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
ZNF362	149076	broad.mit.edu	37	1	33747326	33747326	+	Silent	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33747326G>A	uc001bxc.1	+	6	992	c.822G>A	c.(820-822)CTG>CTA	p.L274L		NM_152493	NP_689706	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	274	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CCCAGCACCTGCGCATCCACC	0.622													9	208	---	---	---	---	PASS
COL8A2	1296	broad.mit.edu	37	1	36565682	36565682	+	Silent	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36565682C>T	uc001bzv.1	-	1	169	c.162G>A	c.(160-162)CCG>CCA	p.P54P	COL8A2_uc001bzw.1_Intron	NM_005202	NP_005193	P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2 precursor	54	Nonhelical region (NC2).				angiogenesis|cell-cell adhesion|extracellular matrix organization	basement membrane|collagen	extracellular matrix structural constituent|protein binding, bridging			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CACGGAAGGGCGGTCCCACAG	0.677											OREG0013361	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	68	---	---	---	---	PASS
TIE1	7075	broad.mit.edu	37	1	43773140	43773140	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43773140G>C	uc001ciu.2	+	6	889	c.810G>C	c.(808-810)GAG>GAC	p.E270D	TIE1_uc010okd.1_Missense_Mutation_p.E270D|TIE1_uc010oke.1_Missense_Mutation_p.E225D|TIE1_uc009vwq.2_Missense_Mutation_p.E226D|TIE1_uc010okf.1_5'UTR|TIE1_uc010okg.1_5'UTR|TIE1_uc010okc.1_Missense_Mutation_p.E270D	NM_005424	NP_005415	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and	270	Extracellular (Potential).|EGF-like 2.				mesoderm development	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GCTGCCAGGAGCAGTGCCCAG	0.637													14	51	---	---	---	---	PASS
USP24	23358	broad.mit.edu	37	1	55563707	55563707	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55563707C>A	uc001cyg.3	-	44	5024	c.5024G>T	c.(5023-5025)TGT>TTT	p.C1675F		NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24	1835					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						CAAACTCTGACAAGAAGTCAC	0.353													3	76	---	---	---	---	PASS
SLAMF7	57823	broad.mit.edu	37	1	160719769	160719769	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160719769A>G	uc001fwq.2	+	3	550	c.535A>G	c.(535-537)ATC>GTC	p.I179V	SLAMF7_uc010pjn.1_Missense_Mutation_p.I72V|SLAMF7_uc001fws.2_Missense_Mutation_p.I72V|SLAMF7_uc001fwr.2_Missense_Mutation_p.I179V|SLAMF7_uc010pjo.1_Intron|SLAMF7_uc010pjp.1_Missense_Mutation_p.I72V|SLAMF7_uc010pjq.1_Intron|SLAMF7_uc010pjr.1_Missense_Mutation_p.I72V	NM_021181	NP_067004	Q9NQ25	SLAF7_HUMAN	SLAM family member 7	179	Ig-like C2-type.|Extracellular (Potential).				cell adhesion|natural killer cell activation|natural killer cell mediated cytotoxicity	integral to membrane	receptor activity			skin(2)|ovary(1)	3	all_cancers(52;2.63e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			TAATGGGTCCATCCTCCCCAT	0.527													22	143	---	---	---	---	PASS
C1orf112	55732	broad.mit.edu	37	1	169773348	169773348	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169773348G>C	uc001ggp.2	+	7	755	c.445G>C	c.(445-447)GAT>CAT	p.D149H	C1orf112_uc001ggj.2_RNA|C1orf112_uc001ggo.2_Missense_Mutation_p.D149H|C1orf112_uc001ggq.2_Missense_Mutation_p.D149H|C1orf112_uc009wvt.2_5'UTR|C1orf112_uc010plu.1_Missense_Mutation_p.D120H|C1orf112_uc009wvu.1_Missense_Mutation_p.D120H|C1orf112_uc001ggr.2_Missense_Mutation_p.D14H|C1orf112_uc010plv.1_Missense_Mutation_p.D91H	NM_018186	NP_060656	Q9NSG2	CA112_HUMAN	hypothetical protein LOC55732	149											0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCCTTTAGTAGATGACAATGA	0.368													43	303	---	---	---	---	PASS
BAT2L2	23215	broad.mit.edu	37	1	171510332	171510332	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171510332G>A	uc010pmg.1	+	16	3987	c.3721G>A	c.(3721-3723)GAA>AAA	p.E1241K	BAT2L2_uc010pmh.1_Missense_Mutation_p.E218K	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	1241							protein C-terminus binding				0						ACAGCGAGAAGAAAGTGAAAC	0.488													16	79	---	---	---	---	PASS
NAV1	89796	broad.mit.edu	37	1	201789098	201789098	+	3'UTR	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201789098G>A	uc001gwu.2	+	29					NAV1_uc001gwx.2_3'UTR	NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1						cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4						ACAGCAGAACGCTGGCATCAG	0.547													14	48	---	---	---	---	PASS
