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
MST1P9	11223	broad.mit.edu	37	1	17087591	17087591	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17087591C>T	uc010ock.1	-	2	74	c.74G>A	c.(73-75)CGC>CAC	p.R25H	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_5'Flank	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						CGATGGCGAGCGCTGCCCTGC	0.577													7	46	---	---	---	---	PASS
CLDN19	149461	broad.mit.edu	37	1	43200699	43200699	+	3'UTR	SNP	A	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43200699A>T	uc001cht.1	-	5					CLDN19_uc001chu.2_3'UTR|CLDN19_uc010ojv.1_3'UTR	NM_148960	NP_683763	Q8N6F1	CLD19_HUMAN	claudin 19 isoform a						calcium-independent cell-cell adhesion|response to stimulus|visual perception	basolateral plasma membrane|integral to membrane|tight junction	identical protein binding				0	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTTCCAAAAAAATATGAAACA	0.547													8	14	---	---	---	---	PASS
MAST2	23139	broad.mit.edu	37	1	46493409	46493409	+	Silent	SNP	A	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46493409A>T	uc001cov.2	+	17	2209	c.1926A>T	c.(1924-1926)CTA>CTT	p.L642L	MAST2_uc001cow.2_Silent_p.L642L|MAST2_uc001coy.1_Silent_p.L316L|MAST2_uc001coz.1_Silent_p.L527L|MAST2_uc001cpa.2_RNA	NM_015112	NP_055927	Q6P0Q8	MAST2_HUMAN	microtubule associated serine/threonine kinase	642	Protein kinase.				regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CCAGCCTCCTAATTACATCCA	0.423													29	69	---	---	---	---	PASS
JAK1	3716	broad.mit.edu	37	1	65300335	65300335	+	Nonsense_Mutation	SNP	A	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65300335A>C	uc001dbu.1	-	25	3624	c.3375T>G	c.(3373-3375)TAT>TAG	p.Y1125*	JAK1_uc009wam.1_Nonsense_Mutation_p.Y1113*|JAK1_uc009wal.1_Nonsense_Mutation_p.Y302*	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1	1125	Protein kinase 2.				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		TCATAAGTTGATAAACCTGTA	0.303			Mis		ALL								3	66	---	---	---	---	PASS
JAK1	3716	broad.mit.edu	37	1	65301865	65301865	+	Missense_Mutation	SNP	A	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65301865A>C	uc001dbu.1	-	23	3423	c.3174T>G	c.(3172-3174)TTT>TTG	p.F1058L	JAK1_uc009wam.1_Missense_Mutation_p.F1046L|JAK1_uc009wal.1_Missense_Mutation_p.F235L	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1	1058	Protein kinase 2.				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		AGGCAATATAAAATTTAGATT	0.423			Mis		ALL								3	35	---	---	---	---	PASS
OLFML3	56944	broad.mit.edu	37	1	114523513	114523513	+	Intron	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114523513C>T	uc001eer.1	+						OLFML3_uc001ees.1_Intron|OLFML3_uc001eet.1_5'UTR	NM_020190	NP_064575	Q9NRN5	OLFL3_HUMAN	olfactomedin-like 3 precursor						multicellular organismal development	extracellular region					0	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-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)		TGGGGGAGTTCCTGCTGGAGG	0.488													4	8	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144612173	144612173	+	5'Flank	SNP	A	G	G	rs2653681	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144612173A>G	uc009wig.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_5'Flank|NBPF9_uc010oyf.1_5'Flank|NBPF9_uc010oyg.1_5'Flank|NBPF9_uc009wii.1_5'Flank|NBPF9_uc009wif.1_Intron|C1orf152_uc001elf.3_RNA	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						TGTGTGGAGTAATGACTCCTG	0.542													2	5	---	---	---	---	PASS
RIT1	6016	broad.mit.edu	37	1	155870061	155870061	+	3'UTR	SNP	T	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155870061T>C	uc001fmh.1	-	6					RIT1_uc010pgr.1_3'UTR	NM_006912	NP_008843	Q92963	RIT1_HUMAN	Ras-like without CAAX 1						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			breast(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)			AAACTCCTAGTAGGCATGTCC	0.373													4	21	---	---	---	---	PASS
NES	10763	broad.mit.edu	37	1	156639636	156639636	+	Silent	SNP	G	A	A	rs11549292	byFrequency	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156639636G>A	uc001fpq.2	-	4	4477	c.4344C>T	c.(4342-4344)GCC>GCT	p.A1448A		NM_006617	NP_006608	P48681	NEST_HUMAN	nestin	1448	Tail.				brain development|embryonic camera-type eye development|G2/M transition of mitotic cell cycle|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation|stem cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AGCTACTCAGGGCCTGGAGGC	0.483													3	38	---	---	---	---	PASS
FAM78B	149297	broad.mit.edu	37	1	166039642	166039642	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166039642G>A	uc001gdr.2	-	3	1212	c.622C>T	c.(622-624)CGG>TGG	p.R208W	FAM78B_uc010plc.1_RNA|FAM78B_uc001gdq.2_5'Flank	NM_001017961	NP_001017961	Q5VT40	FA78B_HUMAN	hypothetical protein LOC149297	208										central_nervous_system(1)|skin(1)	2	all_hematologic(923;0.0813)|Acute lymphoblastic leukemia(8;0.155)					AGCCGGGCCCGCTGCCCCAAG	0.582													24	62	---	---	---	---	PASS
FMO1	2326	broad.mit.edu	37	1	171250000	171250000	+	Missense_Mutation	SNP	T	C	C	rs148980563	byFrequency	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171250000T>C	uc009wvz.2	+	6	839	c.703T>C	c.(703-705)TTC>CTC	p.F235L	FMO1_uc010pme.1_Missense_Mutation_p.F172L|FMO1_uc001ghl.2_Missense_Mutation_p.F235L|FMO1_uc001ghm.2_Missense_Mutation_p.F235L|FMO1_uc001ghn.2_Missense_Mutation_p.F235L	NM_002021	NP_002012	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	235					NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum lumen|integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GGACATGGTGTTCATGACACG	0.493													18	61	---	---	---	---	PASS
FCAMR	83953	broad.mit.edu	37	1	207133044	207133044	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207133044T>C	uc001hfa.3	-	7	2053	c.1553A>G	c.(1552-1554)AAG>AGG	p.K518R	FCAMR_uc001hfb.2_Missense_Mutation_p.S251G|FCAMR_uc009xca.1_Missense_Mutation_p.S251G|FCAMR_uc001hfc.2_Missense_Mutation_p.K493R	NM_001122980	NP_001116452	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity isoform 2	473	Cytoplasmic (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(1)	1						TCTCCAGAGCTTCCTTTGCAA	0.527													37	151	---	---	---	---	PASS
PTPN14	5784	broad.mit.edu	37	1	214656164	214656164	+	Intron	SNP	A	G	G	rs58782956		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214656164A>G	uc001hkk.1	-						PTPN14_uc010pty.1_Intron|uc010ptz.1_RNA	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		TTAAAAGAGGACAGGTTTGGC	0.388													3	40	---	---	---	---	PASS
JMJD4	65094	broad.mit.edu	37	1	227920349	227920349	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227920349T>G	uc001hrb.2	-	6	1136	c.1136A>C	c.(1135-1137)AAC>ACC	p.N379T	SNAP47_uc001hqz.2_Intron|SNAP47_uc001hra.2_Intron|SNAP47_uc001hrd.2_5'Flank|SNAP47_uc001hre.2_5'Flank|SNAP47_uc001hrf.2_5'Flank|LOC100130093_uc001hqx.3_RNA|LOC100130093_uc001hqy.3_RNA|JMJD4_uc001hrc.2_Missense_Mutation_p.N363T	NM_023007	NP_075383	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4 isoform 1	379											0		Prostate(94;0.0885)				CTCTTCAAAGTTGATGCCCGA	0.572													8	36	---	---	---	---	PASS
AHCTF1	25909	broad.mit.edu	37	1	247014376	247014376	+	Silent	SNP	G	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247014376G>C	uc001ibu.1	-	32	4939	c.4932C>G	c.(4930-4932)GCC>GCG	p.A1644A	AHCTF1_uc001ibv.1_Silent_p.A1653A|AHCTF1_uc009xgs.1_Silent_p.A505A|AHCTF1_uc001ibw.1_RNA	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	1644	Mediates transcriptional activity (By similarity).|Necessary for nuclear localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CACTAGTTACGGCAGATGGCA	0.363													7	164	---	---	---	---	PASS
FAHD2B	151313	broad.mit.edu	37	2	97749407	97749407	+	3'UTR	SNP	C	T	T	rs79549240		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97749407C>T	uc002sxm.2	-	8						NM_199336	NP_955368	Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing								hydrolase activity|metal ion binding				0						CTGGCACCTGCCCACACCTGC	0.597													6	20	---	---	---	---	PASS
CCDC93	54520	broad.mit.edu	37	2	118715997	118715997	+	Missense_Mutation	SNP	G	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118715997G>C	uc002tlj.2	-	12	1075	c.949C>G	c.(949-951)CGG>GGG	p.R317G	CCDC93_uc010fld.1_Missense_Mutation_p.R317G	NM_019044	NP_061917	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	317	Potential.									large_intestine(1)|ovary(1)	2						ATGACTTTCCGGCGATGTAGC	0.398													14	42	---	---	---	---	PASS
