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
KLHL21	9903	broad.mit.edu	37	1	6655551	6655551	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6655551C>T	uc001aoa.2	-	3	1546	c.1494G>A	c.(1492-1494)ATG>ATA	p.M498I	KLHL21_uc001anz.1_Missense_Mutation_p.M498I|KLHL21_uc009vme.2_Missense_Mutation_p.M131I	NM_014851	NP_055666	Q9UJP4	KLH21_HUMAN	kelch-like 21	498	Kelch 5.				anaphase|cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex|cytoplasm|polar microtubule				central_nervous_system(1)	1	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)		TTACCTGATTCATGGACGGGA	0.552													12	39	---	---	---	---	PASS
CLSTN1	22883	broad.mit.edu	37	1	9809930	9809930	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9809930G>T	uc001aqh.2	-	6	1450	c.691C>A	c.(691-693)CAT>AAT	p.H231N	CLSTN1_uc001aqi.2_Missense_Mutation_p.H221N|CLSTN1_uc010oag.1_Missense_Mutation_p.H231N	NM_001009566	NP_001009566	O94985	CSTN1_HUMAN	calsyntenin 1 isoform 1	231	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		TTATATTGATGTTCTTTCCCG	0.423													18	68	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974745	16974745	+	RNA	SNP	G	A	A	rs28526603	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974745G>A	uc010och.1	+	7		c.1205G>A			MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						CCTGGAACCGGAGGGCCGGGG	0.711													4	34	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974758	16974758	+	RNA	SNP	G	A	A	rs28484638	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974758G>A	uc010och.1	+	7		c.1218G>A			MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						GGCCGGGGCGGGGTCTCGGCC	0.716													5	28	---	---	---	---	PASS
ARID1A	8289	broad.mit.edu	37	1	27107213	27107213	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27107213T>C	uc001bmv.1	+	20	7197	c.6824T>C	c.(6823-6825)ATT>ACT	p.I2275T	ARID1A_uc001bmu.1_Missense_Mutation_p.I2058T|ARID1A_uc001bmx.1_Missense_Mutation_p.I1121T|ARID1A_uc009vsm.1_Missense_Mutation_p.I603T|ARID1A_uc009vsn.1_Missense_Mutation_p.I517T	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	2275					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TCACAAGTCATTTGTGATGTA	0.498			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								50	118	---	---	---	---	PASS
SLC9A1	6548	broad.mit.edu	37	1	27440753	27440753	+	Nonsense_Mutation	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27440753G>C	uc001bnm.2	-	2	1003	c.377C>G	c.(376-378)TCA>TGA	p.S126*	SLC9A1_uc010ofk.1_Intron|SLC9A1_uc001bnn.2_Nonsense_Mutation_p.S126*	NM_003047	NP_003038	P19634	SL9A1_HUMAN	solute carrier family 9, isoform A1	126	Helical; Name=M2; (Potential).				regulation of pH	integral to membrane	sodium:hydrogen antiporter activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	GACGATGCTTGAGATAGTGGG	0.637													10	76	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34052715	34052715	+	Missense_Mutation	SNP	C	T	T	rs143826784		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34052715C>T	uc001bxn.1	-	46	6945	c.6916G>A	c.(6916-6918)GTC>ATC	p.V2306I	CSMD2_uc001bxm.1_Missense_Mutation_p.V2304I	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2306	Sushi 13.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TTCTCTGTGACGACTTCGGCG	0.527													7	17	---	---	---	---	PASS
ZMYM1	79830	broad.mit.edu	37	1	35580008	35580008	+	Silent	SNP	C	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35580008C>A	uc001bym.2	+	11	2725	c.2577C>A	c.(2575-2577)GTC>GTA	p.V859V	ZMYM1_uc001byn.2_Silent_p.V859V|ZMYM1_uc010ohu.1_Silent_p.V840V|ZMYM1_uc001byo.2_Silent_p.V499V|ZMYM1_uc009vut.2_Silent_p.V784V	NM_024772	NP_079048	Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM domain containing 1	859						nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTGAATTTGTCTTTTGTTTGA	0.323													22	82	---	---	---	---	PASS
BCAR3	8412	broad.mit.edu	37	1	94048304	94048304	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94048304T>C	uc001dpz.2	-	7	1515	c.1240A>G	c.(1240-1242)AAG>GAG	p.K414E	BCAR3_uc001dqa.2_Missense_Mutation_p.K414E|BCAR3_uc001dqb.2_Missense_Mutation_p.K414E|BCAR3_uc001dpx.3_Missense_Mutation_p.K90E|BCAR3_uc001dpy.2_Missense_Mutation_p.K323E|BCAR3_uc009wdm.1_Missense_Mutation_p.K90E	NM_003567	NP_003558	O75815	BCAR3_HUMAN	breast cancer antiestrogen resistance 3	414					response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		GAGGGAACCTTGAGGAACGGC	0.627													47	86	---	---	---	---	PASS
BCAR3	8412	broad.mit.edu	37	1	94048425	94048425	+	Silent	SNP	G	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94048425G>T	uc001dpz.2	-	7	1394	c.1119C>A	c.(1117-1119)GCC>GCA	p.A373A	BCAR3_uc001dqa.2_Silent_p.A373A|BCAR3_uc001dqb.2_Silent_p.A373A|BCAR3_uc001dpx.3_Silent_p.A49A|BCAR3_uc001dpy.2_Silent_p.A282A|BCAR3_uc009wdm.1_Silent_p.A49A	NM_003567	NP_003558	O75815	BCAR3_HUMAN	breast cancer antiestrogen resistance 3	373					response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		CTGGGCTCAGGGCAGGCTCGC	0.642													26	59	---	---	---	---	PASS
NOTCH2	4853	broad.mit.edu	37	1	120468210	120468210	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120468210C>T	uc001eik.2	-	25	4485	c.4229G>A	c.(4228-4230)CGC>CAC	p.R1410H		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	1410	Extracellular (Potential).|EGF-like 35.				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAGTTCACAGCGGCTACCCGA	0.647			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				32	75	---	---	---	---	PASS
PSMB4	5692	broad.mit.edu	37	1	151373481	151373481	+	Intron	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151373481C>T	uc001eyc.1	+						PSMB4_uc010pda.1_3'UTR|PSMB4_uc001eyb.1_3'UTR	NM_002796	NP_002787	P28070	PSB4_HUMAN	proteasome beta 4 subunit						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity			ovary(2)	2	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GGTGTTGACACTGATTCCAGT	0.458													11	25	---	---	---	---	PASS
PGLYRP3	114771	broad.mit.edu	37	1	153283179	153283179	+	5'UTR	SNP	A	G	G	rs3006473	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153283179A>G	uc001fbn.1	-	1						NM_052891	NP_443123	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3 precursor						defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGTGGACGGCAGCCCTGGAAG	0.562													6	138	---	---	---	---	PASS
RC3H1	149041	broad.mit.edu	37	1	173934019	173934019	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173934019A>G	uc001gju.3	-	9	1661	c.1574T>C	c.(1573-1575)ATA>ACA	p.I525T	RC3H1_uc010pms.1_Missense_Mutation_p.I525T|RC3H1_uc001gjv.2_Missense_Mutation_p.I525T|RC3H1_uc010pmt.1_Missense_Mutation_p.I525T	NM_172071	NP_742068	Q5TC82	RC3H1_HUMAN	roquin	525					cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway	cytoplasmic mRNA processing body|stress granule	mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						CAGATGATCTATTTTTCCTGG	0.423													74	123	---	---	---	---	PASS
RNASEL	6041	broad.mit.edu	37	1	182544563	182544563	+	Silent	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182544563A>G	uc001gpj.1	-	6	2357	c.2190T>C	c.(2188-2190)GCT>GCC	p.A730A	RNASEL_uc009wxz.1_Silent_p.A730A	NM_021133	NP_066956	Q05823	RN5A_HUMAN	ribonuclease L	730					mRNA processing|response to virus|type I interferon-mediated signaling pathway	mitochondrion	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding			ovary(4)|stomach(1)	5						TGGCCCCACCAGCTCCATCAC	0.413									Hereditary_Prostate_Cancer				66	157	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215799083	215799083	+	3'UTR	SNP	A	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215799083A>T	uc001hku.1	-	72						NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATGGGTGCAGACCTTGCATTC	0.413										HNSCC(13;0.011)			21	55	---	---	---	---	PASS
EMILIN1	11117	broad.mit.edu	37	2	27307380	27307380	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27307380G>C	uc002rii.3	+	5	2966	c.2538G>C	c.(2536-2538)GAG>GAC	p.E846D	EMILIN1_uc002rik.3_Missense_Mutation_p.E81D|KHK_uc002ril.2_5'Flank|KHK_uc002rim.2_5'Flank|KHK_uc002rin.2_5'Flank|KHK_uc002rio.2_5'Flank	NM_007046	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1 precursor	846	Collagen-like.|Potential.				cell adhesion	collagen				pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACGGGCAAGAGGGCCCCATCG	0.697													32	79	---	---	---	---	PASS
SLC5A6	8884	broad.mit.edu	37	2	27424293	27424293	+	Silent	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27424293A>G	uc002rjd.2	-	15	1964	c.1573T>C	c.(1573-1575)TTG>CTG	p.L525L	SLC5A6_uc010eyv.1_Silent_p.L525L	NM_021095	NP_066918	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium-dependent	525					biotin metabolic process|pantothenate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|Lipoic Acid(DB00166)	AAGTAAGACAAGGAATAGAAC	0.522													4	83	---	---	---	---	PASS
KCNH7	90134	broad.mit.edu	37	2	163236424	163236424	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163236424T>G	uc002uch.1	-	14	3282	c.3070A>C	c.(3070-3072)AGC>CGC	p.S1024R		NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,	1024	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	GTGAGGTCGCTTTCGGTTTCA	0.507													97	224	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179427281	179427281	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179427281C>G	uc010zfg.1	-	275	76098	c.75874G>C	c.(75874-75876)GTG>CTG	p.V25292L	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V18987L|TTN_uc010zfi.1_Missense_Mutation_p.V18920L|TTN_uc010zfj.1_Missense_Mutation_p.V18795L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	26219							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)			GGTTCAGACACTTTAACGGGT	0.438													38	80	---	---	---	---	PASS
GPBAR1	151306	broad.mit.edu	37	2	219127645	219127645	+	Silent	SNP	G	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219127645G>T	uc010zjw.1	+	2	445	c.198G>T	c.(196-198)CTG>CTT	p.L66L	GPBAR1_uc010zjx.1_Silent_p.L66L|GPBAR1_uc010zjy.1_Silent_p.L66L	NM_170699	NP_733800	Q8TDU6	GPBAR_HUMAN	G protein-coupled bile acid receptor 1	66	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;7.19e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCACGGGTCTGGCATTGCCCA	0.652													12	22	---	---	---	---	PASS
RNPEPL1	57140	broad.mit.edu	37	2	241514017	241514017	+	Silent	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241514017C>T	uc002vzi.2	+	6	1160	c.567C>T	c.(565-567)GTC>GTT	p.V189V	RNPEPL1_uc010fzf.2_Silent_p.V95V|RNPEPL1_uc002vzj.2_5'Flank	NM_018226	NP_060696	Q9HAU8	RNPL1_HUMAN	arginyl aminopeptidase (aminopeptidase B)-like	189					leukotriene biosynthetic process|proteolysis		aminopeptidase activity|metallopeptidase activity|zinc ion binding			large_intestine(1)|skin(1)	2		all_epithelial(40;1.13e-11)|Breast(86;0.000169)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.204)|Melanoma(123;0.238)		Epithelial(32;3.05e-31)|all cancers(36;8.2e-29)|OV - Ovarian serous cystadenocarcinoma(60;8.55e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.12e-06)|Lung(119;0.00168)|Colorectal(34;0.005)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.0322)		ACAGCCCGGTCAGCAAACTGC	0.647													6	21	---	---	---	---	PASS
FAM19A4	151647	broad.mit.edu	37	3	68802104	68802104	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68802104G>A	uc003dnh.1	-	4	639	c.196C>T	c.(196-198)CGC>TGC	p.R66C	FAM19A4_uc003dni.1_Missense_Mutation_p.R66C	NM_182522	NP_872328	Q96LR4	F19A4_HUMAN	family with sequence similarity 19 (chemokine	66						extracellular region				skin(2)	2		Lung NSC(201;0.0198)		BRCA - Breast invasive adenocarcinoma(55;1.38e-05)|Epithelial(33;0.000124)|LUSC - Lung squamous cell carcinoma(21;0.0248)|KIRC - Kidney renal clear cell carcinoma(39;0.0729)|Kidney(39;0.0904)		TCTTCTATGCGGTTCTTATTG	0.542													13	97	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	3	159706882	159706882	+	Splice_Site	SNP	A	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159706882A>C	uc003fcw.1	-	9		c.1350_splice	c.e9+1		IL12A_uc003fcx.2_Silent_p.S13S					Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		CACCGCCCTCACCTGCCGCGG	0.652											OREG0015908	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	22	---	---	---	---	PASS
