGAGATGCTGG	0.438									Pendred_syndrome				39	221	---	---	---	---	PASS
MSC	9242	broad.mit.edu	37	8	72756043	72756043	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72756043C>G	uc003xyx.1	-	1	689	c.371G>C	c.(370-372)AGC>ACC	p.S124T	uc011lff.1_Intron|uc003xyy.2_5'Flank	NM_005098	NP_005089	O60682	MUSC_HUMAN	musculin	124	Helix-loop-helix motif.				transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0	Breast(64;0.176)		Epithelial(68;0.137)|BRCA - Breast invasive adenocarcinoma(89;0.203)			GAAGGCTTTGCTCAGCACGCG	0.667											OREG0018826	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	62	20	---	---	---	---	PASS
FAM154A	158297	broad.mit.edu	37	9	19032912	19032912	+	5'UTR	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19032912C>T	uc003zni.1	-	1					FAM154A_uc010mip.1_5'UTR	NM_153707	NP_714918	Q8IYX7	F154A_HUMAN	hypothetical protein LOC158297											pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)		TTCATAGGGGCGATCCTGAGG	0.642													10	14	---	---	---	---	PASS
ENHO	375704	broad.mit.edu	37	9	34521629	34521629	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34521629A>C	uc003zun.1	-	2	489	c.65T>G	c.(64-66)TTG>TGG	p.L22W	ENHO_uc003zuo.2_RNA	NM_198573	NP_940975	Q6UWT2	ENHO_HUMAN	adropin precursor	22						extracellular region					0						CAGCAGCAGCAAGAAGCCCAC	0.632													20	12	---	---	---	---	PASS
STRBP	55342	broad.mit.edu	37	9	125936121	125936121	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125936121C>A	uc004bns.2	-	5	655	c.225G>T	c.(223-225)AAG>AAT	p.K75N	STRBP_uc004bnt.2_Intron|STRBP_uc004bnu.2_Missense_Mutation_p.K61N|STRBP_uc004bnv.2_Missense_Mutation_p.K75N	NM_018387	NP_060857	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	75					multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2						CACCTTGATCCCTAAAAATAA	0.388													79	68	---	---	---	---	PASS
SOHLH1	402381	broad.mit.edu	37	9	138586216	138586216	+	Silent	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138586216C>A	uc004cgl.2	-	7	1024	c.963G>T	c.(961-963)GGG>GGT	p.G321G	SOHLH1_uc010nbe.2_Intron	NM_001012415	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic	321					cell differentiation|multicellular organismal development|oogenesis|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			breast(1)|central_nervous_system(1)	2		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		CAGCCCTGAACCCAGGGCCCC	0.647													29	19	---	---	---	---	PASS
SOHLH1	402381	broad.mit.edu	37	9	138586217	138586217	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138586217C>T	uc004cgl.2	-	7	1023	c.962G>A	c.(961-963)GGG>GAG	p.G321E	SOHLH1_uc010nbe.2_Intron	NM_001012415	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic	321					cell differentiation|multicellular organismal development|oogenesis|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			breast(1)|central_nervous_system(1)	2		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		AGCCCTGAACCCAGGGCCCCA	0.647													28	18	---	---	---	---	PASS
ABCA2	20	broad.mit.edu	37	9	139916407	139916407	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139916407G>C	uc011mem.1	-	6	759	c.611C>G	c.(610-612)TCT>TGT	p.S204C	ABCA2_uc011mel.1_Missense_Mutation_p.S205C|ABCA2_uc004ckl.1_Missense_Mutation_p.S135C|ABCA2_uc004ckm.1_Missense_Mutation_p.S235C|ABCA2_uc004cko.1_5'UTR|ABCA2_uc010nca.2_Missense_Mutation_p.S135C	NM_001606	NP_001597	Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A, member 2	204					cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		GTGGAGGCCAGACTGTGAATC	0.632													5	4	---	---	---	---	PASS
MYST4	23522	broad.mit.edu	37	10	76748798	76748798	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76748798T>A	uc001jwn.1	+	13	3050	c.2557T>A	c.(2557-2559)TAT>AAT	p.Y853N	MYST4_uc001jwm.1_Missense_Mutation_p.Y561N|MYST4_uc001jwo.1_Missense_Mutation_p.Y561N|MYST4_uc001jwp.1_Missense_Mutation_p.Y670N	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	853	Catalytic.|Interaction with BRPF1.				histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)					CCAGCAGAAGTATAATGTCTC	0.448			T	CREBBP	AML								47	151	---	---	---	---	PASS
SMC3	9126	broad.mit.edu	37	10	112335137	112335137	+	Silent	SNP	A	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112335137A>G	uc001kze.2	+	4	300	c.174A>G	c.(172-174)CCA>CCG	p.P58P		NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	58					cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		ATCTTCGTCCAGAACAGCGGT	0.299													44	66	---	---	---	---	PASS
HSPA12A	259217	broad.mit.edu	37	10	118434631	118434631	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118434631C>G	uc001lct.2	-	12	1794	c.1689G>C	c.(1687-1689)TGG>TGC	p.W563C	HSPA12A_uc001lcu.2_Missense_Mutation_p.W480C	NM_025015	NP_079291	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	563							ATP binding			ovary(1)	1				all cancers(201;0.0158)		CGTCGGTGCACCACCGAGTGC	0.642													39	44	---	---	---	---	PASS
RNH1	6050	broad.mit.edu	37	11	499015	499015	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:499015T>C	uc001lpk.1	-	4	2022	c.614A>G	c.(613-615)AAG>AGG	p.K205R	RNH1_uc001lpl.1_Missense_Mutation_p.K205R|RNH1_uc001lpm.1_Missense_Mutation_p.K205R|RNH1_uc001lpn.1_Missense_Mutation_p.K205R|RNH1_uc001lpo.1_Missense_Mutation_p.K205R|RNH1_uc009ybw.1_RNA|RNH1_uc001lpp.1_Missense_Mutation_p.K205R|RNH1_uc001lpt.1_5'UTR|RNH1_uc001lpq.1_Missense_Mutation_p.K205R|RNH1_uc001lpr.1_Missense_Mutation_p.K205R|RNH1_uc001lps.1_Missense_Mutation_p.K205R	NM_203389	NP_976323	P13489	RINI_HUMAN	ribonuclease/angiogenin inhibitor	205	LRR 7.				mRNA catabolic process|regulation of angiogenesis	angiogenin-PRI complex|cytoplasm	protein binding|ribonuclease inhibitor activity				0		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGTGCCTACTTGAGCGCCTC	0.662													34	34	---	---	---	---	PASS
RPL27A	6157	broad.mit.edu	37	11	8704257	8704257	+	5'UTR	SNP	A	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8704257A>G	uc001mgs.3	+	1					uc001mgo.2_5'Flank|SNORA3_uc001mgq.1_5'Flank|SNORA45_uc001mgr.1_5'Flank	NM_000990	NP_000981	P46776	RL27A_HUMAN	ribosomal protein L27a						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0				Epithelial(150;3.24e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GCCCCGCCCGAAGCCCGGCCT	0.662													16	55	---	---	---	---	PASS
ARNTL	406	broad.mit.edu	37	11	13375946	13375946	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13375946A>G	uc001mkr.2	+	5	499	c.91A>G	c.(91-93)AGT>GGT	p.S31G	ARNTL_uc001mko.2_5'UTR|ARNTL_uc001mkp.2_Missense_Mutation_p.S31G|ARNTL_uc001mkq.2_Missense_Mutation_p.S31G|ARNTL_uc001mks.2_5'UTR|ARNTL_uc001mkt.2_Missense_Mutation_p.S31G|ARNTL_uc001mku.2_RNA|ARNTL_uc009ygm.1_5'UTR|ARNTL_uc001mkv.1_5'UTR|ARNTL_uc001mkw.2_5'UTR|ARNTL_uc001mkx.2_5'Flank	NM_001178	NP_001169	O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear	31					circadian rhythm|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	aryl hydrocarbon receptor binding|DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0				Epithelial(150;0.0243)		TCTTGGTACCAGTGGTGTGGA	0.398													8	56	---	---	---	---	PASS
E2F8	79733	broad.mit.edu	37	11	19247052	19247052	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19247052C>T	uc001mpm.2	-	12	2659	c.2137G>A	c.(2137-2139)GGG>AGG	p.G713R	E2F8_uc009yhv.2_RNA|E2F8_uc001mpn.3_Missense_Mutation_p.G713R	NM_024680	NP_078956	A0AVK6	E2F8_HUMAN	E2F family member 8	713					cell cycle	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1						GGGCTGTTCCCGACAGGTACG	0.522													17	64	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	30953424	30953424	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30953424C>A	uc009yjk.1	-	10	1204	c.1135G>T	c.(1135-1137)GAG>TAG	p.E379*	uc009yjl.1_3'UTR					RecName: Full=Doublecortin domain-containing protein 5;																		GCATATGGCTCTGTTGTCTTA	0.443													26	37	---	---	---	---	PASS
MALAT1	378938	broad.mit.edu	37	11	65270349	65270349	+	RNA	SNP	T	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65270349T>C	uc010roh.1	+	1		c.5117T>C			uc001ody.2_RNA|MALAT1_uc001odz.2_RNA	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0						TCTACCATTTTAAAGTTAATT	0.308													4	7	---	---	---	---	PASS
LRRC32	2615	broad.mit.edu	37	11	76371567	76371567	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76371567C>T	uc001oxq.3	-	3	1313	c.1070G>A	c.(1069-1071)CGG>CAG	p.R357Q	LRRC32_uc001oxr.3_Missense_Mutation_p.R357Q|LRRC32_uc010rsf.1_Missense_Mutation_p.R357Q	NM_005512	NP_005503	Q14392	LRC32_HUMAN	leucine rich repeat containing 32 precursor	357	Extracellular (Potential).|LRR 12.					integral to plasma membrane					0						GCCTAAGCGCCGGGCCTCAAA	0.592													9	52	---	---	---	---	PASS