MIR663B	100302269	broad.mit.edu	37	2	133014552	133014552	+	RNA	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133014552C>T	hsa-mir-663b|MI0006336	-			c.102C>T			NCRNA00164_uc002ttj.3_Intron																	0						ACCTCAGGCACGGCCGGGCCA	0.731													5	34	---	---	---	---	PASS
YSK4	80122	broad.mit.edu	37	2	135743788	135743788	+	Missense_Mutation	SNP	C	A	A	rs140658941	byFrequency	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135743788C>A	uc002tue.1	-	7	2685	c.2654G>T	c.(2653-2655)CGA>CTA	p.R885L	YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Missense_Mutation_p.R772L|YSK4_uc010zbg.1_Intron|YSK4_uc002tuh.3_Missense_Mutation_p.R613L|YSK4_uc002tui.3_Missense_Mutation_p.R902L	NM_025052	NP_079328	Q56UN5	YSK4_HUMAN	Yeast Sps1/Ste20-related kinase 4 isoform 1	885							ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)		AGTTAAAATTCGGCTGGCATT	0.378													11	66	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179537132	179537132	+	Splice_Site	SNP	A	G	G			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179537132A>G	uc010zfg.1	-	149	31251	c.31027_splice	c.e149+1	p.G10343_splice	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Splice_Site_p.G7004_splice|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								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)			TTCCAAAAATACCTTTAGCTG	0.328													10	264	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179543217	179543217	+	Silent	SNP	C	T	T	rs35112591	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179543217C>T	uc010zfg.1	-	141	30326	c.30102G>A	c.(30100-30102)GAG>GAA	p.E10034E	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.E6695E|TTN_uc010fre.1_Silent_p.E691E|TTN_uc002una.1_RNA|TTN_uc010frf.1_RNA	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	10961							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)			TCTTGGGTACCTCTGGCACTT	0.373													8	9	---	---	---	---	PASS
IL5RA	3568	broad.mit.edu	37	3	3133896	3133896	+	Intron	SNP	T	G	G	rs7640267	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3133896T>G	uc011ask.1	-						IL5RA_uc010hbq.2_Intron|IL5RA_uc010hbr.2_Intron|IL5RA_uc010hbs.2_Intron|IL5RA_uc011asl.1_Intron|IL5RA_uc011asm.1_Intron|IL5RA_uc010hbt.2_Intron|IL5RA_uc011asn.1_3'UTR|IL5RA_uc010hbu.2_3'UTR|IL5RA_uc010hbp.2_Intron	NM_000564	NP_000555	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha isoform 1						cell proliferation	extracellular space|integral to membrane|plasma membrane	interleukin-5 receptor activity			ovary(1)	1				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		AAAATAAACATAAGCTACTTA	0.438													3	64	---	---	---	---	PASS
ANKRD28	23243	broad.mit.edu	37	3	15727591	15727591	+	Missense_Mutation	SNP	G	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15727591G>C	uc003caj.1	-	20	2140	c.1997C>G	c.(1996-1998)ACA>AGA	p.T666R	ANKRD28_uc003cai.1_Missense_Mutation_p.T512R|ANKRD28_uc011avz.1_Missense_Mutation_p.T512R|ANKRD28_uc003cak.1_RNA|ANKRD28_uc011awa.1_RNA|ANKRD28_uc003cal.1_Missense_Mutation_p.T696R|ANKRD28_uc003cam.2_Missense_Mutation_p.T699R	NM_015199	NP_056014	O15084	ANR28_HUMAN	ankyrin repeat domain 28	666	ANK 19.					nucleoplasm	protein binding			breast(1)	1						AACACAGTCTGTGTGCCCGTT	0.458													4	22	---	---	---	---	PASS
PARP14	54625	broad.mit.edu	37	3	122418827	122418827	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122418827G>A	uc003efq.3	+	6	1485	c.1426G>A	c.(1426-1428)GGC>AGC	p.G476S	PARP14_uc010hrk.2_RNA|PARP14_uc003efr.2_Missense_Mutation_p.G193S|PARP14_uc003efs.1_Missense_Mutation_p.G193S	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	476					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)		CATTTCTCCAGGCAGGTATTT	0.398													10	58	---	---	---	---	PASS
PLCH1	23007	broad.mit.edu	37	3	155199598	155199598	+	Missense_Mutation	SNP	C	A	A	rs150381264	byFrequency	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155199598C>A	uc011bok.1	-	23	4518	c.4241G>T	c.(4240-4242)CGC>CTC	p.R1414L	PLCH1_uc011boj.1_3'UTR|PLCH1_uc011bol.1_Missense_Mutation_p.R1376L	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	1414					lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GACAGAAGGGCGGAGGGTCTC	0.398													23	101	---	---	---	---	PASS
KPNA4	3840	broad.mit.edu	37	3	160219829	160219829	+	3'UTR	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160219829C>T	uc003fdn.2	-	17						NM_002268	NP_002259	O00629	IMA4_HUMAN	karyopherin alpha 4						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			tatatatatacacacacacat	0.313													6	41	---	---	---	---	PASS
TBCK	93627	broad.mit.edu	37	4	107216263	107216263	+	Missense_Mutation	SNP	C	G	G			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107216263C>G	uc010ilv.2	-	3	619	c.254G>C	c.(253-255)AGG>ACG	p.R85T	TBCK_uc003hye.2_Missense_Mutation_p.R85T|TBCK_uc003hyc.2_Missense_Mutation_p.R85T|TBCK_uc003hyd.2_5'UTR|TBCK_uc003hyf.2_Missense_Mutation_p.R85T	NM_001163435	NP_001156907	Q8TEA7	TBCK_HUMAN	TBC domain-containing protein kinase-like	85	Protein kinase.					intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5						CACAGGTTTCCTTTCTCGAAG	0.378													36	137	---	---	---	---	PASS
LEF1	51176	broad.mit.edu	37	4	109084812	109084812	+	Nonsense_Mutation	SNP	G	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109084812G>T	uc003hyt.1	-	3	981	c.326C>A	c.(325-327)TCG>TAG	p.S109*	LEF1_uc011cfj.1_5'UTR|LEF1_uc011cfk.1_Nonsense_Mutation_p.S41*|LEF1_uc003hyu.1_Nonsense_Mutation_p.S109*|LEF1_uc003hyv.1_Nonsense_Mutation_p.S109*|LEF1_uc010imb.1_RNA	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1	109	Pro-rich.				canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		GGAATAACTCGAGTAGGAGGG	0.433													4	68	---	---	---	---	PASS
BBS12	166379	broad.mit.edu	37	4	123663744	123663744	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123663744C>A	uc003ieu.2	+	2	890	c.697C>A	c.(697-699)CAC>AAC	p.H233N		NM_152618	NP_689831	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	233					cellular protein metabolic process	cilium	ATP binding			ovary(2)	2						AATACTAATCCACAGTAGGCA	0.388									Bardet-Biedl_syndrome				4	64	---	---	---	---	PASS
TMEM144	55314	broad.mit.edu	37	4	159156622	159156622	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159156622G>T	uc003ipx.2	+	8	1048	c.528G>T	c.(526-528)TGG>TGT	p.W176C	TMEM144_uc010iqi.2_Intron	NM_018342	NP_060812	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	176						integral to membrane					0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		CCTGTTCCTGGGTGGATAAAC	0.383													4	57	---	---	---	---	PASS
WWC2	80014	broad.mit.edu	37	4	184182184	184182184	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184182184T>C	uc010irx.2	+	11	1590	c.1408T>C	c.(1408-1410)TAT>CAT	p.Y470H	WWC2_uc003ivk.3_Missense_Mutation_p.Y265H|WWC2_uc003ivl.3_RNA|WWC2_uc010iry.2_Missense_Mutation_p.Y152H|WWC2_uc003ivn.3_Missense_Mutation_p.Y34H	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	470	Ser-rich.									ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		CACCGAACTCTATTACAGCAG	0.502													3	55	---	---	---	---	PASS
MATR3	9782	broad.mit.edu	37	5	138643063	138643063	+	5'UTR	SNP	T	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138643063T>A	uc003ldu.2	+	5					MATR3_uc003lds.2_5'UTR|MATR3_uc010jfb.2_5'UTR|MATR3_uc003ldt.2_Intron|MATR3_uc003ldw.2_5'UTR|MATR3_uc003ldx.2_5'UTR|MATR3_uc010jfc.2_5'UTR|MATR3_uc003ldy.2_Intron|MATR3_uc011czb.1_Intron|MATR3_uc003ldz.2_5'UTR|MATR3_uc003lea.2_5'UTR	NM_199189	NP_954659	P43243	MATR3_HUMAN	matrin 3							nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ttaaaaaaattttttttttta	0.368													4	72	---	---	---	---	PASS
PCDHA1	56147	broad.mit.edu	37	5	140242306	140242306	+	Intron	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140242306C>T	uc003lha.2	+						PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|uc003lhy.1_3'UTR	NM_031411	NP_113599	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 3 precursor						homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCGAGTGCGCGCTGTCTAGC	0.642													7	14	---	---	---	---	PASS
RBM27	54439	broad.mit.edu	37	5	145641192	145641192	+	Nonsense_Mutation	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145641192G>A	uc003lnz.3	+	13	2179	c.2013G>A	c.(2011-2013)TGG>TGA	p.W671*	RBM27_uc003lny.2_Nonsense_Mutation_p.W616*	NM_018989	NP_061862	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	671	RRM.				mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding			central_nervous_system(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGTCTTGTGGCATAGGGAAA	0.478													5	158	---	---	---	---	PASS