TNIK	23043	broad.mit.edu	37	3	170893117	170893117	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170893117G>A	uc003fhh.2	-	9	1042	c.697C>T	c.(697-699)CTC>TTC	p.L233F	TNIK_uc003fhi.2_Missense_Mutation_p.L233F|TNIK_uc003fhj.2_Missense_Mutation_p.L233F|TNIK_uc003fhk.2_Missense_Mutation_p.L233F|TNIK_uc003fhl.2_Missense_Mutation_p.L233F|TNIK_uc003fhm.2_Missense_Mutation_p.L233F|TNIK_uc003fhn.2_Missense_Mutation_p.L233F|TNIK_uc003fho.2_Missense_Mutation_p.L233F	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1	233	Protein kinase.				actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			ATGTCACAGAGAGCTGCAAGA	0.557													14	21	---	---	---	---	PASS
LRRC33	375387	broad.mit.edu	37	3	196387275	196387275	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196387275C>T	uc003fwv.2	+	3	865	c.761C>T	c.(760-762)ACG>ATG	p.T254M		NM_198565	NP_940967	Q86YC3	LRC33_HUMAN	leucine rich repeat containing 33 precursor	254	Extracellular (Potential).|LRR 9.					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.9e-23)|all cancers(36;1.76e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		GAGCTGGAGACGCTGGACCTG	0.632													13	79	---	---	---	---	PASS
WDFY3	23001	broad.mit.edu	37	4	85664902	85664902	+	Silent	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85664902G>A	uc003hpd.2	-	37	6432	c.6024C>T	c.(6022-6024)TAC>TAT	p.Y2008Y		NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	2008						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TATCCAAAATGTAAGTTTGAA	0.318													40	75	---	---	---	---	PASS
BANK1	55024	broad.mit.edu	37	4	102751087	102751087	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102751087T>A	uc003hvy.3	+	2	467	c.193T>A	c.(193-195)TTC>ATC	p.F65I	BANK1_uc003hvx.3_Missense_Mutation_p.F50I|BANK1_uc010ill.2_Intron|BANK1_uc003hvz.3_Missense_Mutation_p.F35I	NM_017935	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	65	Interaction with ITPR2.				B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		CTTGGAGAATTTCTCTTTTCG	0.368													55	138	---	---	---	---	PASS
BDH2	56898	broad.mit.edu	37	4	104000886	104000886	+	Silent	SNP	G	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104000886G>T	uc003hwz.2	-	10	816	c.711C>A	c.(709-711)GTC>GTA	p.V237V	NHEDC2_uc003hwx.3_5'Flank|NHEDC2_uc003hwy.2_5'Flank|NHEDC2_uc011cew.1_5'Flank|NHEDC2_uc011cex.1_5'Flank|BDH2_uc003hxa.2_RNA	NM_020139	NP_064524	Q9BUT1	BDH2_HUMAN	3-hydroxybutyrate dehydrogenase, type 2	237					fatty acid beta-oxidation|heme metabolic process|iron ion homeostasis|siderophore biosynthetic process	cytoplasm	3-hydroxybutyrate dehydrogenase activity|NAD binding|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.02e-08)		CATCAATGATGACAGGGTTAC	0.443													32	42	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16711272	16711272	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16711272G>C	uc003jft.3	-	20	2480	c.2012C>G	c.(2011-2013)GCT>GGT	p.A671G	MYO10_uc011cnd.1_Missense_Mutation_p.A28G|MYO10_uc011cne.1_Missense_Mutation_p.A28G|MYO10_uc010itx.2_Missense_Mutation_p.A294G	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	671	Myosin head-like.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						CGCATACCCAGCTTTGCGGAT	0.488													17	57	---	---	---	---	PASS
FYB	2533	broad.mit.edu	37	5	39202090	39202090	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39202090G>C	uc003jls.2	-	1	1040	c.973C>G	c.(973-975)CCA>GCA	p.P325A	FYB_uc003jlt.2_Missense_Mutation_p.P325A|FYB_uc003jlu.2_Missense_Mutation_p.P325A|FYB_uc011cpl.1_Missense_Mutation_p.P335A	NM_199335	NP_955367	O15117	FYB_HUMAN	FYN binding protein (FYB-120/130) isoform 2	325					cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)			TGGCCCCATGGCCCCCCCACT	0.537													11	103	---	---	---	---	PASS
HEATR7B2	133558	broad.mit.edu	37	5	41065513	41065513	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41065513T>G	uc003jmj.3	-	4	771	c.281A>C	c.(280-282)GAA>GCA	p.E94A		NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	94							binding			ovary(6)|central_nervous_system(2)	8						ACTTTGTACTTCATACATCAC	0.428													24	72	---	---	---	---	PASS
IPO11	51194	broad.mit.edu	37	5	61779118	61779118	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61779118A>C	uc003jtc.2	+	10	1209	c.1019A>C	c.(1018-1020)GAA>GCA	p.E340A	IPO11_uc011cqr.1_Missense_Mutation_p.E380A|IPO11_uc003jtb.1_Missense_Mutation_p.E340A	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2	340	HEAT 3.					cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		AAAAATTTTGAAGGTAATTCC	0.264													18	56	---	---	---	---	PASS
MCCC2	64087	broad.mit.edu	37	5	70945080	70945080	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70945080G>A	uc003kbs.3	+	14	1511	c.1373G>A	c.(1372-1374)AGC>AAC	p.S458N	MCCC2_uc003kbt.3_RNA	NM_022132	NP_071415	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)	458	Carboxyltransferase.				leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)	1		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	AGAGCATATAGGTAGGTGTCA	0.438													51	111	---	---	---	---	PASS
RAD50	10111	broad.mit.edu	37	5	131930637	131930637	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131930637A>G	uc003kxi.2	+	12	2257	c.1870A>G	c.(1870-1872)AGT>GGT	p.S624G	RAD50_uc003kxh.2_Missense_Mutation_p.S485G	NM_005732	NP_005723	Q92878	RAD50_HUMAN	RAD50 homolog isoform 1	624					DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCAGTTGTCCAGTTACGAAGA	0.343								Homologous_recombination					135	128	---	---	---	---	PASS
ADRB2	154	broad.mit.edu	37	5	148207220	148207220	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148207220G>C	uc003lpr.1	+	1	1065	c.826G>C	c.(826-828)GGC>CGC	p.G276R	SH3TC2_uc003lpp.1_Intron	NM_000024	NP_000015	P07550	ADRB2_HUMAN	adrenergic, beta-2-, receptor, surface	276	Helical; Name=6.				activation of transmembrane receptor protein tyrosine kinase activity|desensitization of G-protein coupled receptor protein signaling pathway by arrestin|endosome to lysosome transport|positive regulation of MAPKKK cascade|receptor-mediated endocytosis	endosome|integral to plasma membrane|lysosome|receptor complex	beta2-adrenergic receptor activity|norepinephrine binding|potassium channel regulator activity|protein homodimerization activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Alprenolol(DB00866)|Arformoterol(DB01274)|Bambuterol(DB01408)|Bisoprolol(DB00612)|Bitolterol(DB00901)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Nadolol(DB01203)|Norepinephrine(DB00368)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Terbutaline(DB00871)|Timolol(DB00373)	CAAGACGTTAGGCATCATCAT	0.522													13	146	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176562309	176562309	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176562309T>C	uc003mfr.3	+	2	343	c.205T>C	c.(205-207)TAC>CAC	p.Y69H	NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Missense_Mutation_p.Y69H|NSD1_uc011dfx.1_Intron|NSD1_uc003mfp.2_Missense_Mutation_p.Y69H|NSD1_uc003mfq.2_Missense_Mutation_p.Y69H	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	69					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TCCATCTTGTTACATTCCACT	0.413			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			76	91	---	---	---	---	PASS
SYCP2L	221711	broad.mit.edu	37	6	10907856	10907856	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10907856G>C	uc003mzo.2	+	10	1054	c.758G>C	c.(757-759)TGG>TCG	p.W253S	SYCP2L_uc011din.1_Missense_Mutation_p.W94S|SYCP2L_uc010jow.2_5'UTR	NM_001040274	NP_001035364	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	253						nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			GTCCATAAATGGTTTGATGAT	0.373													30	159	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54805594	54805594	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54805594C>T	uc003pck.2	+	5	1941	c.1825C>T	c.(1825-1827)CCA>TCA	p.P609S		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	609										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					GTCAGAGGCACCAAAAATGCA	0.433													30	77	---	---	---	---	PASS
ZNF292	23036	broad.mit.edu	37	6	87969169	87969169	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87969169A>C	uc003plm.3	+	8	5863	c.5822A>C	c.(5821-5823)CAA>CCA	p.Q1941P		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	1941					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AAGAAGAATCAATTGAAATTT	0.348													5	14	---	---	---	---	PASS
AKAP7	9465	broad.mit.edu	37	6	131540937	131540937	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131540937C>A	uc003qck.2	+	7	872	c.839C>A	c.(838-840)TCC>TAC	p.S280Y	AKAP7_uc011ebz.1_Missense_Mutation_p.S258Y|AKAP7_uc003qcl.1_Missense_Mutation_p.S161Y	NM_016377	NP_057461	O43687	AKA7A_HUMAN	A-kinase anchor protein 7 isoform gamma	Error:Variant_position_missing_in_O43687_after_alignment					intracellular signal transduction|ion transport	apical plasma membrane|intracellular|lateral plasma membrane	protein kinase A binding			ovary(2)	2	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		TGTGAATCTTCCATTGTGATT	0.264													20	80	---	---	---	---	PASS
FAM54A	113115	broad.mit.edu	37	6	136562720	136562720	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136562720C>G	uc010kgp.1	-	5	766	c.376G>C	c.(376-378)GAA>CAA	p.E126Q	FAM54A_uc003qgt.1_Missense_Mutation_p.E126Q|FAM54A_uc003qgu.1_Missense_Mutation_p.E83Q	NM_001099286	NP_001092756	Q6P444	FA54A_HUMAN	DUF729 domain containing 1	126										skin(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00228)|OV - Ovarian serous cystadenocarcinoma(155;0.00504)		TTCACAGTTTCTTTCTGTCTT	0.393													28	74	---	---	---	---	PASS
IL20RA	53832	broad.mit.edu	37	6	137322636	137322636	+	3'UTR	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137322636A>G	uc003qhj.2	-	7					IL20RA_uc011edl.1_3'UTR|IL20RA_uc003qhk.2_3'UTR|IL20RA_uc003qhi.2_3'UTR	NM_014432	NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha precursor							integral to membrane	receptor activity			ovary(2)|skin(2)	4	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		TATGGCTGGGATCAAAGGGGT	0.413													20	100	---	---	---	---	PASS
IGF2R	3482	broad.mit.edu	37	6	160471666	160471666	+	Silent	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160471666C>T	uc003qta.2	+	19	2824	c.2676C>T	c.(2674-2676)GTC>GTT	p.V892V		NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor	892	6.|Lumenal (Potential).				receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)		TCCATCTCGTCTGCTCCAGGG	0.557													15	24	---	---	---	---	PASS
ZNF713	349075	broad.mit.edu	37	7	56007482	56007482	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56007482G>A	uc003trc.1	+	4	1114	c.1076G>A	c.(1075-1077)TGT>TAT	p.C359Y	ZNF713_uc003tra.1_Missense_Mutation_p.C372Y|MRPS17_uc003trb.2_Intron	NM_182633	NP_872439	Q8N859	ZN713_HUMAN	zinc finger protein 713	359	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CCTTACGAATGTGGTTTCTGT	0.403													59	174	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94050324	94050324	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94050324C>A	uc003ung.1	+	38	2770	c.2299C>A	c.(2299-2301)CCA>ACA	p.P767T	COL1A2_uc011kib.1_Intron|COL1A2_uc010lfi.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	767			Missing (in OI2A).		axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CATTTAGGGTCCAAATGGTCC	0.443										HNSCC(75;0.22)			45	170	---	---	---	---	PASS