VPS11	55823	broad.mit.edu	37	11	118948939	118948939	+	Silent	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118948939C>T	uc010ryx.1	+	12	1860	c.1818C>T	c.(1816-1818)GCC>GCT	p.A606A	VPS11_uc010ryy.1_Silent_p.A452A	NM_021729	NP_068375	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11	606					protein transport	endocytic vesicle|HOPS complex|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		AGCTGAAAGCCTTCCTAGAGC	0.552													86	265	---	---	---	---	PASS
PDZD3	79849	broad.mit.edu	37	11	119057384	119057384	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119057384C>A	uc001pwb.2	+	2	1037	c.513C>A	c.(511-513)CAC>CAA	p.H171Q	PDZD3_uc001pvy.2_Missense_Mutation_p.H105Q|PDZD3_uc001pvz.2_Missense_Mutation_p.H105Q|PDZD3_uc010rzd.1_Missense_Mutation_p.H92Q|PDZD3_uc001pwa.2_5'UTR			Q86UT5	NHRF4_HUMAN	RecName: Full=Na(+)/H(+) exchange regulatory cofactor NHE-RF4;          Short=NHERF-4; AltName: Full=PDZ domain-containing protein 3; AltName: Full=PDZ domain-containing protein 2; AltName: Full=Intestinal and kidney-enriched PDZ protein; AltName: Full=Sodium-hydrogen exchanger regulatory factor 4;	171	PDZ 1.				cGMP-mediated signaling|ion transport|negative regulation of cGMP biosynthetic process|response to toxin|water transport	apical part of cell|brush border|cytosol|membrane fraction|subapical complex	guanylate cyclase inhibitor activity|ion channel inhibitor activity|protein C-terminus binding			breast(1)	1	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)		TTGTGGAACACGAAGACTATG	0.597													3	57	---	---	---	---	PASS
OR10S1	219873	broad.mit.edu	37	11	123848361	123848361	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123848361G>T	uc001pzm.1	-	1	38	c.38C>A	c.(37-39)ACA>AAA	p.T13K		NM_001004474	NP_001004474	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S,	13	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GTTCTCCGTTGTCATGGTCAT	0.478													59	173	---	---	---	---	PASS
SCNN1A	6337	broad.mit.edu	37	12	6457292	6457292	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6457292C>T	uc001qnx.2	-	13	2046	c.1757G>A	c.(1756-1758)CGA>CAA	p.R586Q	SCNN1A_uc001qnv.2_Missense_Mutation_p.R286Q|SCNN1A_uc001qnw.2_Missense_Mutation_p.R645Q|SCNN1A_uc010sfb.1_Missense_Mutation_p.R609Q	NM_001038	NP_001029	P37088	SCNNA_HUMAN	sodium channel, nonvoltage-gated 1 alpha isoform	586	Cytoplasmic (By similarity).				excretion|response to stimulus|sensory perception of taste	apical plasma membrane	WW domain binding				0					Amiloride(DB00594)|Triamterene(DB00384)	TCGGAACCTTCGGAGCAGCAT	0.478													12	42	---	---	---	---	PASS
AICDA	57379	broad.mit.edu	37	12	8758017	8758017	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8758017C>T	uc001qur.2	-	3	300	c.221G>A	c.(220-222)CGC>CAC	p.R74H	AICDA_uc001qup.1_Missense_Mutation_p.R69H|AICDA_uc001quq.1_Missense_Mutation_p.R69H|AICDA_uc009zgd.1_Intron	NM_020661	NP_065712	Q9GZX7	AICDA_HUMAN	activation-induced cytidine deaminase	74					B cell differentiation|DNA demethylation|mRNA processing|negative regulation of methylation-dependent chromatin silencing	cytoplasm	cytidine deaminase activity|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung SC(5;0.184)					GCGGTAGCAGCGGCCAGGGTC	0.602									Immune_Deficiency_with_Hyper-IgM				45	59	---	---	---	---	PASS
HIST4H4	121504	broad.mit.edu	37	12	14924038	14924038	+	5'UTR	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14924038C>T	uc001rcf.3	-	1					HIST4H4_uc001rce.2_RNA	NM_175054	NP_778224	P62805	H4_HUMAN	histone cluster 4, H4						CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(2)	2						ACAGCGCCTACTCAGCAGAAA	0.562													27	63	---	---	---	---	PASS
PFDN5	5204	broad.mit.edu	37	12	53689313	53689313	+	5'UTR	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53689313G>A	uc001scl.2	+	1					PFDN5_uc001scm.2_5'UTR|PFDN5_uc001scn.2_RNA|PFDN5_uc001sco.2_RNA	NM_002624	NP_002615	Q99471	PFD5_HUMAN	prefoldin subunit 5 isoform alpha						'de novo' posttranslational protein folding|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent	nucleus|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)	1						AGCGTTGCTCGCCGAGAGACT	0.602													35	124	---	---	---	---	PASS
EPYC	1833	broad.mit.edu	37	12	91366748	91366748	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91366748G>C	uc001tbk.2	-	4	443	c.350C>G	c.(349-351)ACC>AGC	p.T117S		NM_004950	NP_004941	Q99645	EPYC_HUMAN	dermatan sulfate proteoglycan 3 precursor	117	LRRNT.				female pregnancy	proteinaceous extracellular matrix	glycosaminoglycan binding			skin(1)	1						CAAAAGACAGGTTGGAAAGTC	0.343													64	91	---	---	---	---	PASS
CCDC41	51134	broad.mit.edu	37	12	94772668	94772668	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94772668A>T	uc001tdd.2	-	7	1286	c.700T>A	c.(700-702)TTA>ATA	p.L234I	CCDC41_uc001tde.2_Missense_Mutation_p.L234I|CCDC41_uc009zsw.1_RNA|CCDC41_uc001tdf.2_Missense_Mutation_p.L234I	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen	226	Potential.										0						TCAGCCTTTAATTCCGCTACT	0.438													129	223	---	---	---	---	PASS
FAM179B	23116	broad.mit.edu	37	14	45431527	45431527	+	5'UTR	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45431527C>T	uc001wvv.2	+	1					FAM179B_uc001wvw.2_5'UTR|FAM179B_uc010anc.2_RNA|KLHL28_uc001wvq.2_5'Flank|KLHL28_uc001wvr.2_5'Flank|FAM179B_uc010anb.1_5'UTR|FAM179B_uc001wvu.2_5'UTR	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116								binding			skin(2)|upper_aerodigestive_tract(1)	3						GCCTCTTCTGCAGCTTGGGGC	0.612													10	5	---	---	---	---	PASS
DLGAP5	9787	broad.mit.edu	37	14	55643874	55643874	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55643874C>A	uc001xbs.2	-	8	1172	c.955G>T	c.(955-957)GGT>TGT	p.G319C	DLGAP5_uc001xbt.2_Missense_Mutation_p.G319C	NM_014750	NP_055565	Q15398	DLGP5_HUMAN	discs large homolog 7 isoform a	319					cell proliferation|cell-cell signaling|mitotic chromosome movement towards spindle pole|positive regulation of mitotic metaphase/anaphase transition	nucleus|spindle pole centrosome	phosphoprotein phosphatase activity|protein binding			ovary(1)|skin(1)	2						GTCTTCAGACCATCCAGTGGC	0.378													4	71	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	66479768	66479768	+	Missense_Mutation	SNP	A	C	C	rs1808975	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66479768A>C	uc001xit.2	-	1	865	c.740T>G	c.(739-741)CTC>CGC	p.L247R						SubName: Full=Nuclease sensitive element binding protein-1;																		CTGTCTTTGGAGAGGAGGGCC	0.532													3	60	---	---	---	---	PASS
SERPINA1	5265	broad.mit.edu	37	14	94844682	94844682	+	3'UTR	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94844682G>A	uc001ycx.3	-	5					SERPINA1_uc001ycw.3_RNA|SERPINA1_uc010auw.2_3'UTR|SERPINA1_uc010aux.2_3'UTR|SERPINA1_uc001ycy.3_3'UTR|SERPINA1_uc010auy.2_3'UTR|SERPINA1_uc001ycz.3_3'UTR|SERPINA1_uc010auz.2_3'UTR|SERPINA1_uc010ava.2_3'UTR|SERPINA1_uc001ydb.3_3'UTR|SERPINA1_uc010avb.2_3'UTR|SERPINA1_uc001ydc.3_3'UTR	NM_000295	NP_000286	P01009	A1AT_HUMAN	serine proteinase inhibitor, clade A, member 1						acute-phase response|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen|proteinaceous extracellular matrix	protease binding|serine-type endopeptidase inhibitor activity			skin(1)	1		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)	Alpha-1-proteinase inhibitor(DB00058)	AAACATGGGAGGGATTTACAG	0.572									Alpha-1-Antitrypsin_Deficiency				5	10	---	---	---	---	PASS
DMXL2	23312	broad.mit.edu	37	15	51791649	51791649	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51791649C>G	uc002abf.2	-	18	3997	c.3772G>C	c.(3772-3774)GGG>CGG	p.G1258R	DMXL2_uc010ufy.1_Missense_Mutation_p.G1258R|DMXL2_uc010bfa.2_Intron	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1258	WD 10.					cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)		ACCAATATCCCATCTCTTACC	0.413													148	91	---	---	---	---	PASS
LDHAL6B	92483	broad.mit.edu	37	15	59499176	59499176	+	Nonsense_Mutation	SNP	A	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59499176A>T	uc002agb.2	+	1	135	c.37A>T	c.(37-39)AGA>TGA	p.R13*	MYO1E_uc002aga.2_Intron	NM_033195	NP_149972	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	13					glycolysis	cytoplasm	L-lactate dehydrogenase activity|protein binding				0					NADH(DB00157)	GGCCAGCCAGAGAGTGAGCTC	0.587													10	8	---	---	---	---	PASS
ADAMTS7	11173	broad.mit.edu	37	15	79058756	79058756	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79058756G>C	uc002bej.3	-	19	3708	c.3497C>G	c.(3496-3498)GCC>GGC	p.A1166G	ADAMTS7_uc010und.1_3'UTR	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1166					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						AAGATCTGGGGCCCCTATGGG	0.632													5	22	---	---	---	---	PASS