OR2G2	81470	broad.mit.edu	37	1	247752478	247752478	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247752478C>A	uc010pyy.1	+	1	817	c.817C>A	c.(817-819)CAG>AAG	p.Q273K		NM_001001915	NP_001001915	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G,	273	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			ATCCAGGGACCAGGGCAAGTT	0.373													43	254	---	---	---	---	PASS
OR2W3	343171	broad.mit.edu	37	1	248059809	248059809	+	Silent	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248059809G>A	uc001idp.1	+	3	1190	c.921G>A	c.(919-921)GGG>GGA	p.G307G	OR2W3_uc010pzb.1_Silent_p.G307G	NM_001001957	NP_001001957	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W,	307	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|pancreas(1)	3	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TGCTTCTGGGGAAGAGAGAGC	0.517													7	43	---	---	---	---	PASS
THADA	63892	broad.mit.edu	37	2	43800089	43800089	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43800089C>A	uc002rsw.3	-	12	2124	c.1772G>T	c.(1771-1773)AGG>ATG	p.R591M	THADA_uc010far.2_5'Flank|THADA_uc002rsx.3_Missense_Mutation_p.R591M|THADA_uc002rsy.3_RNA|THADA_uc010fas.1_RNA|THADA_uc002rsz.2_Missense_Mutation_p.R301M|THADA_uc010fat.1_5'Flank|THADA_uc002rta.2_Missense_Mutation_p.R301M|THADA_uc002rtb.1_Missense_Mutation_p.R591M|THADA_uc002rtc.3_Missense_Mutation_p.R591M|THADA_uc002rtd.2_Missense_Mutation_p.R591M	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	591							binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				CAGAGCCCCCCTGCTATTACA	0.443													23	73	---	---	---	---	PASS
KLRAQ1	129285	broad.mit.edu	37	2	48681713	48681713	+	Intron	SNP	T	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48681713T>C	uc002rwm.2	+						KLRAQ1_uc002rwi.1_Intron|KLRAQ1_uc002rwj.2_Intron|KLRAQ1_uc002rwl.2_5'UTR|KLRAQ1_uc002rwk.2_Intron|KLRAQ1_uc010yok.1_Intron	NM_001135629	NP_001129101	Q6ZMI0	KLRAQ_HUMAN	KLRAQ motif containing 1 isoform 1											ovary(1)	1						TGAGGACCAATCTGTTTTCAC	0.323													14	62	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90192968	90192968	+	Intron	SNP	T	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90192968T>C	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		GGGTCCCCGCTCAGCTCCTGG	0.562													24	109	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152346999	152346999	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152346999C>T	uc010fnx.2	-	147	19807	c.19616G>A	c.(19615-19617)CGA>CAA	p.R6539Q	NEB_uc002txr.2_Missense_Mutation_p.R2869Q|RIF1_uc002txp.2_Intron|NEB_uc010zbz.1_Missense_Mutation_p.R308Q|NEB_uc002txq.2_Missense_Mutation_p.R418Q|NEB_uc010zca.1_Missense_Mutation_p.R370Q|NEB_uc010zcb.1_Missense_Mutation_p.R308Q	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	6539	Interaction with SVIL.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		ACTGGCAGATCGTGACTGCTC	0.502													3	18	---	---	---	---	PASS
IQCA1	79781	broad.mit.edu	37	2	237272567	237272567	+	Silent	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237272567C>T	uc002vvz.1	-	15	1907	c.1725G>A	c.(1723-1725)GGG>GGA	p.G575G	IQCA1_uc002vwb.2_Silent_p.G583G|IQCA1_uc002vwa.1_RNA|IQCA1_uc010zni.1_Silent_p.G534G	NM_024726	NP_079002	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	575	ATP (Potential).						ATP binding			ovary(1)	1						CCCCAGACGGCCCGGCTAACA	0.498													4	90	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191470	10191470	+	Splice_Site	SNP	G	C	C	rs5030817		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191470G>C	uc003bvc.2	+	3	677	c.464_splice	c.e3-1	p.V155_splice	VHL_uc003bvd.2_Splice_Site_p.V114_splice	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						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.?(17)		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)		TGCCCTTCCAGTGTATACTCT	0.493		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				18	32	---	---	---	---	PASS
FBLN2	2199	broad.mit.edu	37	3	13649672	13649672	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13649672A>G	uc011avb.1	+	3	1542	c.1417A>G	c.(1417-1419)AGG>GGG	p.R473G	FBLN2_uc011auz.1_Missense_Mutation_p.R499G|FBLN2_uc011ava.1_Missense_Mutation_p.R473G|FBLN2_uc011avc.1_Missense_Mutation_p.R473G	NM_001998	NP_001989	P98095	FBLN2_HUMAN	fibulin 2 isoform b precursor	473	Anaphylatoxin-like 1.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			CAACGTCTGCAGGTAGGGTGG	0.632													2	3	---	---	---	---	PASS