LMTK2	22853	broad.mit.edu	37	7	97766647	97766647	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97766647G>A	uc003upd.1	+	2	417	c.124G>A	c.(124-126)GAA>AAA	p.E42K		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	42					early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					ACCTGCTGCAGAAGTTTCCTC	0.348													156	73	---	---	---	---	PASS
RBM28	55131	broad.mit.edu	37	7	127961369	127961369	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127961369T>A	uc003vmp.2	-	14	1628	c.1513A>T	c.(1513-1515)AAG>TAG	p.K505*	RBM28_uc003vmo.2_Nonsense_Mutation_p.K122*|RBM28_uc011koj.1_Nonsense_Mutation_p.K364*	NM_018077	NP_060547	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	505	RRM 4.				mRNA processing|RNA splicing	Golgi apparatus|nucleolus|spliceosomal complex	nucleotide binding|RNA binding			ovary(2)	2						AGCAGCAGCTTTCTGAGCTGT	0.507													23	123	---	---	---	---	PASS
SVOPL	136306	broad.mit.edu	37	7	138333763	138333763	+	Silent	SNP	G	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138333763G>T	uc011kqh.1	-	7	654	c.654C>A	c.(652-654)GCC>GCA	p.A218A	SVOPL_uc003vue.2_Silent_p.A66A	NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1	218	Helical; (Potential).					integral to membrane	transmembrane transporter activity				0						CCACCTTGAAGGCCACGATGA	0.542													6	52	---	---	---	---	PASS
UBN2	254048	broad.mit.edu	37	7	138944050	138944050	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138944050A>G	uc011kqr.1	+	5	839	c.839A>G	c.(838-840)AAG>AGG	p.K280R	UBN2_uc003vuv.2_Missense_Mutation_p.K3R	NM_173569	NP_775840	Q6ZU65	UBN2_HUMAN	ubinuclein 2	280	Lys-rich.									ovary(1)|skin(1)	2						GAGATGAAGAAGCGGAAGCGG	0.383													31	76	---	---	---	---	PASS
CUL1	8454	broad.mit.edu	37	7	148454216	148454216	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148454216C>T	uc010lpg.2	+	4	983	c.457C>T	c.(457-459)CGA>TGA	p.R153*	CUL1_uc003wey.2_Nonsense_Mutation_p.R153*|CUL1_uc003wez.2_Nonsense_Mutation_p.R43*	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	153					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			TGACGAAGGACGAAAAGGAAT	0.323													18	108	---	---	---	---	PASS
C8orf74	203076	broad.mit.edu	37	8	10558004	10558004	+	3'UTR	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10558004A>G	uc003wtd.1	+	4					C8orf74_uc003wte.1_RNA	NM_001040032	NP_001035121	Q6P047	CH074_HUMAN	hypothetical protein LOC203076												0				COAD - Colon adenocarcinoma(149;0.0811)		GCCACACGAGACTGACTGGGG	0.562													3	3	---	---	---	---	PASS
MYBL1	4603	broad.mit.edu	37	8	67484765	67484765	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67484765C>A	uc003xwj.2	-	12	2087	c.1680G>T	c.(1678-1680)AAG>AAT	p.K560N	MYBL1_uc003xwl.2_Missense_Mutation_p.K560N|MYBL1_uc003xwk.2_Missense_Mutation_p.K559N	NM_001080416	NP_001073885	P10243	MYBA_HUMAN	v-myb myeloblastosis viral oncogene homolog	560					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)	3			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			CAAGCGCATTCTTAAAAGGAG	0.294													42	26	---	---	---	---	PASS
ARFGEF1	10565	broad.mit.edu	37	8	68111271	68111271	+	Silent	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68111271A>G	uc003xxo.1	-	39	5838	c.5448T>C	c.(5446-5448)ATT>ATC	p.I1816I	ARFGEF1_uc003xxl.1_Intron|ARFGEF1_uc003xxm.1_Silent_p.I219I|ARFGEF1_uc003xxn.1_Silent_p.I761I|ARFGEF1_uc003xxp.1_3'UTR	NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine	1816					exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			GAAGTTCAGGAATCAAGTCAA	0.368													50	226	---	---	---	---	PASS
KANK1	23189	broad.mit.edu	37	9	732501	732501	+	Silent	SNP	T	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:732501T>C	uc003zgl.1	+	10	3778	c.3129T>C	c.(3127-3129)ACT>ACC	p.T1043T	KANK1_uc003zgm.2_3'UTR|KANK1_uc003zgn.1_Silent_p.T1043T|KANK1_uc003zgs.1_Silent_p.T885T|KANK1_uc010mgx.1_5'UTR|KANK1_uc010mgy.1_5'UTR|KANK1_uc003zgt.1_5'Flank	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	1043					negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		ATGAAGACACTCGGGGAATGG	0.473													57	73	---	---	---	---	PASS
TAF1L	138474	broad.mit.edu	37	9	32630111	32630111	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32630111C>A	uc003zrg.1	-	1	5557	c.5467G>T	c.(5467-5469)GGG>TGG	p.G1823W		NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1823					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TTTCCGTGCCCATCCTTGTGT	0.498													3	47	---	---	---	---	PASS
RABGAP1	23637	broad.mit.edu	37	9	125782628	125782628	+	Silent	SNP	T	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125782628T>C	uc011lzh.1	+	13	1818	c.1684T>C	c.(1684-1686)TTA>CTA	p.L562L	RABGAP1_uc004bnl.3_RNA	NM_012197	NP_036329	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	562					cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5						GTTGTCATCCTTAGTAAGAAA	0.413													40	71	---	---	---	---	PASS
C9orf163	158055	broad.mit.edu	37	9	139379131	139379131	+	Silent	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139379131G>A	uc004chy.2	+	1	1185	c.231G>A	c.(229-231)CAG>CAA	p.Q77Q	SEC16A_uc004chx.2_5'Flank|SEC16A_uc010nbo.1_5'Flank	NM_152571	NP_689784	Q8N9P6	CI163_HUMAN	hypothetical protein LOC158055	77							protein binding				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.36e-06)|Epithelial(140;5.65e-06)		TGCCACGCCAGCAGGGCCGCA	0.662													3	30	---	---	---	---	PASS
PRTFDC1	56952	broad.mit.edu	37	10	25145923	25145923	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25145923T>G	uc001ise.1	-	6	454	c.425A>C	c.(424-426)GAT>GCT	p.D142A	PRTFDC1_uc010qdd.1_Missense_Mutation_p.D142A|PRTFDC1_uc001isf.1_RNA|PRTFDC1_uc009xkm.1_RNA	NM_020200	NP_064585	Q9NRG1	PRDC1_HUMAN	phosphoribosyl transferase domain containing 1	142	GMP.	Magnesium (Probable).			adenine salvage|central nervous system neuron development|cerebral cortex neuron differentiation|cytolysis|dendrite morphogenesis|GMP salvage|grooming behavior|hypoxanthine metabolic process|IMP salvage|lymphocyte proliferation|positive regulation of dopamine metabolic process|purine ribonucleoside salvage|response to amphetamine|striatum development	cytosol	hypoxanthine phosphoribosyltransferase activity|magnesium ion binding|nucleotide binding|protein homodimerization activity			ovary(1)	1						TCCGACAACATCCTTTGCAAA	0.398													48	105	---	---	---	---	PASS
GBF1	8729	broad.mit.edu	37	10	104126846	104126846	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104126846G>C	uc001kux.1	+	20	2675	c.2435G>C	c.(2434-2436)TGT>TCT	p.C812S	GBF1_uc001kuy.1_Missense_Mutation_p.C812S|GBF1_uc001kuz.1_Missense_Mutation_p.C813S	NM_004193	NP_004184	Q92538	GBF1_HUMAN	golgi-specific brefeldin A resistant guanine	812	SEC7.				COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		TTTCAGAATTGTAATGGCTCC	0.483													32	154	---	---	---	---	PASS
SEC23IP	11196	broad.mit.edu	37	10	121657969	121657969	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121657969G>C	uc001leu.1	+	2	266	c.194G>C	c.(193-195)AGC>ACC	p.S65T	SEC23IP_uc010qtc.1_Intron	NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125	65	Interaction with SEC23A.				Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		GAGGAGGACAGCTTCCTTGGT	0.448													39	203	---	---	---	---	PASS
GPR123	84435	broad.mit.edu	37	10	134942620	134942620	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134942620C>G	uc001llx.3	+	7	1724	c.1288C>G	c.(1288-1290)CCA>GCA	p.P430A	GPR123_uc001llw.2_Missense_Mutation_p.P1149A	NM_001083909	NP_001077378	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	430	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		TAGCCGGCACCCAGCAGAGGA	0.692													5	5	---	---	---	---	PASS
ZNF215	7762	broad.mit.edu	37	11	6953811	6953811	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6953811A>C	uc001mey.2	+	3	896	c.308A>C	c.(307-309)GAA>GCA	p.E103A	ZNF215_uc010raw.1_Missense_Mutation_p.E103A|ZNF215_uc010rax.1_5'UTR|ZNF215_uc001mez.1_Missense_Mutation_p.E103A	NM_013250	NP_037382	Q9UL58	ZN215_HUMAN	zinc finger protein 215	103	SCAN box.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		CTGCCTGAAGAAGTCAGGACT	0.413													33	87	---	---	---	---	PASS
SLC5A12	159963	broad.mit.edu	37	11	26718743	26718743	+	Silent	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26718743A>G	uc001mra.2	-	8	1321	c.1008T>C	c.(1006-1008)CTT>CTC	p.L336L	SLC5A12_uc001mrb.2_RNA|SLC5A12_uc001mrc.3_Silent_p.L336L	NM_178498	NP_848593	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/glucose	336	Helical; (Potential).				sodium ion transport	apical plasma membrane|integral to membrane	symporter activity			ovary(1)|skin(1)	2						AAGCCACAAAAAGTCCTGGCA	0.373													42	125	---	---	---	---	PASS
NUP160	23279	broad.mit.edu	37	11	47827752	47827752	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47827752A>C	uc001ngm.2	-	20	2644	c.2559T>G	c.(2557-2559)AAT>AAG	p.N853K	NUP160_uc009ylw.2_RNA	NM_015231	NP_056046	Q12769	NU160_HUMAN	nucleoporin 160kDa	853					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7						TTTCAGGCCAATTCAATCCAG	0.353													46	117	---	---	---	---	PASS
ZDHHC5	25921	broad.mit.edu	37	11	57457522	57457522	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57457522C>T	uc001nkx.1	+	5	1660	c.404C>T	c.(403-405)CCC>CTC	p.P135L	ZDHHC5_uc001nky.1_Missense_Mutation_p.P82L|ZDHHC5_uc001nkz.1_5'UTR	NM_015457	NP_056272	Q9C0B5	ZDHC5_HUMAN	zinc finger, DHHC domain containing 5	135	DHHC-type.					integral to membrane	acyltransferase activity|zinc ion binding			skin(1)	1						CATCACTGCCCCTGGGTGAAT	0.458													61	143	---	---	---	---	PASS
SHANK2	22941	broad.mit.edu	37	11	70338536	70338536	+	Silent	SNP	G	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70338536G>T	uc001oqc.2	-	18	2421	c.2343C>A	c.(2341-2343)CCC>CCA	p.P781P	SHANK2_uc010rqn.1_Silent_p.P193P|SHANK2_uc001opz.2_Silent_p.P186P|uc009ysn.1_Intron|SHANK2_uc010rqp.1_Silent_p.P183P|SHANK2_uc001opy.2_5'UTR|SHANK2_uc010rqo.1_5'UTR	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	402					intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			CAGCGCGGGAGGGCTTGGAGG	0.607													6	65	---	---	---	---	PASS
ARHGAP20	57569	broad.mit.edu	37	11	110450017	110450017	+	3'UTR	SNP	C	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110450017C>A	uc001pkz.1	-	16					ARHGAP20_uc001pky.1_3'UTR|ARHGAP20_uc009yyb.1_3'UTR|ARHGAP20_uc001pla.1_3'UTR|ARHGAP20_uc001plb.2_Intron	NM_020809	NP_065860	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		GTATCTTATACAAAGGGGTCA	0.318													10	56	---	---	---	---	PASS
MPZL2	10205	broad.mit.edu	37	11	118133279	118133279	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118133279A>G	uc001psn.2	-	3	451	c.310T>C	c.(310-312)TAC>CAC	p.Y104H	MPZL2_uc001pso.2_Missense_Mutation_p.Y104H|MPZL2_uc001psp.1_Missense_Mutation_p.Y104H	NM_005797	NP_005788	O60487	MPZL2_HUMAN	myelin protein zero-like 2 precursor	104	Extracellular (Potential).|Ig-like V-type.				anatomical structure morphogenesis|homophilic cell adhesion	cytoskeleton|integral to membrane				skin(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		GAGGCATCGTACCGCTCAGGA	0.527													32	66	---	---	---	---	PASS
MLL	4297	broad.mit.edu	37	11	118370617	118370617	+	Silent	SNP	T	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118370617T>A	uc001pta.2	+	24	6161	c.6138T>A	c.(6136-6138)CCT>CCA	p.P2046P	MLL_uc001ptb.2_Silent_p.P2049P	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	2046	FYR N-terminal.				apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		AGCTCTTTCCTATTGGATATC	0.428			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								41	94	---	---	---	---	PASS