C16orf71	146562	broad.mit.edu	37	16	4787820	4787820	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4787820A>C	uc002cxn.2	+	3	611	c.149A>C	c.(148-150)GAG>GCG	p.E50A		NM_139170	NP_631909	Q8IYS4	CP071_HUMAN	hypothetical protein LOC146562	50										central_nervous_system(1)	1						GGGGAAGAGGAGCTGTTCATC	0.597													35	162	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15083531	15083531	+	Intron	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15083531C>A	uc010uzl.1	+						PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002dda.3_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron|uc010bvd.1_5'UTR	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	gccacggggccAGGACCTGGG	0.617													3	13	---	---	---	---	PASS
DNAH3	55567	broad.mit.edu	37	16	21123085	21123085	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21123085G>T	uc010vbe.1	-	14	1961	c.1961C>A	c.(1960-1962)TCC>TAC	p.S654Y	DNAH3_uc002die.2_Missense_Mutation_p.S594Y	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	654	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		GATGTTCATGGATGCAATTTC	0.458													41	99	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	29110458	29110458	+	Intron	SNP	T	C	C	rs151074589	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29110458T>C	uc010vct.1	-						RRN3P2_uc002dsf.3_RNA|RRN3P2_uc002dsg.3_RNA|RRN3P2_uc010vdn.1_RNA					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		GAATTTTGAGTGGATAGTGAT	0.328													5	104	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90161578	90161578	+	Silent	SNP	G	A	A	rs13337896	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90161578G>A	uc002fqp.2	+	3	931	c.453G>A	c.(451-453)ACG>ACA	p.T151T	uc002fqq.2_Silent_p.T168T					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		GCCAAGGGACGCTACACCGAA	0.587													6	42	---	---	---	---	PASS
TNK1	8711	broad.mit.edu	37	17	7291835	7291835	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7291835G>T	uc002ggi.3	+	11	1763	c.1603G>T	c.(1603-1605)GGC>TGC	p.G535C	TNK1_uc002ggj.3_Missense_Mutation_p.G530C|TNK1_uc010cmf.2_RNA|TNK1_uc002ggk.3_Intron	NM_003985	NP_003976	Q13470	TNK1_HUMAN	tyrosine kinase, non-receptor, 1	535	Pro-rich.				protein autophosphorylation	membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(122;0.157)				GGGACCTCCAGGCCTGCCTCC	0.612													17	43	---	---	---	---	PASS
B9D1	27077	broad.mit.edu	37	17	19250621	19250621	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19250621A>C	uc002gvk.3	-	5	529	c.365T>G	c.(364-366)TTT>TGT	p.F122C	B9D1_uc010cqm.1_Missense_Mutation_p.L98V|B9D1_uc002gvl.3_Missense_Mutation_p.L98V|B9D1_uc010vyr.1_Missense_Mutation_p.L142V|B9D1_uc010vys.1_Missense_Mutation_p.L173V|MIR1180_hsa-mir-1180|MI0006273_5'Flank|B9D1_uc010cqn.1_Missense_Mutation_p.L173V	NM_015681	NP_056496	Q9UPM9	B9D1_HUMAN	B9 protein	122	B9.				cilium assembly	centrosome|microtubule basal body	protein binding				0	all_cancers(12;2.04e-05)|all_epithelial(12;0.000806)|Hepatocellular(7;0.00345)|Breast(13;0.143)					TTCTGGGACAAACATGGGGAT	0.463													32	100	---	---	---	---	PASS
PHF12	57649	broad.mit.edu	37	17	27250942	27250942	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27250942T>C	uc002hdg.1	-	4	1230	c.700A>G	c.(700-702)ACC>GCC	p.T234A	PHF12_uc010wbb.1_Missense_Mutation_p.T216A|PHF12_uc002hdi.1_Missense_Mutation_p.T230A|PHF12_uc002hdj.1_Missense_Mutation_p.T234A|PHF12_uc010crw.1_Intron|uc002hdl.2_5'Flank|PHF12_uc002hdh.1_Missense_Mutation_p.T17A	NM_001033561	NP_001028733	Q96QT6	PHF12_HUMAN	PHD finger protein 12 isoform 1	234	Interaction with SIN3A.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	protein binding|zinc ion binding			ovary(1)	1	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			AGTGCAGTGGTACAAGTCAGT	0.562													18	18	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29556075	29556075	+	Silent	SNP	G	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29556075G>A	uc002hgg.2	+	21	2775	c.2442G>A	c.(2440-2442)AAG>AAA	p.K814K	NF1_uc002hgh.2_Silent_p.K814K|NF1_uc010csn.1_Silent_p.K674K|NF1_uc002hgi.1_5'UTR	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	814					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CCATTGTTAAGAGGCGAATGT	0.418			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			17	69	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29687570	29687570	+	Nonsense_Mutation	SNP	C	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29687570C>G	uc002hgg.2	+	57	8559	c.8226C>G	c.(8224-8226)TAC>TAG	p.Y2742*	NF1_uc002hgh.2_Nonsense_Mutation_p.Y2721*|NF1_uc010cso.2_Nonsense_Mutation_p.Y930*|NF1_uc010wbt.1_Nonsense_Mutation_p.Y220*|NF1_uc010wbu.1_RNA	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2742					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTGACACGTACCTGCCTGGAA	0.428			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			79	131	---	---	---	---	PASS
KRTAP4-9	100132386	broad.mit.edu	37	17	39261693	39261693	+	Missense_Mutation	SNP	A	T	T	rs113059833	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39261693A>T	uc010wfp.1	+	1	53	c.53A>T	c.(52-54)GAC>GTC	p.D18V		NM_001146041	NP_001139513	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	18						keratin filament					0						TGCGGCCAAGACCTCTGTCAG	0.627													8	42	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45234696	45234696	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45234696C>A	uc002ild.3	-	6	657	c.530G>T	c.(529-531)AGC>ATC	p.S177I	CDC27_uc002ile.3_Missense_Mutation_p.S177I|CDC27_uc002ilf.3_Missense_Mutation_p.S177I|CDC27_uc010wkp.1_Missense_Mutation_p.S116I|CDC27_uc010wkq.1_RNA	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	177					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						CAGACAGTTGCTAAAGTTCTG	0.398													8	139	---	---	---	---	PASS
RSAD1	55316	broad.mit.edu	37	17	48562232	48562232	+	3'UTR	SNP	T	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48562232T>A	uc002iqw.1	+	9					RSAD1_uc010wmq.1_RNA	NM_018346	NP_060816	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing						porphyrin biosynthetic process	mitochondrion	4 iron, 4 sulfur cluster binding|coproporphyrinogen oxidase activity|metal ion binding				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			ACAAAAATGTTCCTGTGTTCC	0.572													27	19	---	---	---	---	PASS
FBF1	85302	broad.mit.edu	37	17	73913852	73913852	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73913852C>T	uc002jqc.2	-	22	2695	c.2421G>A	c.(2419-2421)ATG>ATA	p.M807I	FBF1_uc002jqa.1_RNA|FBF1_uc010wsp.1_Missense_Mutation_p.M798I|FBF1_uc002jqd.1_Missense_Mutation_p.M808I|FBF1_uc002jqb.2_RNA|FBF1_uc010dgr.1_Missense_Mutation_p.M118I	NM_001080542	NP_001074011	Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	807											0						GCCGTGCCTCCATCTTCCCGA	0.697													7	13	---	---	---	---	PASS
MAP2K7	5609	broad.mit.edu	37	19	7977212	7977212	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7977212C>A	uc002mit.2	+	11	1221	c.1156C>A	c.(1156-1158)CTG>ATG	p.L386M	MAP2K7_uc002miv.2_Missense_Mutation_p.L393M|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Missense_Mutation_p.L393M|MAP2K7_uc010dvv.2_Missense_Mutation_p.L261M	NM_145185	NP_660186	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	386					activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus	ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1)	11					Etoposide(DB00773)	CTACGAGACGCTGGAGGTGGA	0.652													34	51	---	---	---	---	PASS
ZNF347	84671	broad.mit.edu	37	19	53644453	53644453	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53644453C>A	uc002qbb.1	-	5	1697	c.1628G>T	c.(1627-1629)TGT>TTT	p.C543F	ZNF347_uc010eql.1_Missense_Mutation_p.C544F|ZNF347_uc002qbc.1_Missense_Mutation_p.C544F	NM_032584	NP_115973	Q96SE7	ZN347_HUMAN	zinc finger protein 347	543	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0179)		GCACTCATTACACATATAAGG	0.398													128	211	---	---	---	---	PASS
SNRPB	6628	broad.mit.edu	37	20	2448399	2448399	+	Silent	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2448399C>A	uc002wfz.1	-	2	172	c.9G>T	c.(7-9)GTG>GTT	p.V3V	SNRPB_uc002wga.1_Silent_p.V3V|SNRPB_uc010zpv.1_5'UTR|SNRPB_uc002wgb.2_Silent_p.V3V|SNRPB_uc010gan.2_Silent_p.V3V	NM_198216	NP_937859	P14678	RSMB_HUMAN	small nuclear ribonucleoprotein polypeptide B/B'	3					histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|protein binding|RNA binding			ovary(1)	1						TGCTCTTGCCCACCGTCTGCA	0.532													50	83	---	---	---	---	PASS