CPEB4	80315	broad.mit.edu	37	5	173317603	173317603	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173317603G>T	uc003mcs.3	+	1	2273	c.867G>T	c.(865-867)CAG>CAT	p.Q289H	CPEB4_uc010jju.1_Missense_Mutation_p.Q289H|CPEB4_uc010jjv.2_Missense_Mutation_p.Q289H|CPEB4_uc011dfg.1_Missense_Mutation_p.Q289H|CPEB4_uc003mct.3_5'Flank|CPEB4_uc003mcu.3_5'Flank	NM_030627	NP_085130	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding	289							nucleotide binding|RNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GCAGCTACCAGAGTCCGTCAC	0.577													7	227	---	---	---	---	PASS
EXOC2	55770	broad.mit.edu	37	6	497413	497413	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:497413C>T	uc003mtd.2	-	25	2647	c.2513G>A	c.(2512-2514)CGA>CAA	p.R838Q	EXOC2_uc003mte.2_Missense_Mutation_p.R838Q|EXOC2_uc011dho.1_Missense_Mutation_p.R433Q	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein	838					exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		CTGCATCAGTCGACTGAGCTC	0.338													22	90	---	---	---	---	PASS
HIST1H3G	8355	broad.mit.edu	37	6	26271452	26271452	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26271452C>T	uc003nhi.2	-	1	161	c.161G>A	c.(160-162)CGC>CAC	p.R54H	uc003nhj.2_5'Flank|HIST1H2BI_uc003nhk.2_5'Flank	NM_003534	NP_003525	P68431	H31_HUMAN	H3 histone family, member H	54					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding				0						CTTCTGATAGCGGCGAATCTC	0.607													7	105	---	---	---	---	PASS
RPS18	6222	broad.mit.edu	37	6	33243782	33243782	+	Missense_Mutation	SNP	A	G	G	rs144855906	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33243782A>G	uc003odp.1	+	4	275	c.230A>G	c.(229-231)TAC>TGC	p.Y77C	RPS18_uc010jum.1_RNA|RPS18_uc003odq.1_RNA|B3GALT4_uc003odr.2_5'Flank	NM_022551	NP_072045	P62269	RS18_HUMAN	ribosomal protein S18	77					endocrine pancreas development|ribosome biogenesis|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	rRNA binding|structural constituent of ribosome				0						CCACGCCAGTACAAGATCCCA	0.517													3	57	---	---	---	---	PASS
ABCC10	89845	broad.mit.edu	37	6	43411544	43411544	+	Intron	SNP	G	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43411544G>T	uc003ouy.1	+						ABCC10_uc003ouz.1_Intron|ABCC10_uc010jyo.1_5'UTR	NM_033450	NP_258261	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C, member 10							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(6)|central_nervous_system(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			AGGTCTAGGGGTATCCTGCTA	0.557													4	19	---	---	---	---	PASS
BAI3	577	broad.mit.edu	37	6	69758171	69758171	+	Silent	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69758171C>T	uc003pev.3	+	14	2650	c.2202C>T	c.(2200-2202)AAC>AAT	p.N734N	BAI3_uc010kak.2_Silent_p.N734N	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	734	Extracellular (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				GGGCAAGAAACTCAGAAGATA	0.383													9	52	---	---	---	---	PASS
SLC35F1	222553	broad.mit.edu	37	6	118228997	118228997	+	Silent	SNP	C	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118228997C>A	uc003pxx.3	+	1	309	c.108C>A	c.(106-108)GGC>GGA	p.G36G		NM_001029858	NP_001025029	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	36					transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)		GCAGCGGCGGCGGCGGGAGCC	0.612													3	27	---	---	---	---	PASS
PPIL4	85313	broad.mit.edu	37	6	149826610	149826610	+	Silent	SNP	T	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149826610T>C	uc003qmo.1	-	13	1488	c.1458A>G	c.(1456-1458)AAA>AAG	p.K486K	PPIL4_uc010kic.2_Intron	NM_139126	NP_624311	Q8WUA2	PPIL4_HUMAN	peptidylprolyl isomerase-like 4	486					protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)		TAGATTTTTCTTTATCTTTGG	0.338													14	95	---	---	---	---	PASS
MACC1	346389	broad.mit.edu	37	7	20180449	20180449	+	3'UTR	SNP	G	C	C	rs113534252		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20180449G>C	uc003sus.3	-	7					MACC1_uc010kug.2_3'UTR	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						cacacacacagacacacacac	0.164													4	26	---	---	---	---	PASS
ANLN	54443	broad.mit.edu	37	7	36438709	36438709	+	Missense_Mutation	SNP	C	G	G	rs3735400	byFrequency	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36438709C>G	uc003tff.2	+	3	398	c.194C>G	c.(193-195)TCG>TGG	p.S65W	ANLN_uc011kaz.1_Intron|ANLN_uc003tfg.2_Missense_Mutation_p.S65W|ANLN_uc010kxe.2_Missense_Mutation_p.S65W	NM_018685	NP_061155	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	65	Nuclear localization.|Interaction with CD2AP.				cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3						ACAAAACCATCGCCATCAAAA	0.333													3	75	---	---	---	---	PASS
PMS2L5	5383	broad.mit.edu	37	7	74306962	74306962	+	5'UTR	SNP	G	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74306962G>C	uc003ubl.2	+	1					PMS2L5_uc003ubk.2_RNA|PMS2L5_uc010lbw.2_RNA|PMS2L5_uc003ubm.3_RNA|STAG3L2_uc003ubj.3_5'Flank	NR_027775				SubName: Full=Postmeiotic segregation increased 2-like 5;												0						GCTGAGAGCTGGAGGTGAGCT	0.677													3	25	---	---	---	---	PASS
PMS2L11	441263	broad.mit.edu	37	7	76669085	76669085	+	Intron	SNP	T	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76669085T>A	uc011kgn.1	+						LOC100132832_uc003ufy.2_RNA					Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						TTTTGGGTACTTGTTTAAGGA	0.289													4	3	---	---	---	---	PASS
ABCB1	5243	broad.mit.edu	37	7	87179322	87179322	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87179322G>A	uc003uiz.1	-	14	1817	c.1399C>T	c.(1399-1401)CGG>TGG	p.R467W	ABCB1_uc011khc.1_Missense_Mutation_p.R403W	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	467	ABC transporter 1.|Cytoplasmic (Potential).				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	ATGATTTCCCGTAGAAACCTT	0.408													9	121	---	---	---	---	PASS
CLDN12	9069	broad.mit.edu	37	7	90042673	90042673	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90042673C>T	uc003ukp.2	+	5	1319	c.683C>T	c.(682-684)TCT>TTT	p.S228F	CLDN12_uc003ukq.2_Missense_Mutation_p.S228F|CLDN12_uc010leq.2_Missense_Mutation_p.S228F|CLDN12_uc003ukr.2_Missense_Mutation_p.S228F|CLDN12_uc003uks.2_Missense_Mutation_p.S228F	NM_012129	NP_036261	P56749	CLD12_HUMAN	claudin 12	228	Cytoplasmic (Potential).				calcium-independent cell-cell adhesion|tight junction assembly	integral to membrane|tight junction	identical protein binding|structural molecule activity				0						TCAGCACGCTCTCGCCTCTCT	0.423													40	145	---	---	---	---	PASS
ABP1	26	broad.mit.edu	37	7	150554114	150554114	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150554114G>A	uc003why.1	+	3	4774	c.556G>A	c.(556-558)GAT>AAT	p.D186N	ABP1_uc003whz.1_Missense_Mutation_p.D186N|ABP1_uc003wia.1_Missense_Mutation_p.D186N	NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor	186					amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)|skin(2)	6	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)	GGCCTTCACCGATGTGGCCCC	0.587													9	78	---	---	---	---	PASS
ZC3H3	23144	broad.mit.edu	37	8	144623605	144623605	+	5'UTR	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144623605G>A	uc003yyd.2	-	1						NM_015117	NP_055932	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3						mRNA polyadenylation|poly(A)+ mRNA export from nucleus|regulation of mRNA export from nucleus	nucleus	nucleic acid binding|zinc ion binding			skin(1)	1	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			CCGAGTCCGCGACGGCCGGCC	0.706													20	60	---	---	---	---	PASS
DMRT2	10655	broad.mit.edu	37	9	1051731	1051731	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1051731C>T	uc003zha.2	+	2	318	c.118C>T	c.(118-120)CCG>TCG	p.P40S	DMRT2_uc003zgx.3_5'UTR|DMRT2_uc010mgz.2_5'UTR|DMRT2_uc003zgy.3_Intron|DMRT2_uc003zhb.3_Missense_Mutation_p.P40S|DMRT2_uc011llt.1_Missense_Mutation_p.P40S|DMRT2_uc011llu.1_Missense_Mutation_p.P40S|DMRT2_uc011llv.1_Missense_Mutation_p.P40S	NM_181872	NP_870987	Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor	40					male gonad development|sex determination	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		gcccagcccgccgccggcgga	0.284													3	7	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	90746688	90746688	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90746688C>T	uc011lti.1	-	4	1293	c.1264G>A	c.(1264-1266)GTC>ATC	p.V422I						SubName: Full=cDNA FLJ59639;																		ACACTAAAGACGTCCTGAGAT	0.488													7	211	---	---	---	---	PASS