BLID	414899	broad.mit.edu	37	11	121986687	121986687	+	5'UTR	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121986687G>A	uc001pyf.2	-	1					LOC399959_uc009zba.2_Intron	NM_001001786	NP_001001786	Q8IZY5	BLID_HUMAN	BRCC2 protein						apoptosis	mitochondrion					0		Breast(109;0.0164)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;2.08e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.101)		GCTTTATTCAGCAAGTTTTTA	0.383											OREG0021435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	42	---	---	---	---	PASS
WNK1	65125	broad.mit.edu	37	12	936351	936351	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:936351G>C	uc001qio.3	+	3	1583	c.1076G>C	c.(1075-1077)GGC>GCC	p.G359A	WNK1_uc001qin.2_Missense_Mutation_p.G359A|WNK1_uc001qip.3_Missense_Mutation_p.G359A	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	359	Protein kinase.				intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TTTATCACCGGCCCTACTGGC	0.483													73	312	---	---	---	---	PASS
FOXM1	2305	broad.mit.edu	37	12	2983386	2983386	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2983386T>A	uc001qlf.2	-	2	524	c.259A>T	c.(259-261)ATC>TTC	p.I87F	TULP3_uc010sef.1_5'Flank|FOXM1_uc001qle.2_Missense_Mutation_p.I87F|FOXM1_uc001qlg.2_Missense_Mutation_p.I87F|FOXM1_uc009zea.2_Missense_Mutation_p.I87F|FOXM1_uc009zeb.2_Missense_Mutation_p.I87F|C12orf32_uc001qlh.2_5'Flank|C12orf32_uc010see.1_5'Flank|C12orf32_uc001qli.2_5'Flank	NM_021953	NP_068772	Q08050	FOXM1_HUMAN	forkhead box M1 isoform 2	87					cell cycle|embryo development|liver development|negative regulation of cell aging|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|positive regulation of cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell cycle arrest|regulation of cell growth|regulation of cell proliferation|regulation of oxygen and reactive oxygen species metabolic process|regulation of Ras protein signal transduction|regulation of reactive oxygen species metabolic process|regulation of sequence-specific DNA binding transcription factor activity|tissue development|transcription from RNA polymerase II promoter|vasculogenesis	cytoplasm|transcription factor complex	DNA bending activity|DNA binding|DNA binding|double-stranded DNA binding|promoter binding|protein binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|transcription factor binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			GCTGTGATGATGCTGTGAATA	0.517													50	163	---	---	---	---	PASS
DUSP16	80824	broad.mit.edu	37	12	12629998	12629998	+	Silent	SNP	A	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12629998A>T	uc001rao.1	-	7	2399	c.1767T>A	c.(1765-1767)ACT>ACA	p.T589T	DUSP16_uc001ram.1_5'Flank|DUSP16_uc001ran.1_Silent_p.T441T	NM_030640	NP_085143	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	589					inactivation of MAPK activity|MAPK export from nucleus|MAPK phosphatase export from nucleus, leptomycin B sensitive	cytoplasmic membrane-bounded vesicle|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		GGTCTCCGCAAGTGGGCAGCT	0.572													45	206	---	---	---	---	PASS
TRPC4	7223	broad.mit.edu	37	13	38266299	38266299	+	Silent	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38266299C>T	uc001uws.2	-	4	1306	c.1071G>A	c.(1069-1071)CTG>CTA	p.L357L	TRPC4_uc010abv.2_Intron|TRPC4_uc001uwt.2_Silent_p.L357L|TRPC4_uc010tey.1_Silent_p.L357L|TRPC4_uc010abw.2_Silent_p.L184L|TRPC4_uc010abx.2_Silent_p.L357L|TRPC4_uc010aby.2_Silent_p.L357L	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	357	Extracellular (Potential).				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TCCTGATGAACAGTCCAAGTG	0.463													24	81	---	---	---	---	PASS
KIAA0564	23078	broad.mit.edu	37	13	42293563	42293563	+	Intron	SNP	A	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42293563A>C	uc001uyj.2	-						KIAA0564_uc001uyk.2_3'UTR	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)		CCTATAAATAATGCTATTTAA	0.299													6	11	---	---	---	---	PASS
C13orf1	57213	broad.mit.edu	37	13	50489191	50489191	+	3'UTR	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50489191A>G	uc001vdl.2	-	5					C13orf1_uc001vdm.2_3'UTR|C13orf1_uc010tgm.1_RNA	NM_020456	NP_065189	Q5W111	SPRY7_HUMAN	chromosome 13 open reading frame 1 isoform 1												0		Lung NSC(96;7.5e-06)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Acute lymphoblastic leukemia(7;0.117)		GBM - Glioblastoma multiforme(99;1.72e-10)|COAD - Colon adenocarcinoma(199;0.208)		TTTTAAAAACAAATACATTCA	0.294													26	108	---	---	---	---	PASS
RBM26	64062	broad.mit.edu	37	13	79940847	79940847	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79940847A>C	uc001vkz.2	-	7	1070	c.1056T>G	c.(1054-1056)ATT>ATG	p.I352M	RBM26_uc001vky.2_Missense_Mutation_p.I352M|RBM26_uc001vla.2_Missense_Mutation_p.I352M|RBM26_uc001vkx.2_Missense_Mutation_p.I64M|RBM26_uc001vlb.1_RNA	NM_022118	NP_071401	Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	352	Pro-rich.				mRNA processing		nucleotide binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		GGGGTGTAAGAATTGGTGGAG	0.537													59	64	---	---	---	---	PASS
ARGLU1	55082	broad.mit.edu	37	13	107209856	107209856	+	Intron	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107209856C>T	uc001vqk.3	-						ARGLU1_uc010age.1_3'UTR	NM_018011	NP_060481	Q9NWB6	ARGL1_HUMAN	arginine and glutamate rich 1												0	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					TGTATACCTACGTATTCTTTA	0.333													4	23	---	---	---	---	PASS
WHAMML1	339005	broad.mit.edu	37	15	23205094	23205094	+	RNA	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23205094G>A	uc001yvg.2	-	2		c.701C>T			WHAMML1_uc010ayc.2_RNA|WHAMML1_uc010ayd.2_RNA|WHAMML1_uc010aye.1_RNA	NR_003521				Homo sapiens mRNA; cDNA DKFZp313L2232 (from clone DKFZp313L2232).												0						AGTACTGGAAGAACGTGGTTG	0.373													3	22	---	---	---	---	PASS
WDR93	56964	broad.mit.edu	37	15	90276288	90276288	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90276288T>A	uc002boj.2	+	13	1483	c.1382T>A	c.(1381-1383)ATT>AAT	p.I461N	WDR93_uc010bnr.2_Intron|WDR93_uc010upz.1_Missense_Mutation_p.I178N	NM_020212	NP_064597	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	461					electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TGCCAAAGCATTCACTTCCTA	0.478													92	200	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	102304772	102304772	+	5'Flank	SNP	T	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102304772T>C	uc002cbx.1	-						uc002ccc.1_5'Flank|uc002ccf.3_RNA|uc002ccg.3_5'Flank|uc010uth.1_5'Flank|uc002cci.2_5'Flank|uc002ccj.2_5'Flank|uc002cck.2_5'Flank|uc002ccl.1_5'Flank|uc002ccm.1_5'Flank					DQ582460																		CACAGCGGCGTGACGAGACTC	0.587													5	19	---	---	---	---	PASS
LOC100134368	100134368	broad.mit.edu	37	16	436768	436768	+	Intron	SNP	G	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:436768G>T	uc002cgw.1	+						uc002cgx.3_Silent_p.A26A	NR_024453				Homo sapiens cDNA clone IMAGE:3636396, partial cds.												0						ACAAGATGGCGCTGAAAGCAA	0.333													5	100	---	---	---	---	PASS
TBC1D24	57465	broad.mit.edu	37	16	2549923	2549923	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2549923G>A	uc002cql.2	+	6	1434	c.1294G>A	c.(1294-1296)GTG>ATG	p.V432M	TBC1D24_uc002cqk.2_Missense_Mutation_p.V426M|TBC1D24_uc002cqm.2_Intron|TBC1D24_uc010bsm.2_RNA	NM_020705	NP_065756	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	432	TLD.				neuron projection development	cytoplasm	protein binding|Rab GTPase activator activity				0						AGAATGCTTTGTGTTTAGGGT	0.577													26	79	---	---	---	---	PASS
TMEM208	29100	broad.mit.edu	37	16	67261756	67261756	+	Silent	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67261756C>T	uc002esi.2	+	2	130	c.24C>T	c.(22-24)GGC>GGT	p.G8G	LRRC29_uc002ese.2_5'Flank|LRRC29_uc002esf.2_5'Flank|LRRC29_uc002esg.2_5'Flank|LRRC29_uc010vjg.1_5'Flank|TMEM208_uc002esj.2_RNA	NM_014187	NP_054906	Q9BTX3	TM208_HUMAN	HSPC171 protein	8						integral to membrane					0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		GCAAAGTGGGCACGAGAGGGA	0.537													3	15	---	---	---	---	PASS
VAC14	55697	broad.mit.edu	37	16	70834811	70834811	+	Translation_Start_Site	SNP	G	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70834811G>T	uc002ezm.2	-	1	251	c.-7C>A	c.(-9--5)AGCTG>AGATG		VAC14_uc010cfw.2_Translation_Start_Site|VAC14_uc002ezn.2_Translation_Start_Site	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog						interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)				CATGGTGGCAGCTGGGGGAAC	0.557													6	38	---	---	---	---	PASS
CNTNAP4	85445	broad.mit.edu	37	16	76495979	76495979	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76495979C>T	uc002feu.1	+	11	1845	c.1460C>T	c.(1459-1461)TCG>TTG	p.S487L	CNTNAP4_uc002fev.1_Missense_Mutation_p.S351L|CNTNAP4_uc010chb.1_Missense_Mutation_p.S414L|CNTNAP4_uc002fex.1_Missense_Mutation_p.S490L|CNTNAP4_uc002few.2_Missense_Mutation_p.S462L	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	487	Extracellular (Potential).|Laminin G-like 2.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						CAGATTTATTCGGGTGGCACC	0.493													20	62	---	---	---	---	PASS
KIAA0513	9764	broad.mit.edu	37	16	85100597	85100597	+	5'UTR	SNP	C	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85100597C>G	uc002fiu.2	+	2					KIAA0513_uc002fis.3_5'UTR|KIAA0513_uc010voj.1_5'UTR|KIAA0513_uc002fit.2_5'UTR	NM_014732	NP_055547	O60268	K0513_HUMAN	hypothetical protein LOC9764							cytoplasm				breast(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.234)		CTCCTACTAACGCACCTGGGA	0.622													12	24	---	---	---	---	PASS
MIR22	407004	broad.mit.edu	37	17	1617206	1617206	+	RNA	SNP	C	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1617206C>A	hsa-mir-22|MI0000078	-			c.76C>A			C17orf91_uc002ftf.2_5'UTR|C17orf91_uc002ftg.2_5'UTR|WDR81_uc002fth.2_5'Flank|WDR81_uc010vqp.1_5'Flank																	0						GGGCAGAGGGCAACAGTTCTT	0.572													19	51	---	---	---	---	PASS
ACTG1	71	broad.mit.edu	37	17	79478982	79478982	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79478982G>C	uc002kaj.1	-	2	335	c.310C>G	c.(310-312)CTG>GTG	p.L104V	ACTG1_uc002kah.1_5'Flank|ACTG1_uc002kai.1_Missense_Mutation_p.L61V|ACTG1_uc002kak.1_Missense_Mutation_p.L104V|ACTG1_uc010wun.1_Missense_Mutation_p.L104V|ACTG1_uc002kal.1_Missense_Mutation_p.L104V|ACTG1_uc002kag.2_RNA	NM_001614	NP_001605	P63261	ACTG_HUMAN	actin, gamma 1 propeptide	104					adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol	ATP binding|identical protein binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			TCGGTCAGCAGCACTGGGTGC	0.627													10	113	---	---	---	---	PASS
SLC25A10	1468	broad.mit.edu	37	17	79687128	79687128	+	3'UTR	SNP	G	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79687128G>C	uc002kbi.2	+	11					SLC25A10_uc010wut.1_3'UTR|SLC25A10_uc010dif.2_3'UTR|SLC25A10_uc010wuu.1_3'UTR	NM_012140	NP_036272	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier;						gluconeogenesis|mitochondrial transport	integral to membrane|mitochondrial inner membrane|nucleus	protein binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	GAATGGCTGGGCTGCCAGGCC	0.612													9	7	---	---	---	---	PASS
DSG4	147409	broad.mit.edu	37	18	28972163	28972163	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28972163C>T	uc002kwq.2	+	8	1000	c.865C>T	c.(865-867)CGA>TGA	p.R289*	DSG4_uc002kwr.2_Nonsense_Mutation_p.R289*	NM_177986	NP_817123	Q86SJ6	DSG4_HUMAN	desmoglein 4 isoform 2 preproprotein	289	Cadherin 3.|Extracellular (Potential).		Missing (in LAH1).		homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GGAACTGATACGATTACAAGC	0.343													46	119	---	---	---	---	PASS