MAVS	57506	broad.mit.edu	37	20	3845153	3845153	+	Silent	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3845153C>T	uc002wjw.3	+	6	1045	c.876C>T	c.(874-876)AAC>AAT	p.N292N	MAVS_uc002wjx.3_Silent_p.N151N|MAVS_uc002wjy.3_5'UTR	NM_020746	NP_065797	Q7Z434	MAVS_HUMAN	virus-induced signaling adapter	292	Cytoplasmic (Probable).				activation of innate immune response|cellular response to exogenous dsRNA|defense response to bacterium|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of chemokine (C-C motif) ligand 5 production|positive regulation of defense response to virus by host|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interleukin-8 production|positive regulation of IP-10 production|positive regulation of protein import into nucleus, translocation|positive regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|response to virus	integral to membrane|mitochondrial outer membrane	CARD domain binding|protein kinase binding|signal transducer activity				0						CACCTGCCAACTCTCTGCCCT	0.602													33	73	---	---	---	---	PASS
KIF16B	55614	broad.mit.edu	37	20	16359478	16359478	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16359478G>C	uc002wpg.1	-	19	3327	c.3169C>G	c.(3169-3171)CAG>GAG	p.Q1057E	KIF16B_uc002wpe.1_Missense_Mutation_p.Q439E|KIF16B_uc002wpf.1_Missense_Mutation_p.Q439E|KIF16B_uc010gch.1_Missense_Mutation_p.Q1057E|KIF16B_uc010gci.1_Missense_Mutation_p.Q1057E|KIF16B_uc010gcj.1_Missense_Mutation_p.Q1068E	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23	1057	Glu-rich.|Potential.			EQ -> SE (in Ref. 6; AAH34984).	cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity	p.Q1057*(1)		skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						AGGGCTTCCTGCTCAGCCTCC	0.557													107	172	---	---	---	---	PASS
PLTP	5360	broad.mit.edu	37	20	44531163	44531163	+	Silent	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44531163G>T	uc002xqn.1	-	11	1103	c.1023C>A	c.(1021-1023)GGC>GGA	p.G341G	PLTP_uc002xql.1_Silent_p.G253G|PLTP_uc002xqm.1_Silent_p.G361G|PLTP_uc002xqo.1_Silent_p.G289G|PLTP_uc002xqp.1_Silent_p.G341G|PLTP_uc002xqq.1_Silent_p.G310G|PLTP_uc010zxj.1_Silent_p.G246G|PLTP_uc010ghj.1_Silent_p.G341G	NM_006227	NP_006218	P55058	PLTP_HUMAN	phospholipid transfer protein isoform a	341					cellular lipid metabolic process|lipid transport	extracellular region	lipid binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				AGATGGTGGTGCCAGAGGGCT	0.627													29	138	---	---	---	---	PASS
TUBB1	81027	broad.mit.edu	37	20	57599336	57599336	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57599336C>T	uc002yak.2	+	4	1123	c.854C>T	c.(853-855)TCC>TTC	p.S285F		NM_030773	NP_110400	Q9H4B7	TBB1_HUMAN	beta tubulin 1, class VI	285					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity			ovary(1)	1	all_lung(29;0.00711)		Colorectal(105;0.109)		Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	CGAGCCCTCTCCGTGGCCGAG	0.647													20	48	---	---	---	---	PASS
RGS19	10287	broad.mit.edu	37	20	62705068	62705068	+	3'UTR	SNP	C	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62705068C>T	uc002yhy.2	-	6					RGS19_uc002yhz.2_3'UTR|RGS19_uc002yia.2_3'UTR|RGS19_uc002yib.2_3'UTR	NM_005873	NP_005864	P49795	RGS19_HUMAN	G protein signalling regulator 19						autophagy|G-protein coupled receptor protein signaling pathway|negative regulation of signal transduction|small GTPase mediated signal transduction	Golgi apparatus|membrane fraction|plasma membrane	GTPase activator activity|protein binding|signal transducer activity			skin(1)	1	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)					GCACTCCCCACTGGGTCTAGG	0.697													4	4	---	---	---	---	PASS
DMD	1756	broad.mit.edu	37	X	31241191	31241191	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31241191G>T	uc004dda.1	-	64	9578	c.9334C>A	c.(9334-9336)CTC>ATC	p.L3112I	DMD_uc004dcq.1_Missense_Mutation_p.L383I|DMD_uc004dcr.1_Missense_Mutation_p.L652I|DMD_uc004dcs.1_Missense_Mutation_p.L652I|DMD_uc004dct.1_Missense_Mutation_p.L652I|DMD_uc004dcu.1_Missense_Mutation_p.L652I|DMD_uc004dcv.1_Missense_Mutation_p.L652I|DMD_uc004dcw.2_Missense_Mutation_p.L1768I|DMD_uc004dcx.2_Missense_Mutation_p.L1771I|DMD_uc004dcz.2_Missense_Mutation_p.L2989I|DMD_uc004dcy.1_Missense_Mutation_p.L3108I|DMD_uc004ddb.1_Missense_Mutation_p.L3104I|DMD_uc004dcm.1_Missense_Mutation_p.L44I|DMD_uc004dcn.1_Missense_Mutation_p.L44I|DMD_uc004dco.1_Missense_Mutation_p.L44I|DMD_uc004dcp.1_Missense_Mutation_p.L44I|DMD_uc011mkb.1_Missense_Mutation_p.L44I|DMD_uc010ngm.2_Missense_Mutation_p.L44I	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	3112	Interaction with SYNM (By similarity).				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AGTCTTCGGAGTTTCATGGCA	0.383													75	130	---	---	---	---	PASS
CACNA1F	778	broad.mit.edu	37	X	49071873	49071873	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49071873C>A	uc004dnb.2	-	28	3462	c.3400G>T	c.(3400-3402)GGC>TGC	p.G1134C	CACNA1F_uc010nip.2_Missense_Mutation_p.G1123C	NM_005183	NP_005174	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type,	1134	Dihydropyridine binding (By similarity).|III.|Cytoplasmic (Potential).				axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)	ATGACGAAGCCCACGAAGATG	0.502													4	61	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2581	2581	+	5'Flank	SNP	A	G	G			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2581A>G	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		CCGCGGTACCCTAACCGTGCA	0.294													4	5	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	8928	8928	+	RNA	SNP	T	C	C			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:8928T>C	uc011mfi.1	+	1		c.266T>C			uc004cov.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		CAAGGCACACCTACACCCCTT	0.493													3	3	---	---	---	---	PASS
AGRN	375790	broad.mit.edu	37	1	985444	985444	+	Intron	DEL	G	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:985444delG	uc001ack.1	+							NM_198576	NP_940978	O00468	AGRIN_HUMAN	agrin precursor						axon guidance|clustering of voltage-gated sodium channels|muscarinic acetylcholine receptor signaling pathway|receptor clustering	basal lamina	laminin binding|structural constituent of cytoskeleton			central_nervous_system(2)|breast(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		TCTCGGGGCAGGGGGGGGGGG	0.657													4	3	---	---	---	---	
CDK11B	984	broad.mit.edu	37	1	1600092	1600093	+	Intron	DEL	TG	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1600092_1600093delTG	uc001agv.1	-						CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc009vkl.1_Intron|SLC35E2B_uc001ahe.3_Intron|SLC35E2B_uc001ahf.3_Intron|SLC35E2B_uc001ahg.3_Intron|SLC35E2B_uc001ahh.3_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						CTGTTTTTTTTGTTTGTTTGTT	0.317													5	5	---	---	---	---	
SLC35E2B	728661	broad.mit.edu	37	1	1666447	1666448	+	Intron	INS	-	TTTT	TTTT	rs112262693		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1666447_1666448insTTTT	uc001ahh.3	-						SLC35E2_uc009vkm.1_Intron|SLC35E2_uc001ahy.2_Intron|SLC35E2_uc001ahz.2_Intron|SLC35E2_uc001aib.1_Intron	NM_001110781	NP_001104251	P0CK96	S352B_HUMAN	similar to solute carrier family 35, member E2							integral to membrane					0						TCCATTTTCTGTTTTTTGTTTG	0.337													4	2	---	---	---	---	
TARDBP	23435	broad.mit.edu	37	1	11080808	11080808	+	Intron	DEL	A	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11080808delA	uc001art.2	+						TARDBP_uc010oap.1_Intron	NM_007375	NP_031401	Q13148	TADBP_HUMAN	TAR DNA binding protein						3'-UTR-mediated mRNA stabilization|cell death|mRNA processing|negative regulation by host of viral transcription|RNA splicing|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|mRNA 3'-UTR binding|nucleotide binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0578)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.37e-07)|COAD - Colon adenocarcinoma(227;7.38e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)		attaaaatacaaaaaaaaaaa	0.000													9	4	---	---	---	---	
C1orf63	57035	broad.mit.edu	37	1	25573155	25573160	+	In_Frame_Del	DEL	GAACCC	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25573155_25573160delGAACCC	uc001bjw.2	-	2	547_552	c.295_300delGGGTTC	c.(295-300)GGGTTCdel	p.GF99del		NM_020317	NP_064713	Q9BUV0	CA063_HUMAN	hypothetical protein LOC57035	99_100	Arg-rich.									pancreas(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ATCTCCTGGTGAACCCGTAGCGCCTC	0.670													56	36	---	---	---	---	
GMEB1	10691	broad.mit.edu	37	1	29023320	29023320	+	Intron	DEL	T	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29023320delT	uc001bra.2	+						GMEB1_uc001bqz.2_Intron|GMEB1_uc001brb.2_Intron	NM_006582	NP_006573	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|metal ion binding|transcription coactivator activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		TCTAACACTATTAGGTTTCAC	0.418													20	15	---	---	---	---	