CMC1	152100	broad.mit.edu	37	3	28361101	28361101	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28361101A>G	uc003cea.2	+	4	463	c.302A>G	c.(301-303)AAG>AGG	p.K101R		NM_182523	NP_872329	Q7Z7K0	COXAM_HUMAN	COX assembly mitochondrial protein homolog	101						mitochondrion	metal ion binding				0						AGGCTACAGAAGCTTCCAACA	0.348													20	74	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52437782	52437782	+	Nonsense_Mutation	SNP	G	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52437782G>C	uc003ddx.2	-	13	1494	c.1379C>G	c.(1378-1380)TCA>TGA	p.S460*	BAP1_uc003ddw.2_RNA|BAP1_uc010hmg.2_RNA|BAP1_uc010hmh.2_Intron	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	460					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CAGAGGAATTGAGAGGTCCTT	0.587			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								15	69	---	---	---	---	PASS
EAF2	55840	broad.mit.edu	37	3	121591511	121591511	+	Silent	SNP	C	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121591511C>A	uc003een.2	+	5	711	c.612C>A	c.(610-612)TCC>TCA	p.S204S	EAF2_uc003eeo.2_Silent_p.S74S	NM_018456	NP_060926	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	204	Ser-rich.|Necessary for transactivation activity.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	protein binding				0				GBM - Glioblastoma multiforme(114;0.0972)		ATTGCAAATCCTCTACTTCTG	0.393													35	158	---	---	---	---	PASS
ZIC4	84107	broad.mit.edu	37	3	147106623	147106623	+	3'UTR	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147106623C>T	uc003ewd.1	-	5					ZIC4_uc003ewc.1_3'UTR|ZIC4_uc011bno.1_3'UTR	NM_032153	NP_115529	Q8N9L1	ZIC4_HUMAN	zinc finger protein of the cerebellum 4							nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2						AGCGAGATTACCTTGCGAGCA	0.493													14	61	---	---	---	---	PASS
FAM193A	8603	broad.mit.edu	37	4	2698148	2698148	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2698148G>A	uc010icl.2	+	16	2813	c.2462G>A	c.(2461-2463)CGG>CAG	p.R821Q	FAM193A_uc010ick.2_Missense_Mutation_p.R1021Q|FAM193A_uc003gfd.2_Missense_Mutation_p.R821Q|FAM193A_uc011bvm.1_Missense_Mutation_p.R843Q|FAM193A_uc011bvn.1_Missense_Mutation_p.R821Q|FAM193A_uc011bvo.1_RNA|FAM193A_uc010icm.2_RNA|FAM193A_uc003gfe.2_Missense_Mutation_p.R675Q	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	821										ovary(3)	3						CTTCGCTTACGGCTGACCAAG	0.418													5	106	---	---	---	---	PASS
ANKRD17	26057	broad.mit.edu	37	4	73979600	73979600	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73979600C>G	uc003hgp.2	-	24	4427	c.4310G>C	c.(4309-4311)TGT>TCT	p.C1437S	ANKRD17_uc003hgo.2_Missense_Mutation_p.C1324S|ANKRD17_uc003hgq.2_Missense_Mutation_p.C1186S|ANKRD17_uc003hgr.2_Missense_Mutation_p.C1436S|ANKRD17_uc011cbd.1_Missense_Mutation_p.C1002S	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	1437					interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGACTCCATACAAAGATGACA	0.363													45	199	---	---	---	---	PASS
TMEM184C	55751	broad.mit.edu	37	4	148545244	148545244	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148545244G>A	uc003ila.3	+	3	855	c.286G>A	c.(286-288)GAT>AAT	p.D96N		NM_018241	NP_060711	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	96	Helical; (Potential).					integral to membrane					0						TTACAGTTTAGATAGTGTAAG	0.269													13	84	---	---	---	---	PASS
CDKN2AIP	55602	broad.mit.edu	37	4	184367368	184367368	+	Silent	SNP	G	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184367368G>C	uc003ivp.1	+	3	693	c.531G>C	c.(529-531)ACG>ACC	p.T177T	CDKN2AIP_uc003ivq.1_5'UTR	NM_017632	NP_060102	Q9NXV6	CARF_HUMAN	CDKN2A interacting protein	177	Ser-rich.				negative regulation of cell growth|positive regulation of signal transduction|regulation of protein stability	granular component|nucleoplasm	double-stranded RNA binding|p53 binding				0		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		ACAGTTCAACGTGTATAGGGT	0.468													23	92	---	---	---	---	PASS
SKIV2L2	23517	broad.mit.edu	37	5	54635986	54635986	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54635986G>A	uc003jpy.3	+	6	930	c.664G>A	c.(664-666)GCA>ACA	p.A222T	SKIV2L2_uc011cqi.1_Missense_Mutation_p.A121T	NM_015360	NP_056175	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2	222	Helicase ATP-binding.				maturation of 5.8S rRNA	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)|skin(1)	2		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				TAATCCTACGGCATCTTGTCT	0.363													14	257	---	---	---	---	PASS