SLC14A2	8170	broad.mit.edu	37	18	43212331	43212331	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43212331G>T	uc010dnj.2	+	6	859	c.538G>T	c.(538-540)GGA>TGA	p.G180*	SLC14A2_uc002lbb.2_Nonsense_Mutation_p.G180*|SLC14A2_uc002lbe.2_Nonsense_Mutation_p.G180*	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),	180	Helical; (Potential).					apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4						CATTGCCTCAGGACTCCATGG	0.448													46	120	---	---	---	---	PASS
ZNF560	147741	broad.mit.edu	37	19	9578075	9578075	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9578075A>C	uc002mlp.1	-	10	1758	c.1548T>G	c.(1546-1548)TTT>TTG	p.F516L	ZNF560_uc010dwr.1_Missense_Mutation_p.F410L	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560	516	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|pancreas(1)|liver(1)	6						TGTAACACTTAAAGGGCTTCT	0.413													52	163	---	---	---	---	PASS
EMR3	84658	broad.mit.edu	37	19	14755050	14755050	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14755050C>T	uc002mzi.3	-	9	1068	c.920G>A	c.(919-921)TGG>TAG	p.W307*	EMR3_uc010dzp.2_Nonsense_Mutation_p.W255*|EMR3_uc010xnv.1_Nonsense_Mutation_p.W181*	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	307	Extracellular (Potential).|GPS.				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						TGTGCTCTTCCAGTAGACACA	0.433													42	87	---	---	---	---	PASS
ZNF429	353088	broad.mit.edu	37	19	21719682	21719682	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21719682A>C	uc002nqd.1	+	4	964	c.827A>C	c.(826-828)AAG>ACG	p.K276T	ZNF429_uc010ecu.1_Intron	NM_001001415	NP_001001415	Q86V71	ZN429_HUMAN	zinc finger protein 429	276	C2H2-type 5.			Missing (in Ref. 2; AAP30884 and 3; AAK01422).	regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						ACTACCCATAAGAGAATTCAT	0.373													15	92	---	---	---	---	PASS
TSHZ3	57616	broad.mit.edu	37	19	31767620	31767620	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31767620T>C	uc002nsy.3	-	2	3144	c.3079A>G	c.(3079-3081)AAA>GAA	p.K1027E		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	1027					negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					GTCACCATTTTTTCTGACGGT	0.498													18	52	---	---	---	---	PASS
TMEM149	79713	broad.mit.edu	37	19	36230813	36230813	+	Silent	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36230813C>T	uc002obc.2	-	4	620	c.519G>A	c.(517-519)TTG>TTA	p.L173L	TMEM149_uc002obb.2_Intron|TMEM149_uc002obd.3_Silent_p.L173L|TMEM149_uc010xsy.1_RNA|TMEM149_uc010eej.2_Silent_p.L253L	NM_024660	NP_078936	Q9H665	IGFR1_HUMAN	transmembrane protein 149 precursor	173	Helical; (Potential).					integral to membrane|plasma membrane	protein binding|receptor activity				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTATCACCGCCAAGGTCAGGA	0.602													40	94	---	---	---	---	PASS
GGN	199720	broad.mit.edu	37	19	38876071	38876071	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38876071C>T	uc002oij.1	-	3	1966	c.1831G>A	c.(1831-1833)GTC>ATC	p.V611I	GGN_uc002oik.1_RNA|GGN_uc010efy.1_3'UTR	NM_152657	NP_689870	Q86UU5	GGN_HUMAN	gametogenetin	611	Interactions with ZNF403/GGNBP2 and OAZ3 (By similarity).				cell differentiation|multicellular organismal development|spermatogenesis						0	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CAGGCAGAGACGTTGCGTGGC	0.627													11	37	---	---	---	---	PASS
HNRNPUL1	11100	broad.mit.edu	37	19	41808474	41808474	+	Intron	SNP	C	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41808474C>A	uc002oqb.3	+						CYP2F1_uc010xvw.1_Intron|HNRNPUL1_uc002opz.3_Intron|HNRNPUL1_uc002oqa.3_Intron|HNRNPUL1_uc010ehm.2_Intron|HNRNPUL1_uc002oqc.3_Intron|HNRNPUL1_uc002oqe.3_Intron|HNRNPUL1_uc002oqd.3_Intron|HNRNPUL1_uc010ehn.2_Intron|HNRNPUL1_uc010eho.2_Intron|HNRNPUL1_uc010xvy.1_Intron|HNRNPUL1_uc010ehp.2_Intron|HNRNPUL1_uc002oqf.3_Missense_Mutation_p.P55H	NM_007040	NP_008971	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1						nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	enzyme binding|RNA binding			central_nervous_system(1)|skin(1)	2						CACCTTCTCCCTTCTGGAAGG	0.358													13	37	---	---	---	---	PASS
FUT2	2524	broad.mit.edu	37	19	49207301	49207301	+	3'UTR	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49207301C>T	uc002pke.3	+	2					FUT2_uc010emc.2_3'UTR	NM_001097638	NP_001091107	Q10981	FUT2_HUMAN	fucosyltransferase 2						L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	galactoside 2-alpha-L-fucosyltransferase activity			central_nervous_system(1)	1		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.00011)|all cancers(93;0.000238)|GBM - Glioblastoma multiforme(486;0.0164)|Epithelial(262;0.017)		AAGATGAGTGCCCGGGCATGA	0.398													3	30	---	---	---	---	PASS
KLK11	11012	broad.mit.edu	37	19	51525739	51525739	+	3'UTR	SNP	T	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51525739T>G	uc002pvd.1	-	6					KLK10_uc002puy.2_5'Flank|KLK10_uc002puz.2_5'Flank|KLK10_uc002pva.2_5'Flank|KLK11_uc002pvb.1_3'UTR|KLK11_uc002pve.1_3'UTR|KLK11_uc002pvf.1_3'UTR|KLK11_uc002pvc.3_3'UTR	NM_144947	NP_659196	Q9UBX7	KLK11_HUMAN	kallikrein 11 isoform 2 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|GBM - Glioblastoma multiforme(134;0.00878)		ATTAACAGAGTGAACAGGAAC	0.448													42	90	---	---	---	---	PASS
ZNF841	284371	broad.mit.edu	37	19	52569496	52569496	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52569496C>A	uc002pyl.1	-	5	1843	c.1291G>T	c.(1291-1293)GGC>TGC	p.G431C	ZNF841_uc010ydh.1_Missense_Mutation_p.G547C|ZNF841_uc010epk.1_Intron	NM_001136499	NP_001129971	Q6ZN19	ZN841_HUMAN	zinc finger protein 841	431	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AAGACCTTGCCACACACATTA	0.388													4	63	---	---	---	---	PASS
ZNF543	125919	broad.mit.edu	37	19	57835116	57835116	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57835116G>A	uc002qoi.1	+	2	430	c.85G>A	c.(85-87)GCC>ACC	p.A29T		NM_213598	NP_998763	Q08ER8	ZN543_HUMAN	zinc finger protein 543	29	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)|pancreas(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GTTGGATGCAGCCCAGAGAAC	0.517													16	196	---	---	---	---	PASS
SEL1L2	80343	broad.mit.edu	37	20	13845886	13845886	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13845886T>G	uc010gcf.2	-	17	1654	c.1572A>C	c.(1570-1572)AAA>AAC	p.K524N	SEL1L2_uc002woq.3_Missense_Mutation_p.K385N|SEL1L2_uc010zrl.1_Missense_Mutation_p.K469T|SEL1L2_uc002wor.2_RNA	NM_025229	NP_079505	Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 precursor	524	Extracellular (Potential).					integral to membrane	binding			ovary(2)	2						TGTTAGCCTTTTCTAAAAAGA	0.383													12	173	---	---	---	---	PASS
PLAGL2	5326	broad.mit.edu	37	20	30784502	30784502	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30784502G>A	uc002wxn.2	-	3	1461	c.1244C>T	c.(1243-1245)TCC>TTC	p.S415F		NM_002657	NP_002648	Q9UPG8	PLAL2_HUMAN	pleiomorphic adenoma gene-like 2	415						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			CAGTAGGTGGGAGAAGTCCAC	0.647													16	25	---	---	---	---	PASS
SLC25A18	83733	broad.mit.edu	37	22	18070862	18070862	+	Intron	SNP	C	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18070862C>T	uc002zmp.1	+						SLC25A18_uc010gqx.2_Silent_p.D249D|SLC25A18_uc002zmq.1_Intron	NM_031481	NP_113669	Q9H1K4	GHC2_HUMAN	solute carrier							integral to membrane|mitochondrial inner membrane	binding|symporter activity				0				Lung(27;0.124)	L-Glutamic Acid(DB00142)	AGTTGGGAGACGTGTCCTTTC	0.522													6	53	---	---	---	---	PASS
BCR	613	broad.mit.edu	37	22	23606091	23606091	+	Intron	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23606091G>A	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron|BCR_uc010gtx.1_Intron|uc010gty.2_RNA	NM_004327	NP_004318	P11274	BCR_HUMAN	breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12						TTTTGTGACAGGGACGGCTTG	0.527			T	ABL1| FGFR1|JAK2 	CML|ALL|AML								12	31	---	---	---	---	PASS
BCR	613	broad.mit.edu	37	22	23606116	23606116	+	Intron	SNP	C	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23606116C>A	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron|BCR_uc010gtx.1_Intron|uc010gty.2_RNA	NM_004327	NP_004318	P11274	BCR_HUMAN	breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12						GGGCACTTCTCACCCCTGAAA	0.507			T	ABL1| FGFR1|JAK2 	CML|ALL|AML								9	37	---	---	---	---	PASS
CCDC157	550631	broad.mit.edu	37	22	30766638	30766638	+	Silent	SNP	C	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30766638C>G	uc011aku.1	+	5	1404	c.744C>G	c.(742-744)CCC>CCG	p.P248P	CCDC157_uc011akv.1_Silent_p.P248P	NM_001017437	NP_001017437	Q569K6	CC157_HUMAN	coiled-coil domain containing 157	248										central_nervous_system(1)	1						AGAACCTGCCCTCGTCCTTAG	0.657													18	33	---	---	---	---	PASS
SMCR7L	54471	broad.mit.edu	37	22	39907312	39907312	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39907312G>A	uc003axx.2	+	3	511	c.13G>A	c.(13-15)GGT>AGT	p.G5S	SMCR7L_uc003axw.2_Missense_Mutation_p.G5S|SMCR7L_uc010gxz.1_5'UTR|SMCR7L_uc003axy.2_5'UTR	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	5						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)					GGCAGGCGCTGGTGAGCGCAA	0.567													3	59	---	---	---	---	PASS
TNRC6B	23112	broad.mit.edu	37	22	40662303	40662303	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40662303A>C	uc011aor.1	+	5	2280	c.2069A>C	c.(2068-2070)AAA>ACA	p.K690T	TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Missense_Mutation_p.K690T|TNRC6B_uc003ayo.2_Missense_Mutation_p.K494T	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	690					gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0						ACAGAGTGGAAAGACCCCAAG	0.527													5	15	---	---	---	---	PASS
MAOA	4128	broad.mit.edu	37	X	43571993	43571993	+	Silent	SNP	A	G	G			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43571993A>G	uc004dfy.2	+	5	634	c.453A>G	c.(451-453)AAA>AAG	p.K151K	MAOA_uc011mkw.1_Silent_p.K18K	NM_000240	NP_000231	P21397	AOFA_HUMAN	monoamine oxidase A	151	Cytoplasmic.				behavior|neurotransmitter biosynthetic process|neurotransmitter catabolic process|neurotransmitter secretion|xenobiotic metabolic process	integral to membrane|mitochondrial outer membrane	primary amine oxidase activity|protein binding			breast(2)|ovary(1)	3					Almotriptan(DB00918)|Carbidopa(DB00190)|Clonazepam(DB01068)|Dopamine(DB00988)|Fluvoxamine(DB00176)|Ginkgo biloba(DB01381)|Imipramine(DB00458)|Isocarboxazid(DB01247)|Levodopa(DB01235)|Linezolid(DB00601)|Lorazepam(DB00186)|Moclobemide(DB01171)|Nicotine(DB00184)|Norepinephrine(DB00368)|Phenelzine(DB00780)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pseudoephedrine(DB00852)|Rasagiline(DB01367)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)	ATGCTGACAAATGGGACAAAA	0.438													20	17	---	---	---	---	PASS
FMR1NB	158521	broad.mit.edu	37	X	147062896	147062896	+	5'UTR	SNP	C	T	T	rs143097707	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147062896C>T	uc004fcm.2	+	1						NM_152578	NP_689791	Q8N0W7	FMR1N_HUMAN	fragile X mental retardation 1 neighbor							integral to membrane				ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					TGTGAGGCAGCGTCTCAGCGA	0.637													31	24	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14465	14465	+	RNA	SNP	G	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14465G>T	uc004cox.3	+	1		c.2129G>T			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CCATCGCTGTAGTATATCCAA	0.438													3	42	---	---	---	---	PASS
FAM131C	348487	broad.mit.edu	37	1	16386305	16386306	+	Intron	INS	-	C	C	rs143272992		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16386305_16386306insC	uc001axz.3	-						FAM131C_uc010obz.1_Intron	NM_182623	NP_872429	Q96AQ9	F131C_HUMAN	hypothetical protein LOC348487												0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		AGTGATCTGGGCCCCCAAGGAC	0.599													3	7	---	---	---	---	