IPP	3652	broad.mit.edu	37	1	46180107	46180115	+	In_Frame_Del	DEL	ATTGCTGAT	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46180107_46180115delATTGCTGAT	uc001cou.2	-	8	1600_1608	c.1333_1341delATCAGCAAT	c.(1333-1341)ATCAGCAATdel	p.ISN445del	IPP_uc001cos.3_In_Frame_Del_p.ISN445del	NM_005897	NP_005888	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	445_447	Kelch 4.					actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					CTATTCCTTCATTGCTGATGCCCCCAATT	0.388													63	33	---	---	---	---	
IL23R	149233	broad.mit.edu	37	1	67672567	67672568	+	Intron	INS	-	T	T	rs79547341		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67672567_67672568insT	uc001ddo.2	+						IL23R_uc009waz.2_Intron|IL23R_uc001ddp.2_Intron|IL23R_uc010opi.1_Intron|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Intron|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_Intron|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Intron|IL23R_uc001ddr.2_Intron|IL23R_uc010opo.1_Intron|IL23R_uc010opp.1_Intron|IL23R_uc010opq.1_Intron|IL23R_uc010opr.1_Intron|IL23R_uc010ops.1_Intron|IL23R_uc010opt.1_Intron|IL23R_uc010opu.1_Intron|IL23R_uc010opv.1_Intron|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_Intron|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_Intron|IL23R_uc010oqb.1_Intron|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_Intron|IL23R_uc010oqf.1_Intron|IL23R_uc010oqg.1_Intron|IL23R_uc010oqh.1_Intron|IL23R_uc001dds.2_5'Flank|IL23R_uc001ddt.2_5'Flank	NM_144701	NP_653302	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor precursor						inflammatory response|negative regulation of interleukin-10 production|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|response to interferon-gamma|response to lipopolysaccharide	interleukin-23 receptor complex	receptor activity				0						ACAGCCAGGTCttttttttttt	0.351													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149237657	149237662	+	IGR	DEL	TGTGTG	-	-	rs3066030		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149237657_149237662delTGTGTG								LOC645166 (284603 upstream) : LOC388692 (41814 downstream)																							agagccccaatgtgtgtgtgtgtgtg	0.000													4	2	---	---	---	---	
DENND4B	9909	broad.mit.edu	37	1	153911626	153911628	+	Intron	DEL	AAG	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153911626_153911628delAAG	uc001fdd.1	-							NM_014856	NP_055671	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B											ovary(1)	1	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CTCAGGCCCAAAGCCATAATCTC	0.562													6	3	---	---	---	---	
THBS3	7059	broad.mit.edu	37	1	155170157	155170159	+	Intron	DEL	AGA	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155170157_155170159delAGA	uc001fix.2	-						RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Intron|THBS3_uc001fiz.2_Intron|THBS3_uc001fiy.2_Intron|THBS3_uc010pfu.1_Intron|THBS3_uc010pfv.1_Intron	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor						cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TATTTCACAGAGACTTCCTAGCT	0.567													62	68	---	---	---	---	
F5	2153	broad.mit.edu	37	1	169526261	169526262	+	Intron	INS	-	A	A	rs148401141	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169526261_169526262insA	uc001ggg.1	-						F5_uc010plr.1_Intron	NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor						cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	ttgtgccctgcaaaagcagaca	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	227032866	227032869	+	IGR	DEL	AGGA	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227032866_227032869delAGGA								ITPKB (105990 upstream) : PSEN2 (25404 downstream)																							aaagaaaGACaggaaggaaggaag	0.010													3	3	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237944853	237944855	+	Intron	DEL	TCA	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237944853_237944855delTCA	uc001hyl.1	+						RYR2_uc010pya.1_Intron	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AATGCAATGTTCATATTTTCAGG	0.355													19	9	---	---	---	---	
WDR64	128025	broad.mit.edu	37	1	241920952	241920953	+	Intron	DEL	TT	-	-	rs35256499		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241920952_241920953delTT	uc001hzf.1	+						WDR64_uc001hzg.1_Intron	NM_144625	NP_653226	B1ANS9	WDR64_HUMAN	WD repeat domain 64											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			aatggatttgtttttttttttt	0.000													7	4	---	---	---	---	
ITSN2	50618	broad.mit.edu	37	2	24433483	24433484	+	Intron	INS	-	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24433483_24433484insA	uc002rfe.2	-						ITSN2_uc002rff.2_Intron	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1						endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					gactccgtctcaaaaaaaaaaa	0.223													5	4	---	---	---	---	
PPM1G	5496	broad.mit.edu	37	2	27605696	27605697	+	Intron	INS	-	T	T	rs111310967		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27605696_27605697insT	uc002rkl.2	-						ZNF513_uc002rkj.2_5'Flank|ZNF513_uc002rkk.2_5'Flank|PPM1G_uc002rkm.2_Intron	NM_002707	NP_002698	O15355	PPM1G_HUMAN	protein phosphatase 1G						cell cycle arrest|protein dephosphorylation	cytoplasm|nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					agtcttttttgttttttttttt	0.025													4	3	---	---	---	---	
THADA	63892	broad.mit.edu	37	2	43793963	43793964	+	Intron	INS	-	AA	AA			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43793963_43793964insAA	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron|THADA_uc010fat.1_Intron|THADA_uc002rta.2_Intron|THADA_uc002rtb.1_Intron|THADA_uc002rtc.3_Intron|THADA_uc002rtd.2_Intron	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				ATGAAATTCttaaaaaaaaaaa	0.287													13	6	---	---	---	---	
TMEM87B	84910	broad.mit.edu	37	2	112870703	112870706	+	Intron	DEL	TACT	-	-	rs142414944		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112870703_112870706delTACT	uc002thm.2	+							NM_032824	NP_116213	Q96K49	TM87B_HUMAN	transmembrane protein 87B precursor							integral to membrane					0						ACAAGATAAATACTTACTGGTATG	0.294													9	7	---	---	---	---	
NCKAP1	10787	broad.mit.edu	37	2	183867776	183867776	+	Intron	DEL	T	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183867776delT	uc002upc.2	-						NCKAP1_uc002upb.2_Intron	NM_013436	NP_038464	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 1						apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			GAAATACTTATTTTAATCTTT	0.264													62	37	---	---	---	---	
ANKRD44	91526	broad.mit.edu	37	2	197953472	197953473	+	Frame_Shift_Ins	INS	-	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197953472_197953473insT	uc002uua.1	-	12	1211_1212	c.1134_1135insA	c.(1132-1137)AAATTTfs	p.K378fs	ANKRD44_uc002utz.3_Frame_Shift_Ins_p.K110fs|ANKRD44_uc002uub.2_Frame_Shift_Ins_p.K403fs|ANKRD44_uc010zgw.1_Frame_Shift_Ins_p.K331fs	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	403_404	ANK 13.						protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTTCTTCCAAATTTATCTGGGG	0.381													146	66	---	---	---	---	
MLPH	79083	broad.mit.edu	37	2	238419911	238419912	+	Intron	DEL	TT	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238419911_238419912delTT	uc002vwt.2	+						MLPH_uc002vws.2_Intron|MLPH_uc010fyt.1_Intron|MLPH_uc002vwu.2_Intron|MLPH_uc002vwv.2_Intron|MLPH_uc002vww.2_Intron	NM_024101	NP_077006	Q9BV36	MELPH_HUMAN	melanophilin isoform 1								metal ion binding			ovary(1)	1		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		TTCTGGCTGCtttttttttttt	0.104													11	6	---	---	---	---	
SNED1	25992	broad.mit.edu	37	2	242007465	242007465	+	Intron	DEL	A	-	-	rs145826495	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242007465delA	uc002wah.1	+						SNED1_uc002wai.1_Intron|SNED1_uc002waj.1_Intron|SNED1_uc002wak.2_Intron	NM_001080437	NP_001073906	Q8TER0	SNED1_HUMAN	6720455I24Rik homolog precursor						cell-matrix adhesion	extracellular region	calcium ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		TGTGGACTGTACCACCTGCCG	0.652													4	2	---	---	---	---	
COL7A1	1294	broad.mit.edu	37	3	48615597	48615598	+	Intron	INS	-	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48615597_48615598insA	uc003ctz.2	-							NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor						cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		aactccatctcaaaaaaaaaaa	0.213													4	3	---	---	---	---	
C3orf1	51300	broad.mit.edu	37	3	119217940	119217940	+	Intron	DEL	T	-	-	rs34000460		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119217940delT	uc003ecn.2	+						C3orf1_uc003eco.2_Intron|C3orf1_uc003ecp.2_Intron	NM_016589	NP_057673	Q9NPL8	TIDC1_HUMAN	hypothetical protein LOC51300							integral to membrane|mitochondrial inner membrane	protein transporter activity				0				GBM - Glioblastoma multiforme(114;0.186)		tttttctttcttttttttttt	0.184													4	4	---	---	---	---	