KLF4	9314	broad.mit.edu	37	9	110249346	110249346	+	Missense_Mutation	SNP	C	G	G			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110249346C>G	uc004bdh.2	-	3	1923	c.1302G>C	c.(1300-1302)AAG>AAC	p.K434N	KLF4_uc004bdf.1_Missense_Mutation_p.K359N|KLF4_uc004bdg.2_Missense_Mutation_p.K409N	NM_004235	NP_004226	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)	443	C2H2-type 1.				fat cell differentiation|mesodermal cell fate determination|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|stem cell maintenance|transcription from RNA polymerase II promoter	nucleus	RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor recruiting transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(2)|lung(1)	3						GATGGGAACTCTTTGTGTAGG	0.592													12	192	---	---	---	---	PASS
AGPAT2	10555	broad.mit.edu	37	9	139581703	139581703	+	Missense_Mutation	SNP	A	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139581703A>T	uc004cii.1	-	1	209	c.107T>A	c.(106-108)CTG>CAG	p.L36Q	AGPAT2_uc004cij.1_Missense_Mutation_p.L36Q	NM_006412	NP_006403	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	36	Helical; (Potential).				phosphatidic acid biosynthetic process|positive regulation of cytokine production|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		CGTGAAGCACAGCGCGCAGTA	0.527													5	34	---	---	---	---	PASS
ZNF33A	7581	broad.mit.edu	37	10	38345420	38345420	+	Missense_Mutation	SNP	A	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38345420A>T	uc001izh.2	+	5	2543	c.2365A>T	c.(2365-2367)AGC>TGC	p.S789C	ZNF33A_uc001izg.2_Missense_Mutation_p.S790C|ZNF33A_uc010qev.1_Missense_Mutation_p.S796C|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	789						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3						GCCACAAGTCAGCCTCCATAA	0.378													16	59	---	---	---	---	PASS
C10orf129	142827	broad.mit.edu	37	10	96970504	96970504	+	Nonsense_Mutation	SNP	G	T	T	rs141505578	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96970504G>T	uc001kke.2	+	5	834	c.709G>T	c.(709-711)GAG>TAG	p.E237*	C10orf129_uc009xuu.1_Nonsense_Mutation_p.E147*	NM_207321	NP_997204	Q6P461	ACSM6_HUMAN	acyl-coenzyme A synthetase ACSM6, mitochondrial	237					fatty acid metabolic process	mitochondrion	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding				0		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		CAAAATGGTCGAGTATTCCCA	0.502													4	59	---	---	---	---	PASS
KCNIP2	30819	broad.mit.edu	37	10	103599520	103599520	+	Intron	SNP	C	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103599520C>A	uc001kub.2	-						KCNIP2_uc001ktz.2_Silent_p.S26S|KCNIP2_uc009xwu.2_Intron|KCNIP2_uc009xwv.2_Intron|KCNIP2_uc001kuc.2_Intron|KCNIP2_uc001kue.2_Intron|KCNIP2_uc001kud.2_Intron|KCNIP2_uc001kuf.2_Intron|KCNIP2_uc001kua.2_Intron|KCNIP2_uc009xww.2_Intron|KCNIP2_uc010qqh.1_Silent_p.S26S|KCNIP2_uc010qqi.1_Intron	NM_173191	NP_775283	Q9NS61	KCIP2_HUMAN	Kv channel interacting protein 2 isoform 2						clustering of voltage-gated potassium channels|detection of calcium ion|muscle contraction|regulation of heart contraction|signal transduction|synaptic transmission	cytoplasm|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|calcium ion binding|ER retention sequence binding|identical protein binding|protein N-terminus binding				0		Colorectal(252;0.122)		Epithelial(162;4.93e-09)|all cancers(201;2.63e-07)		CTGGGGACAGCGACCCAGTCA	0.652													8	84	---	---	---	---	PASS
PNLIPRP2	5408	broad.mit.edu	37	10	118397884	118397884	+	Splice_Site	SNP	A	G	G	rs4751995	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118397884A>G	uc001lcq.2	+	14	1098	c.1075_splice	c.e14-1	p.R359_splice		NM_005396	NP_005387	P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2						galactolipid catabolic process|lipid digestion|phospholipid catabolic process|triglyceride metabolic process	extracellular space	acylglycerol lipase activity|calcium ion binding|galactolipase activity|phospholipase activity|triglyceride lipase activity			large_intestine(1)	1				all cancers(201;0.015)		GGACAGGTTGAAGATATAAGA	0.333													5	3	---	---	---	---	PASS
PNLIPRP2	5408	broad.mit.edu	37	10	118397894	118397894	+	Missense_Mutation	SNP	A	G	G	rs4751996	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118397894A>G	uc001lcq.2	+	14	1107	c.1084A>G	c.(1084-1086)ATA>GTA	p.I362V		NM_005396	NP_005387	P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2	361	PLAT.				galactolipid catabolic process|lipid digestion|phospholipid catabolic process|triglyceride metabolic process	extracellular space	acylglycerol lipase activity|calcium ion binding|galactolipase activity|phospholipase activity|triglyceride lipase activity			large_intestine(1)	1				all cancers(201;0.015)		AAGATATAAGATATCAGTCAC	0.308													5	3	---	---	---	---	PASS
STK32C	282974	broad.mit.edu	37	10	134145147	134145147	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134145147G>A	uc010quu.1	-	1	210	c.94C>T	c.(94-96)CTT>TTT	p.L32F	STK32C_uc009ybc.1_5'UTR|STK32C_uc009ybd.1_Intron|LRRC27_uc001llf.2_5'Flank|LRRC27_uc010quv.1_5'Flank|LRRC27_uc010quw.1_5'Flank|LRRC27_uc001llg.2_5'Flank|LRRC27_uc001lli.2_5'Flank	NM_173575	NP_775846	Q86UX6	ST32C_HUMAN	serine/threonine kinase 32C	Error:Variant_position_missing_in_Q86UX6_after_alignment							ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		CCGCTCCAAAGGTGGTGCCTC	0.403													21	41	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1221817	1221817	+	Intron	SNP	G	C	C	rs1132440	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1221817G>C	uc009ycr.1	+						uc001lsz.2_RNA|uc009ycs.1_RNA	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TGGGCCGGCGGTGCCCTGCGC	0.701													3	38	---	---	---	---	PASS
PPFIBP2	8495	broad.mit.edu	37	11	7662731	7662731	+	Missense_Mutation	SNP	A	G	G	rs77484205		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7662731A>G	uc001mfj.3	+	16	1785	c.1397A>G	c.(1396-1398)GAC>GGC	p.D466G	PPFIBP2_uc010rbb.1_Missense_Mutation_p.D389G|PPFIBP2_uc001mfk.1_Intron|PPFIBP2_uc010rbc.1_Missense_Mutation_p.D400G|PPFIBP2_uc010rbd.1_Missense_Mutation_p.D308G|PPFIBP2_uc010rbe.1_Missense_Mutation_p.D354G|PPFIBP2_uc001mfl.3_Missense_Mutation_p.D323G|PPFIBP2_uc009yfj.1_Missense_Mutation_p.D110G	NM_003621	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2	466					cell communication|DNA integration	intracellular	DNA binding|integrase activity|protein binding			ovary(2)|breast(2)	4				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		AGTGGCTGGGACGACACTGCT	0.532													9	61	---	---	---	---	PASS
OR5R1	219479	broad.mit.edu	37	11	56185689	56185689	+	Missense_Mutation	SNP	A	G	G	rs7931261	byFrequency	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56185689A>G	uc010rji.1	-	1	20	c.20T>C	c.(19-21)ATT>ACT	p.I7T		NM_001004744	NP_001004744	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R,	7	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)					AGTGACATAAATGATATTAAC	0.398													4	119	---	---	---	---	PASS
SYTL2	54843	broad.mit.edu	37	11	85459457	85459457	+	Silent	SNP	A	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85459457A>T	uc010rth.1	-	2	387	c.111T>A	c.(109-111)CCT>CCA	p.P37P	SYTL2_uc010rtg.1_Silent_p.P37P|SYTL2_uc010rti.1_Silent_p.P37P|SYTL2_uc010rtj.1_5'UTR|SYTL2_uc001pbf.3_Silent_p.P37P	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g	37	RabBD.				intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TAATTTTTTCAGGCAAATGTC	0.393													5	78	---	---	---	---	PASS
IQSEC3	440073	broad.mit.edu	37	12	248155	248155	+	Silent	SNP	C	T	T	rs55923022	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:248155C>T	uc001qhw.1	+	1	723	c.717C>T	c.(715-717)GCC>GCT	p.A239A	IQSEC3_uc001qhu.1_Silent_p.A239A|IQSEC3_uc001qht.1_Silent_p.A324A|uc001qhv.1_Intron	NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	542					regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		AAGCCCCCGCCGTGGGCCGGG	0.706													5	4	---	---	---	---	PASS