IGSF21	84966	broad.mit.edu	37	1	18442393	18442395	+	Intron	DEL	AAG	-	-	rs72242536		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18442393_18442395delAAG	uc001bau.1	+							NM_032880	NP_116269	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21 precursor							extracellular region				ovary(2)|large_intestine(1)|skin(1)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		gaaagaaagaaagaaggagaggg	0.000													3	3	---	---	---	---	
EPB41	2035	broad.mit.edu	37	1	29435710	29435711	+	Intron	INS	-	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29435710_29435711insA	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron|EPB41_uc009vtn.1_Intron	NM_203342	NP_976217	P11171	41_HUMAN	erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		aactccgtctcaaaaaaaaaaa	0.203													4	2	---	---	---	---	
C1orf87	127795	broad.mit.edu	37	1	60506428	60506428	+	Intron	DEL	T	-	-	rs71582611		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60506428delT	uc001czs.1	-							NM_152377	NP_689590	Q8N0U7	CA087_HUMAN	hypothetical protein LOC127795								calcium ion binding			ovary(1)|breast(1)	2						CTGTCTTTAATTTTttttttt	0.199													3	3	---	---	---	---	
ILDR2	387597	broad.mit.edu	37	1	166944274	166944277	+	Intron	DEL	CACA	-	-	rs67253020		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166944274_166944277delCACA	uc001gdx.1	-							NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor							integral to membrane				ovary(1)	1						CTCTCTCTCTcacacacacacaca	0.441													3	3	---	---	---	---	
KIDINS220	57498	broad.mit.edu	37	2	8891387	8891387	+	Intron	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8891387delT	uc002qzc.2	-						KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Intron|KIDINS220_uc010yiw.1_Intron|KIDINS220_uc002qzb.2_5'Flank|KIDINS220_uc002qze.2_Intron	NM_020738	NP_065789	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate of 220 kDa						activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CAGGAttttcttttttttttt	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	40066918	40066921	+	IGR	DEL	GTGT	-	-	rs113110435		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40066918_40066921delGTGT								THUMPD2 (60502 upstream) : SLC8A1 (272366 downstream)																							ggtagctctcgtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	54907447	54907454	+	IGR	DEL	TCTTTCTT	-	-	rs71408782		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54907447_54907454delTCTTTCTT								SPTBN1 (8865 upstream) : EML6 (44695 downstream)																							ttcttttttctctttctttctttctttc	0.130													4	2	---	---	---	---	
SPOPL	339745	broad.mit.edu	37	2	139326739	139326739	+	3'UTR	DEL	G	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139326739delG	uc002tvh.2	+	11						NM_001001664	NP_001001664	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like							nucleus				skin(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0296)		AGCAAGAGTTGTTTCTGTTAT	0.353													59	26	---	---	---	---	
INPP5D	3635	broad.mit.edu	37	2	234079896	234079896	+	Intron	DEL	A	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234079896delA	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		TCCATTAGGCAAAAAAAAAAG	0.438													4	2	---	---	---	---	
CAMK1	8536	broad.mit.edu	37	3	9809372	9809383	+	In_Frame_Del	DEL	TCGTAGATGTCT	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9809372_9809383delTCGTAGATGTCT	uc003bst.2	-	2	229_240	c.51_62delAGACATCTACGA	c.(49-63)AGAGACATCTACGAC>AGC	p.17_21RDIYD>S	CAMK1_uc003bsu.2_RNA	NM_003656	NP_003647	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	17_21	Protein kinase.				cell differentiation|nervous system development|positive regulation of muscle cell differentiation|signal transduction	cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|skin(1)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		ATCTCGGAAGTCGTAGATGTCTCTAATGTCCT	0.608													67	44	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10188204	10188204	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188204delT	uc003bvc.2	+	2	560	c.347delT	c.(346-348)CTTfs	p.L116fs	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	116	Involved in binding to CCT complex.		L -> V (in VHLD).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(2)|p.L116V(1)|p.W117fs*14(1)|p.W117fs*42(1)|p.L116fs*43(1)|p.H115fs*41(1)|p.H115fs*42(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		ATAGGTCACCTTTGGCTCTTC	0.348		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				113	158	---	---	---	---	
C3orf23	285343	broad.mit.edu	37	3	44399953	44399954	+	Intron	INS	-	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44399953_44399954insA	uc010him.2	+						C3orf23_uc003cnd.3_Intron|C3orf23_uc003cne.3_Intron|C3orf23_uc003cnb.3_3'UTR|C3orf23_uc003cnc.3_3'UTR	NM_173826	NP_776187	Q8N3R3	CC023_HUMAN	hypothetical protein LOC285343 isoform 1							mitochondrion				upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(197;0.0468)|Kidney(197;0.0585)		aatattaggggaaaaaaataca	0.025													4	2	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52621512	52621515	+	Frame_Shift_Del	DEL	ACAA	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52621512_52621515delACAA	uc003des.2	-	19	2989_2992	c.2977_2980delTTGT	c.(2977-2982)TTGTATfs	p.L993fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.L993fs|PBRM1_uc003der.2_Frame_Shift_Del_p.L961fs|PBRM1_uc003det.2_Frame_Shift_Del_p.L1008fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.L1008fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.L993fs|PBRM1_uc010hmk.1_Intron|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_Frame_Shift_Del_p.L992fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.L905fs|PBRM1_uc003dfa.1_Frame_Shift_Del_p.L339fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	993_994	BAH 1.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CAACAGCCATACAACCATTTTTCA	0.333			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								43	56	---	---	---	---	
TPRG1	285386	broad.mit.edu	37	3	188923801	188923802	+	Intron	INS	-	TTCCTTCC	TTCCTTCC	rs149478955	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188923801_188923802insTTCCTTCC	uc003frv.1	+						TPRG1_uc003frw.1_Intron	NM_198485	NP_940887	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		TGCAGGTACAtttccttccttc	0.094													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	15768932	15768933	+	IGR	INS	-	T	T	rs111775272		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15768932_15768933insT								BST1 (28999 upstream) : CD38 (10998 downstream)																							CTTTTTATCAAttttttttttt	0.213													4	2	---	---	---	---	
ANK2	287	broad.mit.edu	37	4	114274162	114274162	+	Intron	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114274162delT	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_5'Flank|ANK2_uc011cgb.1_Intron	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TCTTTTTTGATTTCCATTTTA	0.408													64	30	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	144748482	144748483	+	IGR	INS	-	CCTTCCTT	CCTTCCTT			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144748482_144748483insCCTTCCTT								LOC441046 (259169 upstream) : GYPE (43537 downstream)																							ACTAAtttctcccttccttcct	0.094													4	2	---	---	---	---	
FAM149A	25854	broad.mit.edu	37	4	187077514	187077515	+	Intron	INS	-	T	T	rs149797115	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187077514_187077515insT	uc003iyt.3	+						FAM149A_uc011cla.1_Intron|FAM149A_uc010isj.2_Intron|FAM149A_uc010isk.2_Intron|FAM149A_uc003iyu.3_Intron|FAM149A_uc010isl.2_Intron|FAM149A_uc011clb.1_Intron	NM_015398	NP_056213	A5PLN7	F149A_HUMAN	hypothetical protein LOC25854											breast(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		GGACGCTATTGTTTTTTGTGTT	0.282													4	2	---	---	---	---	
KLKB1	3818	broad.mit.edu	37	4	187149200	187149201	+	Intron	INS	-	A	A	rs138397648	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187149200_187149201insA	uc003iyy.2	+						KLKB1_uc011clc.1_Intron|KLKB1_uc011cld.1_Intron	NM_000892	NP_000883	P03952	KLKB1_HUMAN	plasma kallikrein B1 precursor						blood coagulation, intrinsic pathway|Factor XII activation|fibrinolysis|plasminogen activation|positive regulation of fibrinolysis	cytoplasm|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(1)	1		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		ACAAATGTACCAAAAAAAAACC	0.327													4	3	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21344713	21344713	+	Intron	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21344713delT	uc011cnn.1	+											Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						ccttccttcctttccttcctt	0.000													4	2	---	---	---	---	
AGXT2	64902	broad.mit.edu	37	5	35004070	35004072	+	Intron	DEL	TCT	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35004070_35004072delTCT	uc003jjf.2	-						AGXT2_uc003jje.1_Intron|AGXT2_uc011com.1_Intron	NM_031900	NP_114106	Q9BYV1	AGT2_HUMAN	alanine-glyoxylate aminotransferase 2 precursor						glyoxylate metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity|alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(3)|skin(1)	4	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)	TCAATGCCCCTCTTTTTTTTCTC	0.340											OREG0016558	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	9	---	---	---	---	
BDP1	55814	broad.mit.edu	37	5	70828418	70828421	+	Intron	DEL	TTTG	-	-	rs34000891		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70828418_70828421delTTTG	uc003kbp.1	+						BDP1_uc003kbo.2_Intron|BDP1_uc003kbq.1_Intron|BDP1_uc003kbr.1_Intron	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		AAGCAATGATTTTGTTTGTTTGTG	0.279													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	131368633	131368636	+	IGR	DEL	GGAG	-	-	rs59143826		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131368633_131368636delGGAG								ACSL6 (20763 upstream) : IL3 (27711 downstream)																							agagagagaaggagggagggaggg	0.000													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172625957	172625958	+	IGR	INS	-	CC	CC	rs144100476	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172625957_172625958insCC								BNIP1 (34568 upstream) : NKX2-5 (33180 downstream)																							ccttcctccctctctctccttc	0.000													4	2	---	---	---	---	
RMND5B	64777	broad.mit.edu	37	5	177574549	177574549	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177574549delT	uc003mim.2	+	9	1056	c.876delT	c.(874-876)TGTfs	p.C292fs	RMND5B_uc003min.2_Frame_Shift_Del_p.C292fs|RMND5B_uc003mio.2_Frame_Shift_Del_p.C279fs|RMND5B_uc003mip.2_Frame_Shift_Del_p.C292fs|RMND5B_uc011dgf.1_Frame_Shift_Del_p.C333fs|RMND5B_uc003miq.2_Frame_Shift_Del_p.C232fs	NM_022762	NP_073599	Q96G75	RMD5B_HUMAN	required for meiotic nuclear division 5 homolog	292										ovary(1)|skin(1)	2	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCTCTGGCTGTGTGGCGCTGC	0.582													44	29	---	---	---	---	
RPS10	6204	broad.mit.edu	37	6	34389797	34389797	+	Intron	DEL	A	-	-	rs34411335		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34389797delA	uc003ojm.2	-						RPS10_uc003ojn.2_Intron	NM_001014	NP_001005	P46783	RS10_HUMAN	ribosomal protein S10						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding				0						TGCAAATCTGAAAAAAAAAAA	0.323													4	2	---	---	---	---	