GDF9	2661	broad.mit.edu	37	5	132197841	132197841	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132197841C>T	uc003kxz.1	-	2	1057	c.805G>A	c.(805-807)GAC>AAC	p.D269N	GDF9_uc011cxj.1_Missense_Mutation_p.D181N	NM_005260	NP_005251	O60383	GDF9_HUMAN	growth differentiation factor 9 precursor	269					female gamete generation|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			skin(1)	1		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCACTTGTGTCATTCAAATAT	0.458													17	101	---	---	---	---	PASS
GFRA3	2676	broad.mit.edu	37	5	137593484	137593484	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137593484G>A	uc003lcn.2	-	4	769	c.629C>T	c.(628-630)CCC>CTC	p.P210L	GFRA3_uc003lco.2_Missense_Mutation_p.P179L	NM_001496	NP_001487	O60609	GFRA3_HUMAN	GDNF family receptor alpha 3 preproprotein	210					peripheral nervous system development	anchored to membrane|cytoplasm|extrinsic to membrane|intracellular membrane-bounded organelle	receptor binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CTGCGCGTGGGGCTCGGCGGC	0.731													18	44	---	---	---	---	PASS
NR3C1	2908	broad.mit.edu	37	5	142779613	142779613	+	Silent	SNP	A	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142779613A>C	uc003lmz.2	-	2	1284	c.792T>G	c.(790-792)GTT>GTG	p.V264V	NR3C1_uc003lmy.2_Silent_p.V264V|NR3C1_uc003lna.2_Silent_p.V264V|NR3C1_uc003lnb.2_Silent_p.V264V|NR3C1_uc011dbk.1_Intron|NR3C1_uc003lnc.2_Silent_p.V264V|NR3C1_uc003lnd.2_Silent_p.V264V|NR3C1_uc003lne.2_Silent_p.V264V|NR3C1_uc003lnf.2_Silent_p.V264V|NR3C1_uc003lng.2_Silent_p.V264V|NR3C1_uc003lnh.2_Silent_p.V264V|NR3C1_uc003lni.2_Silent_p.V264V	NM_000176	NP_000167	P04150	GCR_HUMAN	glucocorticoid receptor isoform alpha	264	Modulating.				chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter	mitochondrial matrix|nucleoplasm	glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635)	GGCTTGACAAAACCAGATCTC	0.423													71	408	---	---	---	---	PASS
GABRA1	2554	broad.mit.edu	37	5	161302567	161302567	+	Silent	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161302567C>T	uc010jiw.2	+	7	946	c.478C>T	c.(478-480)CTG>TTG	p.L160L	GABRA1_uc010jix.2_Silent_p.L160L|GABRA1_uc010jiy.2_Silent_p.L160L|GABRA1_uc003lyx.3_Silent_p.L160L|GABRA1_uc010jiz.2_Silent_p.L160L|GABRA1_uc010jja.2_Silent_p.L160L|GABRA1_uc010jjb.2_Silent_p.L160L	NM_000806	NP_000797	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha	160	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|pancreas(1)	3	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Alprazolam(DB00404)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Halazepam(DB00801)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Metharbital(DB00463)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Picrotoxin(DB00466)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Zaleplon(DB00962)|Zolpidem(DB00425)	TCCCTTAAGGCTGACAGTGAG	0.363													33	272	---	---	---	---	PASS
ODZ2	57451	broad.mit.edu	37	5	167687305	167687305	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167687305G>A	uc010jjd.2	+	28	7423	c.7423G>A	c.(7423-7425)GTG>ATG	p.V2475M	ODZ2_uc003lzr.3_Missense_Mutation_p.V2245M|ODZ2_uc003lzt.3_Missense_Mutation_p.V1848M|ODZ2_uc010jje.2_Missense_Mutation_p.V1739M	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		AAGCTGGCTTGTGATGTTTGG	0.413													27	162	---	---	---	---	PASS
STC2	8614	broad.mit.edu	37	5	172755100	172755100	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172755100C>A	uc003mco.1	-	1	1407	c.97G>T	c.(97-99)GGT>TGT	p.G33C	STC2_uc003mcn.1_5'Flank	NM_003714	NP_003705	O76061	STC2_HUMAN	stanniocalcin 2 precursor	33					cell surface receptor linked signaling pathway|cell-cell signaling	extracellular region	hormone activity			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TCTTGGGGACCCTCGGGTGGG	0.652													40	141	---	---	---	---	PASS
PRELID1	27166	broad.mit.edu	37	5	176731056	176731056	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176731056C>A	uc003mfx.2	+	1	222	c.70C>A	c.(70-72)CAG>AAG	p.Q24K	RAB24_uc003mfu.2_5'Flank|RAB24_uc003mfv.2_5'Flank|RAB24_uc003mfw.2_5'Flank|PRELID1_uc003mfy.2_Missense_Mutation_p.Q24K	NM_013237	NP_037369	Q9Y255	PRLD1_HUMAN	PRELI domain containing 1 precursor	24					immune response|multicellular organismal development	mitochondrion|nucleus					0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CGCCTTCTGGCAGCGGTACCC	0.587													20	75	---	---	---	---	PASS