DDX12	440081	broad.mit.edu	37	12	9585573	9585573	+	Missense_Mutation	SNP	C	T	T	rs71447582	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9585573C>T	uc010sgs.1	-	8	1067	c.872G>A	c.(871-873)AGC>AAC	p.S291N	DDX12_uc009zgq.1_Missense_Mutation_p.S115N	NM_004400	NP_004391			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12												0						ACCGTGCCTGCTTCTCTGCAT	0.517													4	10	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88514920	88514920	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88514920T>C	uc001tar.2	-	14	1557	c.1213A>G	c.(1213-1215)ACT>GCT	p.T405A	CEP290_uc001tat.2_Missense_Mutation_p.T167A|CEP290_uc009zsl.1_RNA	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	405	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						TTCATATGAGTCTGTTGAGAA	0.383													3	43	---	---	---	---	PASS
ACACB	32	broad.mit.edu	37	12	109639448	109639448	+	Missense_Mutation	SNP	T	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109639448T>A	uc001tob.2	+	19	2974	c.2855T>A	c.(2854-2856)CTG>CAG	p.L952Q	ACACB_uc001toc.2_Missense_Mutation_p.L952Q	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	952	Biotinyl-binding.				acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	GGTGCCGTGCTGGAAGCAGGC	0.552													7	79	---	---	---	---	PASS
TBX5	6910	broad.mit.edu	37	12	114793645	114793645	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114793645G>A	uc001tvo.2	-	9	1744	c.1249C>T	c.(1249-1251)CCC>TCC	p.P417S	TBX5_uc001tvp.2_Missense_Mutation_p.P417S|TBX5_uc001tvq.2_Missense_Mutation_p.P367S	NM_181486	NP_852259	Q99593	TBX5_HUMAN	T-box 5 isoform 1	417					cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(6)|pancreas(1)|skin(1)	8	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		CTGTCCATGGGCTGCACGGTG	0.657													11	46	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	129563125	129563125	+	Missense_Mutation	SNP	A	G	G			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129563125A>G	uc009zyl.1	-	8	2397	c.2069T>C	c.(2068-2070)ATC>ACC	p.I690T	TMEM132D_uc001uia.2_Missense_Mutation_p.I228T	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	690	Extracellular (Potential).					integral to membrane		p.I690I(1)		ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		AGTGGCAAAGATGGCCCTGTT	0.577													5	109	---	---	---	---	PASS
ENOX1	55068	broad.mit.edu	37	13	43872565	43872565	+	Nonsense_Mutation	SNP	C	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43872565C>A	uc001uza.3	-	12	1663	c.1363G>T	c.(1363-1365)GAA>TAA	p.E455*	ENOX1_uc001uzb.3_Nonsense_Mutation_p.E455*|ENOX1_uc001uzc.3_Nonsense_Mutation_p.E455*|ENOX1_uc001uyz.3_Nonsense_Mutation_p.E64*	NM_001127615	NP_001121087	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	455	Potential.				electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		AAAAGCTGTTCTTTTTCTTGT	0.527													38	103	---	---	---	---	PASS
TUBGCP3	10426	broad.mit.edu	37	13	113181286	113181286	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113181286C>A	uc001vse.1	-	13	1712	c.1525G>T	c.(1525-1527)GTG>TTG	p.V509L	TUBGCP3_uc010tjq.1_Missense_Mutation_p.V499L|TUBGCP3_uc001vsf.2_Missense_Mutation_p.V509L	NM_006322	NP_006313	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	509					G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					GACTTGGTCACAGCTATCATC	0.313													3	67	---	---	---	---	PASS
RPL13AP3	645683	broad.mit.edu	37	14	56233307	56233307	+	RNA	SNP	C	T	T	rs56190279	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56233307C>T	uc010aos.2	+	1		c.345C>T				NR_004844				Homo sapiens ribosomal protein L13a pseudogene, mRNA (cDNA clone IMAGE:5271409).												0						AAAGTTTGCCCTTCTGGGGCG	0.552													5	4	---	---	---	---	PASS
TTLL5	23093	broad.mit.edu	37	14	76175666	76175666	+	Intron	SNP	C	A	A	rs8007792	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76175666C>A	uc001xrx.2	+						TTLL5_uc001xrw.1_3'UTR|TTLL5_uc010ask.1_Intron|TTLL5_uc001xry.1_Intron	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)		GTTTTTTTCACATGTATCCTA	0.378													3	9	---	---	---	---	PASS
MAPKBP1	23005	broad.mit.edu	37	15	42109223	42109223	+	Silent	SNP	T	C	C	rs1197689	byFrequency	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42109223T>C	uc001zok.3	+	15	2005	c.1719T>C	c.(1717-1719)GTT>GTC	p.V573V	MAPKBP1_uc001zoj.3_Silent_p.V567V|MAPKBP1_uc010bcj.2_Silent_p.V74V|MAPKBP1_uc010bci.2_Silent_p.V567V|MAPKBP1_uc010udb.1_Silent_p.V406V|MAPKBP1_uc010bck.2_5'UTR|MAPKBP1_uc010bcl.2_Silent_p.V74V	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein	573	WD 9.									central_nervous_system(5)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	10		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		TCACTGCTGTTAAGTTTGCAG	0.607													3	74	---	---	---	---	PASS
USP8	9101	broad.mit.edu	37	15	50785016	50785016	+	Missense_Mutation	SNP	A	G	G	rs148783236	byFrequency	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50785016A>G	uc001zym.3	+	16	2853	c.2353A>G	c.(2353-2355)ACT>GCT	p.T785A	USP8_uc001zyl.3_Missense_Mutation_p.T785A|USP8_uc001zyn.3_Missense_Mutation_p.T785A|USP8_uc010ufh.1_Missense_Mutation_p.T679A|uc001zyo.1_RNA|USP8_uc001zyp.3_5'Flank	NM_001128611	NP_001122083	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	785					cell cycle|cell proliferation|endosome organization|protein K48-linked deubiquitination|protein K63-linked deubiquitination|ubiquitin-dependent protein catabolic process	cytosol|early endosome|extrinsic to plasma membrane|nucleus	cysteine-type endopeptidase activity|SH3 domain binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)|central_nervous_system(1)	2				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		CTTAGGAAATACTTGTTATAT	0.398													6	92	---	---	---	---	PASS
COMMD4	54939	broad.mit.edu	37	15	75631620	75631620	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75631620T>C	uc002azy.2	+	6	374	c.317T>C	c.(316-318)CTG>CCG	p.L106P	COMMD4_uc010umf.1_3'UTR|COMMD4_uc002azz.2_Missense_Mutation_p.C89R|COMMD4_uc002baa.2_Missense_Mutation_p.L106P|COMMD4_uc010umg.1_3'UTR|COMMD4_uc010umh.1_RNA	NM_017828	NP_060298	Q9H0A8	COMD4_HUMAN	COMM domain containing 4	106						cytoplasm	protein binding				0						GCGGCCAGCCTGTGCCGCTGT	0.622													3	45	---	---	---	---	PASS
AP3B2	8120	broad.mit.edu	37	15	83332552	83332552	+	Splice_Site	SNP	C	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83332552C>A	uc010uoh.1	-	19	2556	c.2379_splice	c.e19+1	p.T793_splice	AP3B2_uc010uoi.1_Splice_Site_p.T812_splice|AP3B2_uc010uoj.1_Splice_Site_p.T761_splice|AP3B2_uc010bmp.2_5'Flank|AP3B2_uc010uog.1_Splice_Site_p.T429_splice|AP3B2_uc002biy.1_5'Flank	NM_004644	NP_004635	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)			AAGGCTCTCACTGTTTTCCTG	0.587													3	36	---	---	---	---	PASS
PRKCB	5579	broad.mit.edu	37	16	24104205	24104205	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24104205G>A	uc002dmd.2	+	6	820	c.623G>A	c.(622-624)AGC>AAC	p.S208N	PRKCB_uc002dme.2_Missense_Mutation_p.S208N	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1	208	C2.				apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	AAAAGTGAGAGCAAACAGAAG	0.443													9	104	---	---	---	---	PASS
GTF3C1	2975	broad.mit.edu	37	16	27500375	27500375	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27500375G>T	uc002dov.1	-	21	3458	c.3418C>A	c.(3418-3420)CAG>AAG	p.Q1140K	GTF3C1_uc002dou.2_Missense_Mutation_p.Q1140K	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	1140						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5						TTTTTGGCCTGGTTGATGATG	0.577													5	121	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	29110458	29110458	+	Intron	SNP	T	C	C	rs151074589	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									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													9	63	---	---	---	---	PASS
BRD7	29117	broad.mit.edu	37	16	50368807	50368807	+	Splice_Site	SNP	C	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50368807C>A	uc002egf.1	-	8	770	c.703_splice	c.e8-1	p.E235_splice	BRD7_uc002ege.1_Splice_Site_p.E235_splice	NM_013263	NP_037395	Q9NPI1	BRD7_HUMAN	bromodomain containing 7						cell cycle|negative regulation of cell proliferation|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of histone acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|nucleus	histone acetyl-lysine binding|p53 binding|transcription coactivator activity|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding				0		all_cancers(37;0.0127)				GAATTCTTTCCTAAACATATT	0.373													4	57	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7680786	7680786	+	Nonsense_Mutation	SNP	C	G	G			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7680786C>G	uc002giu.1	+	32	5095	c.5081C>G	c.(5080-5082)TCA>TGA	p.S1694*		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1694	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				AATAAGTATTCAGAAGCCATC	0.507													30	378	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11572560	11572560	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11572560G>A	uc002gne.2	+	16	2979	c.2911G>A	c.(2911-2913)GGC>AGC	p.G971S	DNAH9_uc010coo.2_Missense_Mutation_p.G265S	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	971	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CCCACAAAATGGCTCTCCTCA	0.542													5	125	---	---	---	---	PASS