XPO5	57510	broad.mit.edu	37	6	43533306	43533306	+	Intron	DEL	A	-	-	rs113079021		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43533306delA	uc003ovp.2	-							NM_020750	NP_065801	Q9HAV4	XPO5_HUMAN	exportin 5						gene silencing by RNA	cytosol|nucleoplasm	protein binding|tRNA binding			skin(2)|breast(1)|kidney(1)	4	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			atctcaaaataaaaaaaaaaa	0.139													4	3	---	---	---	---	
SESN1	27244	broad.mit.edu	37	6	109309010	109309010	+	Intron	DEL	T	-	-	rs35465901		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109309010delT	uc003pst.3	-						SESN1_uc003psu.2_Intron	NM_014454	NP_055269	Q9Y6P5	SESN1_HUMAN	sestrin 1						cell cycle arrest|negative regulation of cell proliferation|response to DNA damage stimulus	nucleus				ovary(1)	1		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		AGCAGCTATCttttttttttt	0.169													4	2	---	---	---	---	
STX7	8417	broad.mit.edu	37	6	132793381	132793382	+	Intron	DEL	CA	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132793381_132793382delCA	uc003qdg.2	-						STX7_uc011ecg.1_Intron|STX7_uc011ech.1_Intron	NM_003569	NP_003560	O15400	STX7_HUMAN	syntaxin 7						intracellular protein transport|post-Golgi vesicle-mediated transport	early endosome membrane|integral to membrane	SNAP receptor activity				0	Breast(56;0.0615)			OV - Ovarian serous cystadenocarcinoma(155;0.00532)|GBM - Glioblastoma multiforme(226;0.0114)		GGGTTTTTTTCACATTCAATAC	0.366													43	24	---	---	---	---	
GPR126	57211	broad.mit.edu	37	6	142630823	142630823	+	Intron	DEL	G	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142630823delG	uc010khc.2	+						GPR126_uc010khd.2_Intron|GPR126_uc010khe.2_Intron|GPR126_uc010khf.2_Intron|GPR126_uc003qix.2_Intron	NM_020455	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		TAATCATGATGACATTGTCTG	0.368													6	3	---	---	---	---	
PSMB1	5689	broad.mit.edu	37	6	170844077	170844078	+	Intron	INS	-	AAA	AAA	rs35363030		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170844077_170844078insAAA	uc003qxq.2	-							NM_002793		P20618	PSB1_HUMAN	proteasome beta 1 subunit precursor						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cell junction|cytoplasm|nucleus|proteasome core complex	protein binding|threonine-type endopeptidase activity			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)	ACTTAAAATGCaaaaaaaaaaa	0.272													4	2	---	---	---	---	
C7orf44	55744	broad.mit.edu	37	7	43731021	43731032	+	Intron	DEL	AAAGAAAGAAAG	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43731021_43731032delAAAGAAAGAAAG	uc003tin.1	-						C7orf44_uc003til.2_Intron|C7orf44_uc003tii.2_Intron|C7orf44_uc003tij.2_Intron|C7orf44_uc010kxu.1_Intron|C7orf44_uc003tik.2_Intron|C7orf44_uc003tim.1_Intron|C7orf44_uc003tio.1_Intron|C7orf44_uc003tiq.1_Intron|C7orf44_uc003tip.1_Intron	NM_018224	NP_060694	Q9GZY4	CG044_HUMAN	hypothetical protein LOC55744							integral to membrane				ovary(1)	1						gaagaaagaaaaagaaagaaagaaagaaagaa	0.075													6	3	---	---	---	---	
ZNF138	7697	broad.mit.edu	37	7	64276251	64276254	+	Intron	DEL	AGTG	-	-	rs142497687		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64276251_64276254delAGTG	uc011kdp.1	+						ZNF138_uc003ttg.2_Intron|ZNF138_uc011kdq.1_Intron|ZNF138_uc003tth.2_Intron|ZNF138_uc010kzs.2_Intron	NM_001160183	NP_001153655	B4DFX2	B4DFX2_HUMAN	zinc finger protein 138 isoform 2						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding				0		Lung NSC(55;0.0795)|all_lung(88;0.18)				tcaagttcacagtgagagccaacg	0.167													4	2	---	---	---	---	
TRIM50	135892	broad.mit.edu	37	7	72729266	72729267	+	Intron	INS	-	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72729266_72729267insA	uc010lbd.1	-						FKBP6_uc003twz.2_Intron|TRIM50_uc003txy.1_Intron|TRIM50_uc003txz.1_Intron	NM_178125	NP_835226	Q86XT4	TRI50_HUMAN	tripartite motif protein 50A							cytoplasm|intracellular membrane-bounded organelle	ligase activity|zinc ion binding			skin(1)	1						AATTTTCCTTCAAAAAAAAAAA	0.287													3	4	---	---	---	---	
ZAN	7455	broad.mit.edu	37	7	100373941	100373948	+	Intron	DEL	AGGGAGGG	-	-	rs3991185		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100373941_100373948delAGGGAGGG	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron|ZAN_uc011kke.1_Intron	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			actTGAaggaagggagggagggagggag	0.125													4	2	---	---	---	---	
ATP6V0A4	50617	broad.mit.edu	37	7	138391635	138391640	+	Intron	DEL	TTTTTT	-	-	rs35405334		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138391635_138391640delTTTTTT	uc003vuf.2	-						ATP6V0A4_uc003vug.2_Intron|ATP6V0A4_uc003vuh.2_Intron	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit						cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1						ATCCTGAGGAtttttttttttttttt	0.272													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	2799876	2799878	+	Intron	DEL	AAG	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2799876_2799878delAAG	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		aaaaaaaaaaAAGAACATTGCAT	0.182													4	2	---	---	---	---	
XKR6	286046	broad.mit.edu	37	8	11058892	11058892	+	5'Flank	DEL	C	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11058892delC	uc003wtk.1	-							NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		ggagggacggcgggggggggg	0.249													4	2	---	---	---	---	
CHRNA6	8973	broad.mit.edu	37	8	42620149	42620150	+	Intron	INS	-	T	T	rs28615771		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42620149_42620150insT	uc003xpj.2	-						CHRNA6_uc011lcw.1_Intron	NM_004198	NP_004189	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6							cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)			AAATTCCTTCATTTACCACCTG	0.480													25	28	---	---	---	---	
SDC2	6383	broad.mit.edu	37	8	97620360	97620362	+	Intron	DEL	TGG	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97620360_97620362delTGG	uc003yhv.1	+						SDC2_uc011lgu.1_Intron	NM_002998	NP_002989	P34741	SDC2_HUMAN	syndecan 2 precursor							integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)	GATCATGCGATGGGTGTTGTGCA	0.404													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	6158554	6158555	+	IGR	INS	-	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6158554_6158555insT								RANBP6 (142914 upstream) : IL33 (57252 downstream)																							ttattttttaattttttttgta	0.000													4	2	---	---	---	---	
GABBR2	9568	broad.mit.edu	37	9	101150902	101150905	+	Intron	DEL	TGTG	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101150902_101150905delTGTG	uc004ays.2	-							NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	GCCTGGCCTCtgtgtgtgtgtgtg	0.230													5	3	---	---	---	---	
SUSD1	64420	broad.mit.edu	37	9	114928166	114928169	+	Intron	DEL	AAAG	-	-	rs10622700		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114928166_114928169delAAAG	uc004bfu.2	-						SUSD1_uc010mui.2_Intron|SUSD1_uc010muj.2_Intron	NM_022486	NP_071931	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1 precursor							integral to membrane	calcium ion binding				0						agagaaagaaaaagaaagaaagaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11696232	11696233	+	IGR	INS	-	AGGAAGGAAGGA	AGGAAGGAAGGA			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11696232_11696233insAGGAAGGAAGGA								USP6NL (42553 upstream) : ECHDC3 (88123 downstream)																							AGGaggaggagaggaaggaagg	0.035													4	3	---	---	---	---	
LOC387647	387647	broad.mit.edu	37	10	29719433	29719436	+	Intron	DEL	TCTC	-	-	rs71492595		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29719433_29719436delTCTC	uc001iuo.1	+						LOC387647_uc001iup.2_Intron|LOC387647_uc001iuq.1_Intron					Homo sapiens cDNA FLJ31518 fis, clone NT2RI2000064.												0						ttcctttctttctctctttctctt	0.098													3	3	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	106837280	106837287	+	Intron	DEL	ACACACAC	-	-	rs34110774		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106837280_106837287delACACACAC	uc001kyi.1	+							NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		ACTAAATTAAacacacacacacacacac	0.308													4	2	---	---	---	---	
CPXM2	119587	broad.mit.edu	37	10	125540252	125540255	+	Intron	DEL	CCTT	-	-	rs66915589		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125540252_125540255delCCTT	uc001lhk.1	-						CPXM2_uc001lhj.2_Intron	NM_198148	NP_937791	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2						cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		CATTCATTCCccttccttccttcc	0.343													4	2	---	---	---	---	
C11orf40	143501	broad.mit.edu	37	11	4593180	4593181	+	Intron	INS	-	A	A	rs150576957	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4593180_4593181insA	uc010qyg.1	-							NM_144663	NP_653264	Q8WZ69	CK040_HUMAN	hypothetical protein LOC143501											ovary(2)	2		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		CACAAGAGACCAAAAAAATCAA	0.386													3	3	---	---	---	---	
RRAS2	22800	broad.mit.edu	37	11	14303034	14303056	+	Intron	DEL	AATGCACCATGTGCATTAATCCC	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14303034_14303056delAATGCACCATGTGCATTAATCCC	uc001mlf.3	-						RRAS2_uc009ygq.2_Intron|RRAS2_uc010rco.1_Intron	NM_012250	NP_036382	P62070	RRAS2_HUMAN	related RAS viral (r-ras) oncogene homolog 2							endoplasmic reticulum|plasma membrane	GTP binding|GTPase activity|protein binding			breast(1)	1				Epithelial(150;0.203)		TAAAAATTGTAATGCACCATGTGCATTAATCCCTAGAAAGGAA	0.260													11	5	---	---	---	---	
KIF18A	81930	broad.mit.edu	37	11	28116025	28116025	+	Intron	DEL	A	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28116025delA	uc001msc.2	-							NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A						blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			ovary(2)	2						ttgccaaagtaaaaaAAAAAA	0.095													6	3	---	---	---	---	
OR8H3	390152	broad.mit.edu	37	11	55889645	55889646	+	5'Flank	INS	-	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55889645_55889646insT	uc001nii.1	+							NM_001005201	NP_001005201	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00693)					tgttttgtttattttttttgag	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	58852578	58852578	+	IGR	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58852578delT								GLYATL1 (128062 upstream) : FAM111B (22080 downstream)																							ccctcttgcattttggagctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	2128745	2128746	+	IGR	INS	-	AA	AA	rs139954072	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2128745_2128746insAA								DCP1B (15068 upstream) : CACNA1C (33670 downstream)																							agaaaagaaagagagagagaaa	0.069													2	6	---	---	---	---	
PPHLN1	51535	broad.mit.edu	37	12	42692995	42692996	+	Intron	INS	-	A	A	rs5797787		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42692995_42692996insA	uc001rmy.2	+							NM_201439	NP_958847	Q8NEY8	PPHLN_HUMAN	periphilin 1 isoform 3						keratinization	cytoplasm|nucleus				ovary(1)|breast(1)	2	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		aagactctgtcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
TMEM117	84216	broad.mit.edu	37	12	44271693	44271694	+	Intron	INS	-	ACACAC	ACACAC	rs72317533		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44271693_44271694insACACAC	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632	Q9H0C3	TM117_HUMAN	transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)		gtaaaaacaaaacacacacaca	0.000													4	2	---	---	---	---	
SLC4A8	9498	broad.mit.edu	37	12	51887333	51887334	+	Intron	INS	-	C	C			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51887333_51887334insC	uc001rys.1	+						SLC4A8_uc001rym.2_Intron|SLC4A8_uc001ryn.2_Intron|SLC4A8_uc001ryo.2_Intron|SLC4A8_uc010snj.1_Intron|SLC4A8_uc001ryr.2_Intron	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate						bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)		TTGCTTCTACTCCTAAGTCACC	0.371													11	11	---	---	---	---	