TBC1D9B	23061	broad.mit.edu	37	5	179301968	179301968	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179301968A>T	uc003mlh.2	-	12	2157	c.2120T>A	c.(2119-2121)CTG>CAG	p.L707Q	TBC1D9B_uc003mli.2_Missense_Mutation_p.L707Q|TBC1D9B_uc003mlj.2_Missense_Mutation_p.L707Q|TBC1D9B_uc011dgv.1_5'Flank	NM_198868	NP_942568	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	707						integral to membrane|intracellular	calcium ion binding|Rab GTPase activator activity			breast(1)|skin(1)	2	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTTGGCGTCCAGGACGGCCAG	0.632													27	81	---	---	---	---	PASS
SLC29A1	2030	broad.mit.edu	37	6	44198152	44198152	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44198152C>T	uc003owu.1	+	6	852	c.523C>T	c.(523-525)CCC>TCC	p.P175S	SLC29A1_uc011dvp.1_3'UTR|SLC29A1_uc003owv.1_Missense_Mutation_p.P175S|SLC29A1_uc003oww.1_Missense_Mutation_p.P254S|SLC29A1_uc011dvq.1_3'UTR|SLC29A1_uc003owx.1_Missense_Mutation_p.P175S|SLC29A1_uc003owy.1_Missense_Mutation_p.P175S|SLC29A1_uc003owz.1_Missense_Mutation_p.P175S	NM_004955	NP_004946	Q99808	S29A1_HUMAN	equilibrative nucleoside transporter 1	175	Helical; (Potential).				nucleobase, nucleoside and nucleotide metabolic process	apical plasma membrane|basolateral plasma membrane|integral to plasma membrane|membrane fraction	nucleoside transmembrane transporter activity|protein binding			large_intestine(2)|skin(1)	3	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Troglitazone(DB00197)	CTACACGGCCCCCATCATGAG	0.627													22	71	---	---	---	---	PASS
TDRD6	221400	broad.mit.edu	37	6	46656688	46656688	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46656688G>T	uc003oyj.2	+	1	823	c.823G>T	c.(823-825)GAG>TAG	p.E275*	TDRD6_uc010jze.2_Nonsense_Mutation_p.E269*	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	275					cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)|skin(1)	6			Lung(136;0.192)			CGTCTCGCAGGAGATCCACCG	0.637													4	23	---	---	---	---	PASS
FYN	2534	broad.mit.edu	37	6	111983021	111983021	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111983021G>T	uc003pvj.2	-	13	1875	c.1535C>A	c.(1534-1536)ACT>AAT	p.T512N	FYN_uc003pvi.2_Missense_Mutation_p.T457N|FYN_uc003pvk.2_Missense_Mutation_p.T512N|FYN_uc003pvh.2_Missense_Mutation_p.T509N	NM_002037	NP_002028	P06241	FYN_HUMAN	protein-tyrosine kinase fyn isoform a	512	Protein kinase.				axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	GTACTCAAAAGTGGGGCGTTC	0.572													70	306	---	---	---	---	PASS
SAMD3	154075	broad.mit.edu	37	6	130465867	130465867	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130465867T>A	uc003qbv.2	-	13	1687	c.1361A>T	c.(1360-1362)GAG>GTG	p.E454V	SAMD3_uc003qbx.2_Missense_Mutation_p.E454V|SAMD3_uc003qbw.2_Missense_Mutation_p.E454V	NM_001017373	NP_001017373	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3 isoform	454										ovary(1)	1				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		TGTGAGCCTCTCCCTTTCTAA	0.443													28	104	---	---	---	---	PASS
MED23	9439	broad.mit.edu	37	6	131914170	131914170	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131914170G>A	uc003qcs.1	-	24	3548	c.3374C>T	c.(3373-3375)GCC>GTC	p.A1125V	MED23_uc003qcq.2_Missense_Mutation_p.A1131V|MED23_uc003qcr.1_5'UTR	NM_004830	NP_004821	Q9ULK4	MED23_HUMAN	mediator complex subunit 23 isoform a	1125					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		ATTTAGAAGGGCATTCCCAAC	0.393													4	116	---	---	---	---	PASS
GUSB	2990	broad.mit.edu	37	7	65439619	65439619	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65439619C>T	uc003tun.2	-	7	1214	c.1138G>A	c.(1138-1140)GCT>ACT	p.A380T	GUSB_uc011kdt.1_Missense_Mutation_p.A234T	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor	380					glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0						GTACGGAAAGCGTTGGCACCA	0.592													12	48	---	---	---	---	PASS
CFTR	1080	broad.mit.edu	37	7	117171014	117171014	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117171014A>C	uc003vjd.2	+	4	467	c.335A>C	c.(334-336)GAT>GCT	p.D112A	CFTR_uc011knq.1_5'UTR	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	112	ABC transmembrane type-1 1.|Extracellular (Potential).				respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)	TATGACCCGGATAACAAGGAG	0.428									Cystic_Fibrosis				4	100	---	---	---	---	PASS
EXOC4	60412	broad.mit.edu	37	7	133689775	133689775	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133689775A>C	uc003vrk.2	+	16	2494	c.2459A>C	c.(2458-2460)GAT>GCT	p.D820A	EXOC4_uc011kpo.1_Missense_Mutation_p.D719A|EXOC4_uc003vrl.2_Missense_Mutation_p.D430A|EXOC4_uc011kpp.1_Missense_Mutation_p.D352A|EXOC4_uc011kpq.1_Missense_Mutation_p.D108A	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a	820					vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				CTCAACAAAGATATCAGCGCC	0.493													35	129	---	---	---	---	PASS