POLQ	10721	broad.mit.edu	37	3	121238522	121238523	+	Intron	INS	-	A	A	rs80321773		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121238522_121238523insA	uc003eee.3	-							NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta						DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		gactccgtctcaaaaaaaaaaa	0.099								DNA_polymerases_(catalytic_subunits)					8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	57554288	57554290	+	IGR	DEL	AGG	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57554288_57554290delAGG								HOPX (6416 upstream) : SPINK2 (121744 downstream)																							gaaggaaaaaaggagggagggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	68265711	68265711	+	IGR	DEL	C	-	-	rs55759050		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68265711delC								None (None upstream) : CENPC1 (72278 downstream)																							acgaaggacacaaagaggtcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84326631	84326632	+	IGR	DEL	GT	-	-	rs71659573		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84326631_84326632delGT								HPSE (70325 upstream) : HELQ (1869 downstream)																							TGATAGAAGAgtgtgtgtgtgt	0.297													4	2	---	---	---	---	
EGF	1950	broad.mit.edu	37	4	110925370	110925371	+	Intron	DEL	AT	-	-	rs35428416		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110925370_110925371delAT	uc003hzy.3	+						EGF_uc011cfu.1_Intron|EGF_uc011cfv.1_Intron|EGF_uc010imk.2_Intron	NM_001963	NP_001954	P01133	EGF_HUMAN	epidermal growth factor precursor						angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)	ATGGGcatacatacacacacac	0.193													4	2	---	---	---	---	
LRBA	987	broad.mit.edu	37	4	151642665	151642666	+	Intron	INS	-	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151642665_151642666insT	uc010ipj.2	-						LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron	NM_006726	NP_006717	P50851	LRBA_HUMAN	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)					GAAGAACTGGGTTTTTTTTTTT	0.282													3	3	---	---	---	---	
PDZD2	23037	broad.mit.edu	37	5	32077366	32077366	+	Intron	DEL	A	-	-	rs34030551		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32077366delA	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						tttagagttgaaaaaaatgga	0.000													4	2	---	---	---	---	
RAPGEF6	51735	broad.mit.edu	37	5	130996913	130996914	+	Intron	INS	-	TG	TG	rs34731837		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130996913_130996914insTG	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		tgtctttgttttgtgtgtgtgt	0.000													4	2	---	---	---	---	
FLT4	2324	broad.mit.edu	37	5	180051227	180051227	+	Intron	DEL	G	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180051227delG	uc003mma.3	-						FLT4_uc003mlz.3_Intron|FLT4_uc003mmb.1_Intron|FLT4_uc011dgy.1_Intron	NM_002020	NP_002011	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 2						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|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)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)	GGACTTTGGTGtttttttttt	0.313									Congenital_Hereditary_Lymphedema				10	5	---	---	---	---	
BTNL9	153579	broad.mit.edu	37	5	180486891	180486892	+	3'UTR	INS	-	G	G	rs151240170	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180486891_180486892insG	uc003mmt.2	+	11						NM_152547	NP_689760	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9 precursor							integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGACTGGCCCCGGGGGGCCCCC	0.683													2	11	---	---	---	---	
DST	667	broad.mit.edu	37	6	56333733	56333733	+	Intron	DEL	A	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56333733delA	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pcw.3_5'Flank|DST_uc003pcx.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AATTAAAGTTAAAAAAAAATC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57659470	57659471	+	IGR	DEL	TA	-	-	rs79867563	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57659470_57659471delTA								ZNF716 (126205 upstream) : None (None downstream)																							GCGTTGATCTTACAGTCTGGTG	0.371													8	5	---	---	---	---	
TTC26	79989	broad.mit.edu	37	7	138857972	138857972	+	Intron	DEL	T	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138857972delT	uc003vus.2	+						TTC26_uc011kqn.1_Intron|TTC26_uc011kqo.1_Intron|TTC26_uc011kqp.1_Intron|TTC26_uc003vut.2_Intron|TTC26_uc011kqq.1_Intron	NM_024926	NP_079202	A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26 isoform 1								binding			ovary(1)	1						CAAAGTCACCttttttttttt	0.204													4	3	---	---	---	---	
OR2A9P	441295	broad.mit.edu	37	7	143980083	143980083	+	Intron	DEL	G	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143980083delG	uc003wec.1	-											SubName: Full=Seven transmembrane helix receptor;												0						CACAGCCATAGGGCTTGGGAA	0.532													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	4985367	4985367	+	IGR	DEL	T	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4985367delT								CSMD1 (133039 upstream) : None (None downstream)																							ctgacgcttcttttttttttt	0.224													3	3	---	---	---	---	
MED30	90390	broad.mit.edu	37	8	118535435	118535435	+	Intron	DEL	T	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118535435delT	uc003yoj.2	+						MED30_uc011lib.1_Intron	NM_080651	NP_542382	Q96HR3	MED30_HUMAN	TRAP/Mediator complex component TRAP25						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding				0	all_cancers(13;3.41e-25)|Lung NSC(37;3.02e-05)|Ovarian(258;0.00163)		STAD - Stomach adenocarcinoma(47;0.0266)			CAAAGCCAACTTTTTTTTTTT	0.303													4	5	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139701401	139701402	+	Intron	INS	-	G	G	rs149093007	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139701401_139701402insG	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GCTGCTCTCCCGGGGGGGGGGC	0.545										HNSCC(7;0.00092)			6	3	---	---	---	---	
MRC1	4360	broad.mit.edu	37	10	18122472	18122473	+	Intron	INS	-	AA	AA			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18122472_18122473insAA	uc001ipm.2	+							NM_002438	NP_002429	P22897	MRC1_HUMAN	mannose receptor C type 1 precursor						receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0						gactctgtctcaaaaaaaaaaa	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	27620447	27620448	+	IGR	INS	-	TT	TT	rs142562667	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27620447_27620448insTT								LOC387646 (79212 upstream) : PTCHD3 (66669 downstream)																							ACTCAGGCTTCTTTCCGCCAAG	0.465													4	2	---	---	---	---	
ANKRD1	27063	broad.mit.edu	37	10	92676188	92676189	+	Intron	DEL	TG	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92676188_92676189delTG	uc001khe.1	-							NM_014391	NP_055206	Q15327	ANKR1_HUMAN	cardiac ankyrin repeat protein						cellular lipid metabolic process|defense response|signal transduction		DNA binding				0		Colorectal(252;0.0475)				CTAAATTACAtgtgtgtgtgtg	0.248													4	2	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	128836112	128836112	+	Intron	DEL	C	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128836112delC	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		CTTTTTGGGTCtttttttttt	0.393													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119723392	119723393	+	IGR	INS	-	GA	GA			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119723392_119723393insGA								PVRL1 (123957 upstream) : TRIM29 (258602 downstream)																							tgtgtgtgtgtgtgCAAGTGCT	0.089													3	4	---	---	---	---	
FOXRED1	55572	broad.mit.edu	37	11	126141134	126141135	+	Intron	INS	-	AAGG	AAGG	rs141438450	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126141134_126141135insAAGG	uc001qdi.2	+						SRPR_uc001qdh.2_5'Flank|SRPR_uc010sbm.1_5'Flank|FOXRED1_uc010sbn.1_Intron|FOXRED1_uc010sbo.1_Intron|FOXRED1_uc010sbp.1_Intron|FOXRED1_uc010sbq.1_Intron|FOXRED1_uc001qdj.2_Intron|FOXRED1_uc010sbr.1_Intron|FOXRED1_uc001qdk.2_5'UTR	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing							integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		CAATGCATGAAGAGACTGATGG	0.342													3	5	---	---	---	---	
CLEC1A	51267	broad.mit.edu	37	12	10225700	10225701	+	Intron	DEL	AC	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10225700_10225701delAC	uc001qxb.2	-						CLEC1A_uc009zhf.2_Intron|CLEC1A_uc001qxc.2_Intron|CLEC1A_uc001qxd.2_Intron|CLEC1A_uc010sgx.1_Intron	NM_016511	NP_057595	Q8NC01	CLC1A_HUMAN	C-type lectin-like receptor-1						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane|intracellular	sugar binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2						AAACGAACAAACACACACACAC	0.223													4	2	---	---	---	---	