PSPC1	55269	broad.mit.edu	37	13	20279633	20279634	+	Intron	INS	-	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20279633_20279634insA	uc001uml.2	-						PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron	NM_001042414	NP_001035879	Q8WXF1	PSPC1_HUMAN	paraspeckle protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		ctctctgtctcaaaaaaaaaaa	0.129													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	54942527	54942534	+	IGR	DEL	GAAAAAAG	-	-	rs9527197	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54942527_54942534delGAAAAAAG								MIR1297 (56344 upstream) : None (None downstream)																							aaggaaggaagaaaaaagaaagaaagaa	0.058													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	77920460	77920461	+	IGR	DEL	GT	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77920460_77920461delGT								MYCBP2 (19283 upstream) : SCEL (189348 downstream)																							GCCTCAAAGCgtgtgtgtgtgt	0.292													4	2	---	---	---	---	
YLPM1	56252	broad.mit.edu	37	14	75230625	75230626	+	Frame_Shift_Ins	INS	-	CC	CC			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75230625_75230626insCC	uc001xqj.3	+	1	557_558	c.433_434insCC	c.(433-435)TCCfs	p.S145fs		NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	145	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		GGAGCTGGAATCCCCCCCTGAA	0.619													14	10	---	---	---	---	
AQR	9716	broad.mit.edu	37	15	35210390	35210390	+	Intron	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35210390delT	uc001ziv.2	-							NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius							catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		CTGCCTATAATTGCCAATTAT	0.338													51	28	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40921686	40921688	+	Intron	DEL	GCC	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40921686_40921688delGCC	uc010bbs.1	+						CASC5_uc010bbt.1_Intron	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		ttttttttttgccttttcttttt	0.123													6	3	---	---	---	---	
SPTBN5	51332	broad.mit.edu	37	15	42144805	42144805	+	Intron	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42144805delT	uc001zos.2	-							NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5						actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CCACCAGCCCTCAGCCCCTAG	0.602													153	87	---	---	---	---	
DUOX2	50506	broad.mit.edu	37	15	45400613	45400614	+	Intron	INS	-	C	C	rs144393243	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45400613_45400614insC	uc010bea.2	-						DUOX2_uc001zun.2_Intron	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor						cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CCACGGTAACACCACGGTCAGG	0.589													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78675656	78675656	+	IGR	DEL	T	-	-	rs112849950		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78675656delT								CRABP1 (35084 upstream) : IREB2 (54862 downstream)																							ATAAGGAGAAttttttttttt	0.209													8	4	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7323198	7323205	+	Intron	DEL	CCTCCCTC	-	-	rs79339377	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7323198_7323205delCCTCCCTC	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		tcccttccttcctccctcccttccttcc	0.048													4	2	---	---	---	---	
MYH11	4629	broad.mit.edu	37	16	15932288	15932288	+	Intron	DEL	A	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15932288delA	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002deb.3_Intron	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						GAGACCACCCAAAGGCCCTTC	0.318			T	CBFB	AML								3	3	---	---	---	---	
NAE1	8883	broad.mit.edu	37	16	66839540	66839541	+	Intron	INS	-	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66839540_66839541insA	uc002eqf.2	-						NAE1_uc002eqe.2_Intron|NAE1_uc002eqg.2_Intron|NAE1_uc010cdv.2_Intron	NM_003905	NP_003896	Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1 isoform a						apoptosis|cell cycle|DNA replication|mitotic cell cycle DNA replication checkpoint|protein neddylation|signal transduction	cytoplasm|insoluble fraction|plasma membrane	catalytic activity|protein heterodimerization activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)	gactgcgtctcaaaaaaaaaaa	0.124													4	2	---	---	---	---	
CYB5B	80777	broad.mit.edu	37	16	69482267	69482267	+	Intron	DEL	T	-	-	rs71672468		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69482267delT	uc002exg.1	+						CYB5B_uc002exf.2_3'UTR|CYB5B_uc010cfl.1_Intron	NM_030579	NP_085056	O43169	CYB5B_HUMAN	cytochrome b5 outer mitochondrial membrane						electron transport chain|transport	integral to membrane|mitochondrial outer membrane	heme binding				0		Ovarian(137;0.101)				CTTTATACGCTTTTTTTTTTT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87256041	87256043	+	Intron	DEL	CAC	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87256041_87256043delCAC	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																		ccaccaccatcaccaccaccacc	0.000													4	2	---	---	---	---	
OR1E1	8387	broad.mit.edu	37	17	3302504	3302515	+	5'Flank	DEL	GAAGGAAGGAAG	-	-	rs4790137		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3302504_3302515delGAAGGAAGGAAG	uc002fvj.1	-							NM_003553	NP_003544	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						aagaaagaaagaaggaaggaaggaaggaagga	0.000													4	2	---	---	---	---	
USP6	9098	broad.mit.edu	37	17	5035457	5035457	+	Intron	DEL	G	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5035457delG	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron|USP6_uc002gaw.2_Intron|uc002gay.1_5'Flank	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5						CCCCATGCCAGGGGCCCCAGT	0.637			T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								4	2	---	---	---	---	
C17orf76	388341	broad.mit.edu	37	17	16359634	16359636	+	Intron	DEL	AGA	-	-	rs62076299		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16359634_16359636delAGA	uc010cph.1	-						C17orf76_uc002gqh.2_Intron|NCRNA00188_uc010vwl.1_Intron|NCRNA00188_uc010vwm.1_Intron|NCRNA00188_uc010vwn.1_Intron|NCRNA00188_uc010cpe.2_Intron|NCRNA00188_uc010vwo.1_Intron|NCRNA00188_uc010vwp.1_Intron	NM_001113567	NP_001107039	Q8NAA5	CQ076_HUMAN	hypothetical protein LOC388341 isoform 1												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)		gaggaagaggagaagaaggaaga	0.000													3	4	---	---	---	---	
NLK	51701	broad.mit.edu	37	17	26449400	26449400	+	Intron	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26449400delT	uc010crj.2	+						NLK_uc010cri.1_Intron	NM_016231	NP_057315	Q9UBE8	NLK_HUMAN	nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		TAGACAGGGATTTTTTTTTTT	0.338													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39063535	39063538	+	IGR	DEL	TTCC	-	-	rs71764584		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39063535_39063538delTTCC								KRT20 (22056 upstream) : KRT23 (15414 downstream)																							cctccctcctttccttccttcctt	0.181													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68974725	68974726	+	IGR	INS	-	GGGA	GGGA			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68974725_68974726insGGGA								KCNJ2 (798544 upstream) : None (None downstream)																							aggaaaagaaggggagggaggg	0.084													5	6	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	37248431	37248454	+	Intron	DEL	AGGGAGGAAGGAAGGAAGGAAGGA	-	-	rs11270312	by1000genomes	TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37248431_37248454delAGGGAGGAAGGAAGGAAGGAAGGA	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						ggagggagggagggaggaaggaaggaaggaaggaaggaaggaag	0.098													11	7	---	---	---	---	
ATP9B	374868	broad.mit.edu	37	18	77030300	77030301	+	Intron	DEL	CT	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77030300_77030301delCT	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933	O43861	ATP9B_HUMAN	ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		TATGTGGCAGCTCtgtgtgtgt	0.282													3	3	---	---	---	---	
ZNF20	7568	broad.mit.edu	37	19	12246275	12246275	+	Intron	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12246275delT	uc002mtf.1	-						ZNF20_uc002mte.1_Intron|ZNF20_uc002mtg.1_Intron	NM_021143	NP_066966	P17024	ZNF20_HUMAN	zinc finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CATTTTAAGATTTTCTAGAGG	0.204													65	28	---	---	---	---	
RYR1	6261	broad.mit.edu	37	19	38994748	38994750	+	Intron	DEL	CCT	-	-	rs34529638		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38994748_38994750delCCT	uc002oit.2	+						RYR1_uc002oiu.2_Intron|RYR1_uc002oiv.1_Intron	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1						muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	ATAACCCACACCTCCTTCATAAT	0.443													4	4	---	---	---	---	
BCAM	4059	broad.mit.edu	37	19	45318165	45318165	+	Intron	DEL	G	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45318165delG	uc002ozu.2	+						BCAM_uc002ozt.1_Intron	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1						cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				TTTTTTGGttgtttttttttt	0.259													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37426125	37426125	+	IGR	DEL	T	-	-			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37426125delT								ACTR5 (25036 upstream) : PPP1R16B (8223 downstream)																							ccttccttcctttctttcttt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58889874	58889875	+	Intron	INS	-	CATT	CATT			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58889874_58889875insCATT	uc002ybl.2	+						uc010gjw.1_Intron					Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																		atccatcctcccatcctcccat	0.000													5	3	---	---	---	---	
IFNGR2	3460	broad.mit.edu	37	21	34793638	34793639	+	Intron	INS	-	A	A			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34793638_34793639insA	uc002yrp.3	+						IFNGR2_uc002yrq.3_Intron|IFNGR2_uc010gma.2_Intron|IFNGR2_uc002yrr.3_Intron	NM_005534	NP_005525	P38484	INGR2_HUMAN	interferon gamma receptor 2 precursor						regulation of interferon-gamma-mediated signaling pathway|response to virus	endoplasmic reticulum|integral to plasma membrane	interferon-gamma receptor activity				0					Interferon gamma-1b(DB00033)	aactccatctcaaaaaaaaaaa	0.163													4	2	---	---	---	---	
SLC2A11	66035	broad.mit.edu	37	22	24199261	24199261	+	Intron	DEL	G	-	-	rs71184919		TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24199261delG	uc002zyn.3	+						SLC2A11_uc002zyl.1_Intron|SLC2A11_uc002zym.3_Intron|SLC2A11_uc002zyo.3_Intron|SLC2A11_uc011ajc.1_5'UTR|SLC2A11_uc011ajd.1_5'Flank|SLC2A11_uc002zyp.3_5'Flank	NM_001024938	NP_001020109	Q9BYW1	GTR11_HUMAN	glucose transporter protein 10 isoform c							integral to membrane|plasma membrane	sugar transmembrane transporter activity			ovary(1)	1						GTGTGTGTGTGGGGGGGGGGG	0.612													4	4	---	---	---	---	
MCF2	4168	broad.mit.edu	37	X	138713416	138713417	+	Intron	INS	-	T	T			TCGA-CJ-4912-01A-01D-1429-08	TCGA-CJ-4912-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138713416_138713417insT	uc004fau.2	-						MCF2_uc004fav.2_Intron|MCF2_uc011mwl.1_Intron|MCF2_uc010nsh.1_Intron|MCF2_uc011mwm.1_Intron|MCF2_uc011mwn.1_Intron|MCF2_uc004faw.2_Intron|MCF2_uc011mwo.1_Intron	NM_005369	NP_005360	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|membrane|membrane fraction	protein binding|Rho guanyl-nucleotide exchange factor activity			lung(1)|pleura(1)	2	Acute lymphoblastic leukemia(192;0.000127)					ATGTATGTGAAAAATGAGGGCC	0.327													23	12	---	---	---	---	