ESRP1	54845	broad.mit.edu	37	8	95680227	95680227	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95680227G>C	uc003ygq.3	+	10	1165	c.982G>C	c.(982-984)GTC>CTC	p.V328L	ESRP1_uc003ygr.3_Missense_Mutation_p.V328L|ESRP1_uc003ygs.3_Missense_Mutation_p.V328L|ESRP1_uc003ygt.3_Missense_Mutation_p.V328L|ESRP1_uc003ygu.3_Missense_Mutation_p.V328L|ESRP1_uc003ygv.2_Missense_Mutation_p.V168L|ESRP1_uc003ygw.2_Missense_Mutation_p.V168L	NM_017697	NP_060167	Q6NXG1	ESRP1_HUMAN	RNA binding motif protein 35A isoform 1	328	RRM 2.				mRNA processing|regulation of RNA splicing|RNA splicing	nucleus|plasma membrane	mRNA binding|nucleotide binding		ESRP1/RAF1(4)	prostate(4)	4						TCAAGTCATTGTCCGCATGCG	0.483													8	76	---	---	---	---	PASS
ASB6	140459	broad.mit.edu	37	9	132401522	132401522	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132401522A>G	uc004byf.1	-	4	636	c.470T>C	c.(469-471)CTC>CCC	p.L157P	ASB6_uc004bye.1_Missense_Mutation_p.L82P|ASB6_uc004byg.1_Intron|ASB6_uc011mbt.1_Missense_Mutation_p.L78P|ASB6_uc010myx.1_Missense_Mutation_p.L157P	NM_017873	NP_060343	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box-containing 6 isoform	157	ANK 3.				intracellular signal transduction	cytoplasm					0		Ovarian(14;0.00556)				AAGGTCCAGGAGGCGCTGCAG	0.647													29	139	---	---	---	---	PASS
LAMC3	10319	broad.mit.edu	37	9	133944413	133944413	+	Missense_Mutation	SNP	G	A	A	rs142124517		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133944413G>A	uc004caa.1	+	16	2964	c.2866G>A	c.(2866-2868)GGC>AGC	p.G956S		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	956	Laminin EGF-like 10.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GGGTTTCTTCGGCTTCTCCAT	0.667													8	137	---	---	---	---	PASS
FRMD4A	55691	broad.mit.edu	37	10	13699459	13699459	+	Silent	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13699459G>A	uc001ims.2	-	22	2482	c.2130C>T	c.(2128-2130)TCC>TCT	p.S710S	FRMD4A_uc009xjf.1_Silent_p.S710S	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	710	Ser-rich.					cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						ACTCCAGGCTGGAGCTCCGGT	0.677													8	36	---	---	---	---	PASS
ZNF438	220929	broad.mit.edu	37	10	31134379	31134379	+	Silent	SNP	T	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31134379T>C	uc010qdz.1	-	8	2433	c.1998A>G	c.(1996-1998)TTA>TTG	p.L666L	ZNF438_uc001ivn.2_Silent_p.L617L|ZNF438_uc010qdy.1_Silent_p.L656L|ZNF438_uc001ivo.3_Silent_p.L230L|ZNF438_uc009xlg.2_Silent_p.L666L|ZNF438_uc001ivp.3_Silent_p.L656L|ZNF438_uc010qea.1_Silent_p.L666L|ZNF438_uc010qeb.1_Silent_p.L666L	NM_182755	NP_877432	Q7Z4V0	ZN438_HUMAN	zinc finger protein 438 isoform a	666					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2		Prostate(175;0.0587)				GAACATCAAGTAAATGAAATT	0.458													50	205	---	---	---	---	PASS
TM9SF3	56889	broad.mit.edu	37	10	98312748	98312748	+	Silent	SNP	A	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98312748A>T	uc001kmm.3	-	6	946	c.729T>A	c.(727-729)ATT>ATA	p.I243I	TM9SF3_uc010qot.1_Silent_p.I243I|TM9SF3_uc001kmn.1_Silent_p.I12I	NM_020123	NP_064508	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3 precursor	243	Helical; (Potential).					integral to membrane	binding				0		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		TTCTCATTAAAATCATTGAAA	0.299													24	124	---	---	---	---	PASS
ZRANB1	54764	broad.mit.edu	37	10	126662867	126662867	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126662867T>A	uc001lic.2	+	5	1698	c.1327T>A	c.(1327-1329)TGC>AGC	p.C443S	ZRANB1_uc010qug.1_Missense_Mutation_p.C469S	NM_017580	NP_060050	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1	443	OTU.|TRAF-binding.	Nucleophile (By similarity).		C->S: Abolishes the deubiquitinating activity but not the binding to ubiquitin chains.	positive regulation of Wnt receptor signaling pathway|protein K63-linked deubiquitination|Wnt receptor signaling pathway	aggresome|centrosome|intermediate filament cytoskeleton|nucleolus	cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|kidney(1)	2		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)		TGCAGGAGACTGCCTACTTGA	0.468													41	172	---	---	---	---	PASS