CCDC144A	9720	broad.mit.edu	37	17	16594036	16594036	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16594036G>T	uc002gqk.1	+	1	398	c.322G>T	c.(322-324)GAC>TAC	p.D108Y		NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	108											0						CACTGGCGTGGACAAGAGGGA	0.657													27	245	---	---	---	---	PASS
FLII	2314	broad.mit.edu	37	17	18151872	18151872	+	Missense_Mutation	SNP	G	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18151872G>C	uc002gsr.1	-	18	2233	c.2182C>G	c.(2182-2184)CTG>GTG	p.L728V	FLII_uc002gsq.1_Missense_Mutation_p.L599V|FLII_uc010cpy.1_Missense_Mutation_p.L717V|FLII_uc010vxn.1_Missense_Mutation_p.L697V|FLII_uc010vxo.1_Missense_Mutation_p.L673V|FLII_uc002gss.1_Missense_Mutation_p.L727V	NM_002018	NP_002009	Q13045	FLII_HUMAN	flightless I homolog	728	Interaction with ACTL6A.				multicellular organismal development|muscle contraction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleus	actin binding			central_nervous_system(1)|skin(1)	2	all_neural(463;0.228)					ACCTTGTACAGCTTGGGCTGC	0.622											OREG0024225	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	61	---	---	---	---	PASS
KRT24	192666	broad.mit.edu	37	17	38855747	38855747	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38855747C>A	uc002hvd.2	-	6	1367	c.1310G>T	c.(1309-1311)CGC>CTC	p.R437L		NM_019016	NP_061889	Q2M2I5	K1C24_HUMAN	keratin 24	437	Rod.|Coil 2.					cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.00526)				CACCTCCAGGCGTGTCTTGAT	0.502													30	158	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45234300	45234300	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45234300G>T	uc002ild.3	-	7	948	c.821C>A	c.(820-822)GCT>GAT	p.A274D	CDC27_uc002ile.3_Missense_Mutation_p.A274D|CDC27_uc002ilf.3_Missense_Mutation_p.A274D|CDC27_uc010wkp.1_Missense_Mutation_p.A213D|CDC27_uc010wkq.1_RNA	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	274					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						TGGACTAAGAGCTGCTGGTCC	0.363													5	51	---	---	---	---	PASS
ABCA5	23461	broad.mit.edu	37	17	67252297	67252297	+	Splice_Site	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67252297C>T	uc002jif.2	-	28	5076	c.3858_splice	c.e28+1	p.E1286_splice	ABCA5_uc002jib.2_Splice_Site_p.E252_splice|ABCA5_uc002jic.2_Splice_Site_p.E509_splice|ABCA5_uc002jid.2_Splice_Site_p.E203_splice|ABCA5_uc002jie.2_Splice_Site|ABCA5_uc002jig.2_Splice_Site_p.E1286_splice	NM_018672	NP_061142	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5						cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)					GAATAAATTACCTCCTCACAA	0.353													7	134	---	---	---	---	PASS
MAP2K6	5608	broad.mit.edu	37	17	67513026	67513026	+	Silent	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67513026C>T	uc002jij.2	+	3	402	c.114C>T	c.(112-114)TGC>TGT	p.C38C	MAP2K6_uc002jii.2_Silent_p.C38C|MAP2K6_uc002jik.2_Silent_p.C68C	NM_002758	NP_002749	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6	38					activation of MAPK activity|cell cycle arrest|DNA damage induced protein phosphorylation|innate immune response|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of muscle cell differentiation|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|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|pancreas(1)	5	Breast(10;6.05e-10)					CCAAGGCTTGCATTTCTATTG	0.363													5	106	---	---	---	---	PASS
PSG3	5671	broad.mit.edu	37	19	43237124	43237124	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43237124G>A	uc002oue.2	-	3	653	c.521C>T	c.(520-522)CCG>CTG	p.P174L	PSG3_uc002ouf.2_RNA|PSG1_uc002oug.1_Intron|PSG3_uc010eil.2_Missense_Mutation_p.P196L	NM_021016	NP_066296	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	174	Ig-like C2-type 1.				defense response|female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)				GCTTGCGTCCGGAGTCTCAGG	0.522													12	277	---	---	---	---	PASS
GLTSCR2	29997	broad.mit.edu	37	19	48254189	48254189	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48254189C>A	uc002phm.2	+	4	447	c.423C>A	c.(421-423)AAC>AAA	p.N141K	GLTSCR2_uc002phk.2_Missense_Mutation_p.N141K|GLTSCR2_uc002phl.2_Missense_Mutation_p.N141K|GLTSCR2_uc010elj.2_Missense_Mutation_p.N141K|GLTSCR2_uc010elk.1_5'Flank	NM_015710	NP_056525	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	141						nucleolus				central_nervous_system(1)	1		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		AGGTCCCCAACGCCAAGAAGC	0.706													3	5	---	---	---	---	PASS
MIR516B1	574490	broad.mit.edu	37	19	54240136	54240136	+	RNA	SNP	C	G	G	rs79235448	byFrequency	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54240136C>G	hsa-mir-516b-1|MI0003172	+			c.38C>G			MIR518A2_hsa-mir-518a-2|MI0003173_5'Flank																	0						GAAGCACTTTCTGTTTTGTGA	0.413													7	120	---	---	---	---	PASS
HSPBP1	23640	broad.mit.edu	37	19	55789207	55789207	+	Missense_Mutation	SNP	T	C	C			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55789207T>C	uc002qjx.2	-	2	466	c.356A>G	c.(355-357)CAG>CGG	p.Q119R	HSPBP1_uc002qjy.2_Missense_Mutation_p.Q73R|HSPBP1_uc002qkb.2_Missense_Mutation_p.Q73R|HSPBP1_uc002qka.2_Missense_Mutation_p.Q73R|HSPBP1_uc002qkd.2_Missense_Mutation_p.Q73R|HSPBP1_uc002qkc.2_Missense_Mutation_p.Q73R	NM_012267	NP_036399	Q9NZL4	HPBP1_HUMAN	hsp70-interacting protein	76					positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein folding		enzyme inhibitor activity|protein binding				0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		CTGCAGCCACTGACGCCTCTG	0.577													7	21	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29625885	29625885	+	Missense_Mutation	SNP	A	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29625885A>T	uc010ztl.1	+	2	71	c.39A>T	c.(37-39)AAA>AAT	p.K13N	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						TCGCCCTGAAATCTGGCTATG	0.353													6	113	---	---	---	---	PASS
KRTAP10-4	386672	broad.mit.edu	37	21	45993895	45993895	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45993895C>T	uc002zfk.1	+	1	290	c.260C>T	c.(259-261)CCC>CTC	p.P87L	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198687	NP_941960	P60372	KR104_HUMAN	keratin associated protein 10-4	87	36 X 5 AA repeats of C-C-X(3).					keratin filament					0						TCCTGCACGCCCTCGTGCTGC	0.682													16	85	---	---	---	---	PASS
DGCR14	8220	broad.mit.edu	37	22	19120172	19120172	+	3'UTR	SNP	G	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19120172G>A	uc002zou.2	-	10					DGCR14_uc002zot.2_3'UTR|DGCR14_uc002zov.2_RNA	NM_022719	NP_073210	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region protein 14						nervous system development	catalytic step 2 spliceosome				ovary(1)	1	Colorectal(54;0.0993)					CAGCAAAGACGTTCCTTACTG	0.463													3	4	---	---	---	---	PASS
ARSF	416	broad.mit.edu	37	X	3002395	3002395	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3002395G>T	uc004cre.1	+	6	739	c.518G>T	c.(517-519)TGC>TTC	p.C173F	ARSF_uc004crf.1_Missense_Mutation_p.C173F	NM_004042	NP_004033	P54793	ARSF_HUMAN	arylsulfatase F precursor	173						extracellular region	arylsulfatase activity|metal ion binding			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GTTGACAGCTGCTGGCCGGAC	0.527													6	50	---	---	---	---	PASS
VCX3B	425054	broad.mit.edu	37	X	8434311	8434311	+	Missense_Mutation	SNP	A	G	G			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8434311A>G	uc010ndo.2	+	4	845	c.538A>G	c.(538-540)ATG>GTG	p.M180V	VCX3B_uc004csd.1_Missense_Mutation_p.M160V	NM_001001888	NP_001001888	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	180	8.|11 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.					nucleolus					0						GGAGAGCGAGATGGAAGAACC	0.567													8	310	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	26179532	26179532	+	IGR	SNP	A	G	G	rs5943854	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26179532A>G								MAGEB18 (20680 upstream) : MAGEB6 (31025 downstream)																							GGTCTCTCCAATGAAGGAAGT	0.517													4	74	---	---	---	---	PASS