CSDA	8531	broad.mit.edu	37	12	10870901	10870901	+	Intron	DEL	C	-	-	rs11309033		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10870901delC	uc001qyt.2	-						CSDA_uc001qyu.2_Intron	NM_003651	NP_003642	P16989	DBPA_HUMAN	cold shock domain protein A isoform a						negative regulation of transcription from RNA polymerase II promoter|response to cold	cytoplasm|nucleus	double-stranded DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|lung(1)|large_intestine(1)	4	Glioma(1;0.155)					CCACAGGCCACCCACCTTCCT	0.418													1	6	---	---	---	---	
FAIM2	23017	broad.mit.edu	37	12	50291547	50291548	+	Intron	INS	-	C	C	rs144837790	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50291547_50291548insC	uc001rvj.1	-						FAIM2_uc001rvi.1_Intron|FAIM2_uc001rvk.1_Intron	NM_012306	NP_036438	Q9BWQ8	FAIM2_HUMAN	Fas apoptotic inhibitory molecule 2						anti-apoptosis|apoptosis	cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|ovary(1)|skin(1)	3						AGCCAAGCGCACCCCCCCCCAG	0.564													1	5	---	---	---	---	
CDK2	1017	broad.mit.edu	37	12	56363264	56363265	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56363264_56363265delGA	uc001sit.3	+	5	729_730	c.492_493delGA	c.(490-495)GTGACCfs	p.V164fs	CDK2_uc001siu.3_Intron|CDK2_uc010spy.1_Intron	NM_001798	NP_001789	P24941	CDK2_HUMAN	cyclin-dependent kinase 2 isoform 1	164_165	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|blood coagulation|cell division|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA replication|G1/S transition of mitotic cell cycle|G2 phase of mitotic cell cycle|G2/M transition of mitotic cell cycle|histone phosphorylation|M/G1 transition of mitotic cell cycle|mitosis|positive regulation of cell proliferation|Ras protein signal transduction|regulation of DNA replication|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|traversing start control point of mitotic cell cycle	cyclin-dependent protein kinase holoenzyme complex|cytosol	ATP binding|cyclin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2			UCEC - Uterine corpus endometrioid carcinoma (6;0.123)|OV - Ovarian serous cystadenocarcinoma(18;0.235)			CTCAGGTGGTGACCCTGTGGTA	0.535													68	37	---	---	---	---	
MON2	23041	broad.mit.edu	37	12	62950042	62950043	+	Intron	DEL	TC	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62950042_62950043delTC	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srf.2_Intron	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		tacagaCGATTCTTTTAGAGTC	0.208													14	10	---	---	---	---	
FRS2	10818	broad.mit.edu	37	12	69965989	69965989	+	Frame_Shift_Del	DEL	T	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69965989delT	uc001suy.2	+	9	1014	c.504delT	c.(502-504)CCTfs	p.P168fs	FRS2_uc001suz.2_Frame_Shift_Del_p.P168fs|FRS2_uc009zrj.2_Frame_Shift_Del_p.P168fs|FRS2_uc009zrk.2_Frame_Shift_Del_p.P168fs	NM_006654	NP_006645	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	168					activation of MAPKK activity|activation of phospholipase C activity|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|transmembrane receptor protein tyrosine phosphatase signaling pathway	endomembrane system|endosome|integral to plasma membrane|membrane fraction	fibroblast growth factor receptor binding|insulin receptor binding|phosphatase activator activity|transmembrane receptor protein tyrosine kinase adaptor activity			prostate(1)|kidney(1)	2	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			GCAGACATCCTTCTGTGGGAA	0.478													102	86	---	---	---	---	
HIP1R	9026	broad.mit.edu	37	12	123338888	123338888	+	Intron	DEL	A	-	-	rs34386328		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123338888delA	uc001udj.1	+						HIP1R_uc001udg.1_Intron|HIP1R_uc001udi.1_Intron|HIP1R_uc001udk.1_5'Flank	NM_003959	NP_003950	O75146	HIP1R_HUMAN	huntingtin interacting protein-1-related						receptor-mediated endocytosis	clathrin coated vesicle membrane|coated pit|perinuclear region of cytoplasm	actin binding|phosphatidylinositol binding			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		atattttatgaaaaaaaaaaa	0.045													6	3	---	---	---	---	
PIBF1	10464	broad.mit.edu	37	13	73372279	73372279	+	Intron	DEL	G	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73372279delG	uc001vjc.2	+						PIBF1_uc001vja.1_Intron|PIBF1_uc010aeo.1_Intron|PIBF1_uc001vjb.2_Intron|PIBF1_uc010aep.2_Intron	NM_006346	NP_006337	Q8WXW3	PIBF1_HUMAN	progesterone-induced blocking factor 1							centrosome				ovary(1)|breast(1)	2		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		ACTATGGGATGGTGACTGCTA	0.398													33	34	---	---	---	---	
SNW1	22938	broad.mit.edu	37	14	78185057	78185058	+	Intron	DEL	TT	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78185057_78185058delTT	uc001xuf.2	-						SNW1_uc010tvm.1_Intron|SNW1_uc010asu.2_Intron|SNW1_uc010tvn.1_Intron	NM_012245	NP_036377	Q13573	SNW1_HUMAN	SKI-interacting protein						negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|regulation of transcription from RNA polymerase II promoter	catalytic step 2 spliceosome|nucleoplasm	Notch binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CTTTGGAttctttttttttttt	0.153													6	3	---	---	---	---	
CYP1A2	1544	broad.mit.edu	37	15	75046942	75046943	+	Intron	INS	-	A	A			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75046942_75046943insA	uc002ayr.1	+							NM_000761	NP_000752	P05177	CP1A2_HUMAN	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)	gagggtgtctcaaaaaaaaaaa	0.158													4	3	---	---	---	---	
IREB2	3658	broad.mit.edu	37	15	78763031	78763032	+	Intron	DEL	CT	-	-	rs67871183		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78763031_78763032delCT	uc002bdr.2	+						IREB2_uc010unb.1_Intron|IREB2_uc002bdq.2_Intron	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2								4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		TTTTCttttccttttttttttt	0.099													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32471773	32471774	+	IGR	INS	-	A	A	rs149995933	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32471773_32471774insA								HERC2P4 (307899 upstream) : TP53TG3B (213067 downstream)																							TATCACTTGCTAAAAAAAAATC	0.252													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32823484	32823484	+	IGR	DEL	G	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32823484delG								TP53TG3B (134606 upstream) : SLC6A10P (65313 downstream)																							GAGGCGCGGTGGGGGGAGAAA	0.652													4	2	---	---	---	---	
CDH8	1006	broad.mit.edu	37	16	61689777	61689778	+	Intron	INS	-	T	T	rs35413525		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61689777_61689778insT	uc002eog.1	-							NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CGTCTCCGCACttttttttttt	0.223													3	4	---	---	---	---	
PRMT7	54496	broad.mit.edu	37	16	68371179	68371179	+	Intron	DEL	T	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68371179delT	uc002evy.1	+						PRMT7_uc002evx.1_Intron|PRMT7_uc010vlg.1_Intron|PRMT7_uc002evz.1_Intron	NM_019023	NP_061896	Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7						cell differentiation|DNA methylation involved in gamete generation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|spliceosomal snRNP assembly|transcription, DNA-dependent	cytosol|nucleus	[myelin basic protein]-arginine N-methyltransferase activity|histone methyltransferase activity (H4-R3 specific)|protein-arginine omega-N monomethyltransferase activity|protein-arginine omega-N symmetric methyltransferase activity|ribonucleoprotein binding				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		tacatatggattttttttttt	0.065													4	2	---	---	---	---	
AKAP10	11216	broad.mit.edu	37	17	19861142	19861143	+	Intron	INS	-	CTCCAGATATCC	CTCCAGATATCC	rs144770708	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19861142_19861143insCTCCAGATATCC	uc002gwo.2	-						AKAP10_uc002gwp.1_Intron|AKAP10_uc010cqw.1_Intron|AKAP10_uc010vze.1_Intron	NM_007202	NP_009133	O43572	AKA10_HUMAN	A-kinase anchor protein 10 precursor						blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					AGGTCCAGTCACTCCTGCTCCT	0.371													4	3	---	---	---	---	
CCDC144C	348254	broad.mit.edu	37	17	20254234	20254235	+	Intron	INS	-	T	T			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20254234_20254235insT	uc010cqy.1	+							NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0						AAGAGGAATTGTTTTTTTTTTT	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25275047	25275047	+	IGR	DEL	C	-	-	rs111754023		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25275047delC								None (None upstream) : WSB1 (346059 downstream)																							cactcgTCTTCCCCATTTTGT	0.090													4	3	---	---	---	---	