FANCF	2188	broad.mit.edu	37	11	22646676	22646676	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22646676G>C	uc001mql.1	-	1	712	c.681C>G	c.(679-681)CAC>CAG	p.H227Q		NM_022725	NP_073562	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	227					DNA repair	nucleoplasm	protein binding			skin(1)	1						CAGGTGATTTGTGGATGCCGG	0.582			N|F			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	32	114	---	---	---	---	PASS
PDE2A	5138	broad.mit.edu	37	11	72300797	72300797	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72300797G>A	uc010rrc.1	-	11	1114	c.871C>T	c.(871-873)CCC>TCC	p.P291S	PDE2A_uc001oso.2_Missense_Mutation_p.P270S|PDE2A_uc010rra.1_Missense_Mutation_p.P284S|PDE2A_uc001osn.2_Intron|PDE2A_uc010rrb.1_Missense_Mutation_p.P282S|PDE2A_uc010rrd.1_Missense_Mutation_p.P176S	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1	291	GAF 1.				platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	GGACTCACGGGAAAGCTGACC	0.577											OREG0021197	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	24	---	---	---	---	PASS
GDPD5	81544	broad.mit.edu	37	11	75160647	75160647	+	Silent	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75160647C>T	uc001owo.3	-	9	1020	c.483G>A	c.(481-483)GCG>GCA	p.A161A	GDPD5_uc001owp.3_Silent_p.A161A|GDPD5_uc001own.3_5'UTR|GDPD5_uc009yuc.2_Silent_p.A23A|GDPD5_uc009yud.2_Silent_p.A42A|GDPD5_uc009yue.1_Silent_p.A49A	NM_030792	NP_110419	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain	161	Helical; (Potential).				glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1						GCAGGAATGGCGCTGTGCCCT	0.617													3	7	---	---	---	---	PASS
KCNA1	3736	broad.mit.edu	37	12	5021702	5021702	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5021702G>T	uc001qnh.2	+	2	2263	c.1158G>T	c.(1156-1158)AAG>AAT	p.K386N		NM_000217	NP_000208	Q09470	KCNA1_HUMAN	potassium voltage-gated channel subfamily A	386					synaptic transmission	juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium ion transmembrane transporter activity			ovary(1)|skin(1)	2					Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TTGGAGGCAAGATCGTGGGCT	0.522													154	449	---	---	---	---	PASS
LST-3TM12	338821	broad.mit.edu	37	12	21172281	21172281	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21172281T>C	uc010sin.1	+	2	185	c.185T>C	c.(184-186)ATT>ACT	p.I62T	SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron	NM_001009562	NP_001009562	Q71QF0	Q71QF0_HUMAN	liver-specific organic anion transporter 3TM12	62						membrane	transporter activity				0						ACTGGAAGTATTTTGATGGCT	0.328													11	123	---	---	---	---	PASS
KRAS	3845	broad.mit.edu	37	12	25380275	25380275	+	Missense_Mutation	SNP	T	G	G	rs17851045		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25380275T>G	uc001rgp.1	-	3	364	c.183A>C	c.(181-183)CAA>CAC	p.Q61H	KRAS_uc001rgq.1_Missense_Mutation_p.Q61H	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	61	GTP.		Q -> R (in a colorectal cancer sample; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.Q61H(140)|p.Q61L(51)|p.Q61R(44)|p.Q61K(24)|p.Q61P(11)|p.Q61E(10)|p.Q61D(1)		large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	21052	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			TGTACTCCTCTTGACCTGCTG	0.423	Q61H(T3M4_PANCREAS)|Q61H(HS766T_PANCREAS)|Q61H(NCIH460_LUNG)|Q61H(NCIH1155_LUNG)|Q61H(CL11_LARGE_INTESTINE)	119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			5	162	---	---	---	---	PASS
ITPR2	3709	broad.mit.edu	37	12	26540497	26540497	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26540497G>T	uc001rhg.2	-	55	8144	c.7727C>A	c.(7726-7728)ACG>AAG	p.T2576K	ITPR2_uc009zjg.1_Missense_Mutation_p.T727K	NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	2576	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					AAATGAAACCGTTTTATTATC	0.348													19	107	---	---	---	---	PASS
AQP2	359	broad.mit.edu	37	12	50344571	50344571	+	5'UTR	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50344571C>T	uc001rvn.2	+	1						NM_000486	NP_000477	P41181	AQP2_HUMAN	aquaporin 2						cellular response to copper ion|cellular response to mercury ion|excretion	apical plasma membrane|integral to membrane|transport vesicle membrane	glycerol transmembrane transporter activity|water channel activity			ovary(2)	2						CCGGAGCATCCTGGCCCTGAG	0.627													37	110	---	---	---	---	PASS
KRT82	3888	broad.mit.edu	37	12	52788815	52788815	+	Missense_Mutation	SNP	G	A	A	rs139996519		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52788815G>A	uc001sai.1	-	9	1601	c.1486C>T	c.(1486-1488)CGG>TGG	p.R496W		NM_033033	NP_149022	Q9NSB4	KRT82_HUMAN	keratin 82	496	Tail.					keratin filament	protein binding|structural constituent of epidermis			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.193)		CTGGATTTCCGCCCGCTCCCA	0.642													26	69	---	---	---	---	PASS