GDI1	2664	broad.mit.edu	37	X	153665594	153665594	+	5'UTR	SNP	C	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153665594C>T	uc004fli.3	+	1					GDI1_uc011mzo.1_5'UTR	NM_001493	NP_001484	P31150	GDIA_HUMAN	GDP dissociation inhibitor 1						protein transport|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|midbody	GTPase activator activity|protein binding				0	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGCACCGAGGCCTGACCATGG	0.547													18	9	---	---	---	---	PASS
RERE	473	broad.mit.edu	37	1	8555372	8555373	+	Intron	INS	-	T	T	rs111493554		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8555372_8555373insT	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc010nzx.1_Intron|RERE_uc001aph.1_Intron	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		CTCTGCTCCTAttttttttttt	0.228													4	2	---	---	---	---	
PTPN22	26191	broad.mit.edu	37	1	114401266	114401266	+	Intron	DEL	T	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114401266delT	uc001eds.2	-						uc001edv.1_Intron|PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron|PTPN22_uc001edu.2_Intron	NM_015967	NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		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)		CTCCGCTTCCttttttttttt	0.234													4	2	---	---	---	---	
C1orf56	54964	broad.mit.edu	37	1	151022895	151022896	+	Intron	INS	-	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151022895_151022896insT	uc001ewn.2	+							NM_017860	NP_060330	Q9BUN1	CA056_HUMAN	hypothetical protein LOC54964 precursor							extracellular region					0	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CTTTTTCTCTATTTTTTTTTCT	0.436													112	7	---	---	---	---	
TUFT1	7286	broad.mit.edu	37	1	151518480	151518480	+	Intron	DEL	T	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151518480delT	uc001eyl.2	+						TUFT1_uc001eym.2_Intron|TUFT1_uc010pdf.1_Intron|TUFT1_uc010pdg.1_Intron	NM_020127	NP_064512	Q9NNX1	TUFT1_HUMAN	tuftelin 1 isoform 1						bone mineralization|odontogenesis	cytoplasm|extracellular region	structural constituent of tooth enamel				0	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			catttttttcttttttttttt	0.139													4	2	---	---	---	---	
IMMT	10989	broad.mit.edu	37	2	86385653	86385653	+	Intron	DEL	T	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86385653delT	uc002sqz.3	-						IMMT_uc002sqy.3_Intron|IMMT_uc002srb.3_Intron|IMMT_uc002sra.3_Intron|IMMT_uc010ytd.1_Intron|IMMT_uc010yte.1_Intron|IMMT_uc002src.1_Intron|IMMT_uc002srd.2_3'UTR	NM_006839	NP_006830	Q16891	IMMT_HUMAN	inner membrane protein, mitochondrial isoform 1							integral to mitochondrial inner membrane	protein binding			skin(1)	1						ATGAAGCAAGTTTAGATTCAT	0.368													2	4	---	---	---	---	
RAPH1	65059	broad.mit.edu	37	2	204302738	204302739	+	3'UTR	INS	-	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204302738_204302739insA	uc002vad.2	-	14						NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains						cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10						AAAATTCACAGAAAAAAGCATA	0.366													3	3	---	---	---	---	
OR5H14	403273	broad.mit.edu	37	3	97868429	97868429	+	Frame_Shift_Del	DEL	C	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97868429delC	uc003dsg.1	+	1	200	c.200delC	c.(199-201)GCTfs	p.A67fs		NM_001005514	NP_001005514	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H,	67	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						GGGAATTTAGCTTTTGTGGAT	0.398													296	10	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79205383	79205384	+	Intron	INS	-	T	T	rs75951231		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79205383_79205384insT	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron|FRAS1_uc003hky.1_Intron|FRAS1_uc003hkz.2_Intron|FRAS1_uc003hla.1_5'Flank	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						ATTGGAATGTAttttttttttt	0.347													11	5	---	---	---	---	
LEF1	51176	broad.mit.edu	37	4	108999640	108999640	+	Intron	DEL	G	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108999640delG	uc003hyt.1	-						LEF1_uc011cfj.1_Intron|LEF1_uc011cfk.1_Intron|LEF1_uc003hyu.1_Intron|LEF1_uc003hyv.1_Intron|LEF1_uc010imb.1_Intron|LEF1_uc010ima.1_5'Flank|LEF1_uc003hyw.1_Intron	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1						canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		GCTACACTCAGGATGGCGACA	0.517													42	22	---	---	---	---	
FAM134B	54463	broad.mit.edu	37	5	16572323	16572323	+	Intron	DEL	T	-	-	rs68191869		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16572323delT	uc003jfs.2	-							NM_001034850	NP_001030022	Q9H6L5	F134B_HUMAN	hypothetical protein LOC54463 isoform 1						sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3						ATGATTTCACttttttttttt	0.144													4	2	---	---	---	---	
FAM65B	9750	broad.mit.edu	37	6	24851127	24851127	+	Intron	DEL	T	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24851127delT	uc003neo.1	-						FAM65B_uc011djs.1_Intron|FAM65B_uc011dju.1_Intron|FAM65B_uc003nep.2_Intron|FAM65B_uc011djt.1_Intron	NM_014722	NP_055537	Q9Y4F9	FA65B_HUMAN	hypothetical protein LOC9750 isoform 1						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1						GGGAGGAGACttttttttttt	0.289													8	5	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38800028	38800029	+	Intron	INS	-	AT	AT			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38800028_38800029insAT	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						CACTTGTTGGAATAGAATTGTA	0.312													5	3	---	---	---	---	
BAIAP2L1	55971	broad.mit.edu	37	7	98015040	98015041	+	Intron	INS	-	T	T	rs144554018	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98015040_98015041insT	uc003upj.2	-							NM_018842	NP_061330	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			ATCAACATTTCTTTTTTTTGTT	0.178													9	4	---	---	---	---	
MTUS1	57509	broad.mit.edu	37	8	17613213	17613215	+	In_Frame_Del	DEL	GGT	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17613213_17613215delGGT	uc003wxv.2	-	2	576_578	c.102_104delACC	c.(100-105)CCACCT>CCT	p.34_35PP>P	MTUS1_uc010lsy.2_RNA|MTUS1_uc003wxw.2_In_Frame_Del_p.34_35PP>P|MTUS1_uc010lsz.2_In_Frame_Del_p.34_35PP>P	NM_001001924	NP_001001924	Q9ULD2	MTUS1_HUMAN	mitochondrial tumor suppressor 1 isoform 1	34_35						Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)		GTTTTGTGTAGGTGGTGATTTCG	0.399													158	10	---	---	---	---	
CSPP1	79848	broad.mit.edu	37	8	68066164	68066165	+	Intron	INS	-	A	A	rs11784423	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68066164_68066165insA	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672	Q1MSJ5	CSPP1_HUMAN	centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			tttttttttttaaaaatgaatt	0.262													4	2	---	---	---	---	
UBR5	51366	broad.mit.edu	37	8	103358988	103358988	+	Intron	DEL	A	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103358988delA	uc003ykr.1	-						UBR5_uc003yks.1_Intron	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			ctctcaaaggaaaaaaaaaaa	0.164													4	2	---	---	---	---	
SCRIB	23513	broad.mit.edu	37	8	144894702	144894703	+	Intron	INS	-	T	T	rs149556936	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144894702_144894703insT	uc003yzp.1	-						SCRIB_uc003yzo.1_Intron	NM_015356	NP_056171	Q14160	SCRIB_HUMAN	scribble isoform b						activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction	cell-cell adherens junction|Scrib-APC-beta-catenin complex	protein binding			urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CCTACCTTGCCCCACAAGCCTG	0.658													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44109097	44109098	+	IGR	INS	-	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44109097_44109098insA								FAM75A6 (478367 upstream) : FAM27C (881138 downstream)																							ATAAAGGTCTCAAAAATCCAGA	0.347													5	5	---	---	---	---	
KIN	22944	broad.mit.edu	37	10	7816626	7816627	+	Intron	INS	-	A	A			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7816626_7816627insA	uc001ijt.2	-						KIN_uc010qaz.1_Intron|KIN_uc009xip.2_Intron|KIN_uc010qba.1_Intron	NM_012311	NP_036443	O60870	KIN17_HUMAN	HsKin17 protein						DNA recombination|DNA repair|DNA replication|interspecies interaction between organisms|mRNA processing	cytoplasm|nuclear matrix	double-stranded DNA binding|RNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						ccccatctcttaaaaaaaaaaa	0.119													5	3	---	---	---	---	