RPL23	9349	broad.mit.edu	37	17	37006922	37006923	+	Intron	DEL	TT	-	-	rs34258429		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37006922_37006923delTT	uc002hqx.1	-						RPL23_uc002hqw.1_Intron|RPL23_uc002hqy.1_3'UTR	NM_000978	NP_000969	P62829	RL23_HUMAN	ribosomal protein L23						endocrine pancreas development|ribosomal protein import into nucleus|translational elongation|translational termination|viral transcription	cytosol|ribosome	protein binding|structural constituent of ribosome				0						catgcccagatttttttttttt	0.129													7	4	---	---	---	---	
KRT35	3886	broad.mit.edu	37	17	39636682	39636682	+	Intron	DEL	C	-	-	rs11321036		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39636682delC	uc002hws.2	-							NM_002280	NP_002271	Q92764	KRT35_HUMAN	keratin 35						anatomical structure morphogenesis	intermediate filament	protein binding|structural molecule activity			ovary(1)|skin(1)	2		Breast(137;0.000286)				gggtcgcttacccagcctgaa	0.000													3	3	---	---	---	---	
ACOX1	51	broad.mit.edu	37	17	73969971	73969971	+	Intron	DEL	T	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73969971delT	uc002jqf.2	-						ACOX1_uc010wsq.1_Intron|ACOX1_uc002jqe.2_Intron|ACOX1_uc010wsr.1_Intron	NM_007292	NP_009223	Q15067	ACOX1_HUMAN	acyl-Coenzyme A oxidase 1 isoform b						fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1						GTCAGGAAAATGTAAACCCCC	0.388													7	7	---	---	---	---	
FSCN2	25794	broad.mit.edu	37	17	79498204	79498206	+	Intron	DEL	TGA	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79498204_79498206delTGA	uc010wup.1	+						FSCN2_uc010wuo.1_Intron	NM_012418	NP_036550	O14926	FSCN2_HUMAN	fascin 2 isoform 1						actin filament bundle assembly|anatomical structure morphogenesis|visual perception	actin cytoskeleton|cytoplasm|stereocilium	actin filament binding|protein binding, bridging				0	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			gtggtgatggtgatgatggtggt	0.207													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	110643	110643	+	Intron	DEL	C	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:110643delC	uc002kke.2	+											Homo sapiens Rho-associated, coiled-coil containing protein kinase 1, mRNA (cDNA clone IMAGE:5269982), complete cds.																		cttagatctgcctacatggac	0.000													4	2	---	---	---	---	
PCP2	126006	broad.mit.edu	37	19	7698226	7698227	+	Intron	INS	-	TAAT	TAAT	rs151032321	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7698226_7698227insTAAT	uc002mgz.2	-							NM_174895	NP_777555	Q8IVA1	PCP2_HUMAN	Purkinje cell protein 2						signal transduction		GTPase activator activity				0						GCCCTACAAACTAGTCTTGTCA	0.609													4	3	---	---	---	---	
LDLR	3949	broad.mit.edu	37	19	11233654	11233654	+	Intron	DEL	T	-	-	rs35951147		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11233654delT	uc002mqk.3	+						LDLR_uc010xlk.1_Intron|LDLR_uc010xll.1_Intron|LDLR_uc010xlm.1_Intron|LDLR_uc010xln.1_Intron|LDLR_uc010xlo.1_Intron	NM_000527	NP_000518	P01130	LDLR_HUMAN	low density lipoprotein receptor precursor						cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)|skin(2)	4		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	acctggctaattttttttttt	0.000													6	3	---	---	---	---	
CD97	976	broad.mit.edu	37	19	14492068	14492069	+	5'Flank	INS	-	TGAG	TGAG	rs145201420	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14492068_14492069insTGAG	uc002myl.2	+						CD97_uc002mym.2_5'Flank|CD97_uc002myn.2_5'Flank	NM_078481	NP_510966	P48960	CD97_HUMAN	CD97 antigen isoform 1 precursor						cell adhesion|cell-cell signaling|cellular component movement|immune response|inflammatory response|neuropeptide signaling pathway	extracellular space|integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(3)|breast(1)	4						TTCATTCTTACTGAGTGCACgt	0.416													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31443095	31443098	+	IGR	DEL	CTTT	-	-	rs12459562	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31443095_31443098delCTTT								ZNF536 (394130 upstream) : DKFZp566F0947 (197685 downstream)																							tccttccttcctttcttctttcct	0.005													7	4	---	---	---	---	
CEACAM4	1089	broad.mit.edu	37	19	42126512	42126515	+	Intron	DEL	GATG	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42126512_42126515delGATG	uc002orh.1	-						CEACAM4_uc010xwd.1_Intron	NM_001817	NP_001808	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion							integral to plasma membrane|membrane fraction					0						CTGTGGGGTTGATGGTCCCCCTGC	0.613													2	4	---	---	---	---	
ZNF761	388561	broad.mit.edu	37	19	53946133	53946133	+	Intron	DEL	A	-	-	rs35108555		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53946133delA	uc010eqp.2	+						LOC147804_uc002qbo.2_RNA|LOC147804_uc002qbq.2_RNA|LOC147804_uc002qbp.2_RNA|ZNF761_uc002qbr.2_Intron|ZNF761_uc010ydy.1_5'Flank	NM_001008401	NP_001008401	Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00786)		TCATGTTGTGAAAAAAAAAAT	0.348													6	8	---	---	---	---	
C20orf186	149954	broad.mit.edu	37	20	31677536	31677536	+	Intron	DEL	C	-	-	rs67782664		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31677536delC	uc010zue.1	+							NM_182519	NP_872325	P59827	LPLC4_HUMAN	antimicrobial peptide RY2G5 precursor							cytoplasm|extracellular region	lipid binding				0						CTCCCAAACACCCCCCCCGAG	0.617													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58889651	58889662	+	Intron	DEL	CATTCTCCCATT	-	-	rs114216255	by1000genomes	TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58889651_58889662delCATTCTCCCATT	uc002ybl.2	+						uc010gjw.1_Intron					Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																		tccatccatccattctcccattcatccatcct	0.000													9	5	---	---	---	---	
SF3A1	10291	broad.mit.edu	37	22	30734627	30734627	+	Intron	DEL	C	-	-	rs5844903		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30734627delC	uc003ahl.2	-							NM_005877	NP_005868	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa isoform 1						nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|U2-type spliceosomal complex	protein binding|RNA binding			ovary(3)|large_intestine(1)|pancreas(1)	5						GAGAGAGGTTCCCACTTGCAT	0.527													10	11	---	---	---	---	
C22orf42	150297	broad.mit.edu	37	22	32550003	32550004	+	Intron	DEL	CA	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32550003_32550004delCA	uc003amd.2	-							NM_001010859	NP_001010859	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42											ovary(1)|skin(1)	2						gagaccttTTcacacacacaca	0.099													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35411562	35411563	+	IGR	DEL	AA	-	-	rs67733631		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35411562_35411563delAA								None (None upstream) : ISX (50566 downstream)																							CCCAAGGTGGAAAAAAAAAAAA	0.262													4	2	---	---	---	---	
ARSH	347527	broad.mit.edu	37	X	2942330	2942330	+	Intron	DEL	A	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2942330delA	uc011mhj.1	+							NM_001011719	NP_001011719	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H							integral to membrane	arylsulfatase activity|metal ion binding			lung(1)	1		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				AGCTAGACCGAAAAAAAAAAA	0.373													8	5	---	---	---	---	
FAAH2	158584	broad.mit.edu	37	X	57458220	57458220	+	Intron	DEL	G	-	-	rs6521622		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57458220delG	uc004dvc.2	+							NM_174912	NP_777572	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2							integral to membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|hydrolase activity			ovary(3)	3						ttgtttttttgttttttttgg	0.060										HNSCC(52;0.14)			8	4	---	---	---	---	
DKC1	1736	broad.mit.edu	37	X	154001559	154001559	+	Intron	DEL	C	-	-			TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154001559delC	uc004fmm.2	+						DKC1_uc010nvf.2_Intron|SNORA56_uc004fmo.2_5'Flank	NM_001363	NP_001354	O60832	DKC1_HUMAN	dyskerin isoform 1						cell proliferation|pseudouridine synthesis|rRNA processing|telomere maintenance via telomerase	Cajal body|nucleolus|telomerase holoenzyme complex	protein binding|pseudouridine synthase activity|RNA binding|telomerase activity				0	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CTGCCAGGTTCTTTTTTTTTT	0.269									Congenital_Dyskeratosis				36	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13500860	13500860	+	IGR	DEL	G	-	-	rs76607402		TCGA-A3-3382-01A-01D-0966-08	TCGA-A3-3382-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13500860delG								None (None upstream) : None (None downstream)																							TGATTTCTAAGACTTTTGAAA	0.274													5	3	---	---	---	---	