ARHGAP12	94134	broad.mit.edu	37	10	32141656	32141657	+	Intron	DEL	TC	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32141656_32141657delTC	uc001ivz.1	-						ARHGAP12_uc001ivy.1_Intron|ARHGAP12_uc009xls.2_Intron|ARHGAP12_uc001iwb.1_Intron|ARHGAP12_uc001iwc.1_Intron|ARHGAP12_uc009xlq.1_Intron|ARHGAP12_uc001iwd.1_Intron|ARHGAP12_uc009xlr.1_Intron	NM_018287	NP_060757	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)				AACAAAAAAttctttttttttt	0.114													5	3	---	---	---	---	
NANOS1	340719	broad.mit.edu	37	10	120789635	120789637	+	In_Frame_Del	DEL	GAC	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120789635_120789637delGAC	uc009xzf.1	+	1	408_410	c.322_324delGAC	c.(322-324)GACdel	p.D112del		NM_199461	NP_955631	Q8WY41	NANO1_HUMAN	nanos homolog 1	112					epithelial cell migration	perinuclear region of cytoplasm	protein binding|RNA binding|translation repressor activity|zinc ion binding				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0193)		ctacgacgaggacgacgacgacg	0.389													4	2	---	---	---	---	
C11orf46	120534	broad.mit.edu	37	11	30358034	30358034	+	Intron	DEL	T	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30358034delT	uc001mso.1	+						C11orf46_uc001msp.2_5'Flank	NM_152316	NP_689529	Q8N8R7	CK046_HUMAN	hypothetical protein LOC120534												0						TTTTATCTCCTTTTTTTTTTT	0.284													4	2	---	---	---	---	
GALNT4	8693	broad.mit.edu	37	12	89919737	89919737	+	5'Flank	DEL	G	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89919737delG	uc001tbd.2	-						POC1B_uc001tba.2_5'Flank|POC1B_uc001tbb.2_5'Flank|POC1B_uc001tbc.2_5'UTR|POC1B_uc010sun.1_RNA|GALNT4_uc001tbe.2_5'UTR|GALNT4_uc010suo.1_5'UTR	NM_003774	NP_003765	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4						carbohydrate metabolic process	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0						gggagaggatggggaaggaga	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	55014796	55014797	+	IGR	INS	-	TTTT	TTTT			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55014796_55014797insTTTT								MIR1297 (128613 upstream) : None (None downstream)																							tttcaggttcctttTTTTTTTT	0.188													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	97535721	97535721	+	IGR	DEL	A	-	-	rs148246127	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97535721delA								HS6ST3 (43910 upstream) : OXGR1 (102252 downstream)																							GAACAAAATTAAAAAAAAAAC	0.264													4	2	---	---	---	---	
BTBD7	55727	broad.mit.edu	37	14	93720048	93720048	+	Frame_Shift_Del	DEL	T	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93720048delT	uc001ybo.2	-	7	2023	c.1697delA	c.(1696-1698)AATfs	p.N566fs	BTBD7_uc010aur.2_Frame_Shift_Del_p.N91fs|BTBD7_uc010two.1_Frame_Shift_Del_p.N386fs|BTBD7_uc001ybp.2_Frame_Shift_Del_p.N215fs	NM_001002860	NP_001002860	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7 isoform 1	566										pancreas(1)	1		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		GATGCCAGCATTTTTTTGCCG	0.383													193	7	---	---	---	---	
KLHL25	64410	broad.mit.edu	37	15	86314432	86314433	+	Intron	INS	-	A	A	rs55642980		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86314432_86314433insA	uc002bly.2	-						MIR1276_hsa-mir-1276|MI0006416_5'Flank	NM_022480	NP_071925	Q9H0H3	ENC2_HUMAN	BTB/POZ KELCH domain protein							cytoplasm				ovary(2)	2						AATTAAGCCTGaaaaaaaaaaa	0.406													4	2	---	---	---	---	
CLEC16A	23274	broad.mit.edu	37	16	11064883	11064883	+	Intron	DEL	G	-	-	rs78420628		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11064883delG	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041	Q2KHT3	CL16A_HUMAN	C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2						TTTTTTTTTTGTCTTTTTCTG	0.408													5	3	---	---	---	---	
PMFBP1	83449	broad.mit.edu	37	16	72163921	72163921	+	Intron	DEL	T	-	-	rs67023960		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72163921delT	uc002fcc.3	-						PMFBP1_uc002fcd.2_Intron|PMFBP1_uc002fce.2_Intron|PMFBP1_uc002fcf.2_Intron|PMFBP1_uc010cgo.1_5'Flank	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1											ovary(2)	2		Ovarian(137;0.179)				aatgtttgtattttttttttt	0.000													3	4	---	---	---	---	
CCDC144A	9720	broad.mit.edu	37	17	16623497	16623498	+	Intron	INS	-	T	T			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16623497_16623498insT	uc002gqk.1	+						CCDC144A_uc002gql.1_Intron|LOC162632_uc010cpj.1_Intron	NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A												0						AAAAGGAATTGTTTTTTTTTTT	0.248													4	2	---	---	---	---	
EFCAB5	374786	broad.mit.edu	37	17	28295793	28295793	+	Intron	DEL	T	-	-	rs141990566	by1000genomes	TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28295793delT	uc002het.2	+						EFCAB5_uc010wbi.1_Intron|EFCAB5_uc010wbj.1_Intron|EFCAB5_uc010wbk.1_Intron|EFCAB5_uc010csd.2_Intron|EFCAB5_uc010cse.2_5'Flank|EFCAB5_uc010csf.2_5'Flank	NM_198529	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5 isoform a								calcium ion binding			ovary(1)|skin(1)	2						TACATTTCACTTTTTTTTCCC	0.308													4	2	---	---	---	---	
HEXIM1	10614	broad.mit.edu	37	17	43227525	43227526	+	In_Frame_Ins	INS	-	GGAGCT	GGAGCT			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43227525_43227526insGGAGCT	uc002iig.2	+	1	2842_2843	c.968_969insGGAGCT	c.(967-969)CGG>CGGGAGCTG	p.329_330insEL		NM_006460	NP_006451	O94992	HEXI1_HUMAN	hexamethylene bis-acetamide inducible 1	329_330	Potential.|Required for inhibition of ESR1-dependent transcription.				negative regulation of cyclin-dependent protein kinase activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	cyclin-dependent protein kinase inhibitor activity|protein binding|snRNA binding			ovary(1)	1						GCGCGTGTGCGGGAGCTGGAGC	0.668													114	17	---	---	---	---	
USP36	57602	broad.mit.edu	37	17	76808801	76808801	+	Intron	DEL	G	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76808801delG	uc002jvz.1	-						USP36_uc002jwa.1_Intron|USP36_uc002jwb.1_Intron|USP36_uc002jwc.1_Intron	NM_025090	NP_079366	Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36						ubiquitin-dependent protein catabolic process	nucleolus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			aaaaaaaaaagaaaagaaAAG	0.214													7	6	---	---	---	---	
PLAUR	5329	broad.mit.edu	37	19	44159429	44159429	+	Intron	DEL	A	-	-	rs146818784		TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44159429delA	uc002oxf.1	-						PLAUR_uc002oxd.1_Intron|PLAUR_uc002oxe.1_Intron|PLAUR_uc002oxg.1_Intron	NM_002659	NP_002650	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor						attachment of GPI anchor to protein|blood coagulation|C-terminal protein lipidation|cellular component movement|chemotaxis|fibrinolysis|regulation of proteolysis	anchored to membrane|cell surface|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|extrinsic to membrane|integral to membrane|plasma membrane	enzyme binding|U-plasminogen activator receptor activity			ovary(1)	1		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Urokinase(DB00013)	actccgtctcaaaaaaaaaaa	0.080													4	3	---	---	---	---	
SFRS16	11129	broad.mit.edu	37	19	45567373	45567375	+	In_Frame_Del	DEL	GAG	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45567373_45567375delGAG	uc002pak.2	+	12	1107_1109	c.1009_1011delGAG	c.(1009-1011)GAGdel	p.E338del	SFRS16_uc002pal.2_RNA|SFRS16_uc010xxh.1_In_Frame_Del_p.E276del|SFRS16_uc002pam.2_In_Frame_Del_p.E338del|SFRS16_uc002pan.1_RNA	NM_007056	NP_008987	Q8N2M8	CLASR_HUMAN	splicing factor, arginine/serine-rich 16	338					mRNA processing|RNA splicing	nucleus					0		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GGGCAGCGATGAGGAGGCAGCCG	0.704													35	7	---	---	---	---	
ABCG1	9619	broad.mit.edu	37	21	43639333	43639335	+	5'UTR	DEL	CCG	-	-			TCGA-G9-6363-01	TCGA-G9-6363-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43639333_43639335delCCG	uc002zaq.2	+	1					ABCG1_uc002zan.2_Intron|ABCG1_uc002zam.2_Intron|ABCG1_uc002zao.2_Intron|ABCG1_uc002zap.2_5'UTR|ABCG1_uc002zar.2_5'Flank|ABCG1_uc011aev.1_5'Flank	NM_004915	NP_004906	P45844	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1						amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|recycling endosome	ADP binding|ATP binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)|central_nervous_system(1)	3					Adenosine triphosphate(DB00171)	AGCCTCGTCCccgccgccgccgc	0.596													5	4	---	---	---	---	