PDE1B	5153	broad.mit.edu	37	12	54962995	54962995	+	Silent	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54962995G>A	uc001sgd.1	+	4	421	c.255G>A	c.(253-255)CTG>CTA	p.L85L	PDE1B_uc010soz.1_5'UTR|PDE1B_uc010spa.1_Silent_p.L44L|PDE1B_uc001sgf.2_Intron|PDE1B_uc001sge.2_Silent_p.L65L|PDE1B_uc009znq.2_Intron	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	phosphodiesterase 1B isoform 1	85					activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						AGGACGAGCTGCAGGAGCTGC	0.642													33	139	---	---	---	---	PASS
MYL6B	140465	broad.mit.edu	37	12	56548877	56548877	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56548877G>C	uc001sjs.2	+	4	368	c.241G>C	c.(241-243)GAT>CAT	p.D81H	MYL6B_uc009zoo.2_Missense_Mutation_p.D81H|MYL6B_uc001sjt.2_Missense_Mutation_p.D81H|MYL6B_uc001sju.1_Missense_Mutation_p.D81H	NM_002475	NP_002466	P14649	MYL6B_HUMAN	smooth muscle and non-muscle myosin alkali light	81	EF-hand 1.				muscle filament sliding|skeletal muscle tissue development	cytosol|muscle myosin complex|unconventional myosin complex	calcium ion binding|motor activity|protein binding|structural constituent of muscle				0			OV - Ovarian serous cystadenocarcinoma(18;0.0979)			CCGAGTGGGGGATGGCAAGAT	0.577													74	282	---	---	---	---	PASS
PTPRB	5787	broad.mit.edu	37	12	70953090	70953090	+	Intron	SNP	T	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70953090T>G	uc001swb.3	-						PTPRB_uc010sto.1_Intron|PTPRB_uc010stp.1_Intron|PTPRB_uc001swc.3_Intron|PTPRB_uc001swa.3_Intron|PTPRB_uc001swd.3_Missense_Mutation_p.M1582L	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B						angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CTCTACTCCATTTGAGAAATA	0.373													40	188	---	---	---	---	PASS
UHRF1BP1L	23074	broad.mit.edu	37	12	100496634	100496634	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100496634G>C	uc001tgq.2	-	4	477	c.248C>G	c.(247-249)TCC>TGC	p.S83C	UHRF1BP1L_uc001tgr.2_Missense_Mutation_p.S83C	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a	83										ovary(2)	2						TTTATCCAGGGACTAATAAAA	0.294													28	88	---	---	---	---	PASS
CRYL1	51084	broad.mit.edu	37	13	21006205	21006205	+	Intron	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21006205G>T	uc001une.2	-						CRYL1_uc001unf.2_Intron|CRYL1_uc001ung.2_Intron|CRYL1_uc010tcp.1_Silent_p.S97S	NM_015974	NP_057058	Q9Y2S2	CRYL1_HUMAN	lambda-crystallin						fatty acid metabolic process	cytosol	3-hydroxyacyl-CoA dehydrogenase activity|L-gulonate 3-dehydrogenase activity|NAD+ binding|protein homodimerization activity				0		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)		gagggagaaaggaagggaggg	0.433													5	35	---	---	---	---	PASS
ATP12A	479	broad.mit.edu	37	13	25285760	25285760	+	3'UTR	SNP	A	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25285760A>T	uc001upp.2	+	23					ATP12A_uc010aaa.2_3'UTR	NM_001676	NP_001667	P54707	AT12A_HUMAN	hydrogen/potassium-exchanging ATPase 12A						ATP biosynthetic process	hydrogen:potassium-exchanging ATPase complex	ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1)	6		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)	Esomeprazole(DB00736)|Pantoprazole(DB00213)	AGACATCGTCAAAATTCAGAC	0.438													6	22	---	---	---	---	PASS
RPL36AL	6166	broad.mit.edu	37	14	50085461	50085461	+	3'UTR	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50085461C>T	uc001wwq.1	-	2					SDCCAG1_uc010anj.1_Intron|MGAT2_uc001wwr.2_5'Flank	NM_001001	NP_000992	Q969Q0	RL36L_HUMAN	ribosomal protein L36a-like protein						translation	ribosome	structural constituent of ribosome				0	all_epithelial(31;0.0021)|Breast(41;0.0124)					TCTATGGCTTCACCATTTTCT	0.338													9	37	---	---	---	---	PASS
RTL1	388015	broad.mit.edu	37	14	101351082	101351082	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101351082T>C	uc010txj.1	-	1	103	c.44A>G	c.(43-45)CAT>CGT	p.H15R	uc010txk.1_RNA|MIR136_hsa-mir-136|MI0000475_RNA	NM_001134888	NP_001128360	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	15										pancreas(1)	1						TGGATTCTTATGCTCCATCAT	0.527													15	71	---	---	---	---	PASS
GATM	2628	broad.mit.edu	37	15	45654249	45654249	+	3'UTR	SNP	C	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45654249C>A	uc001zvc.2	-	9					GATM_uc001zvb.2_3'UTR	NM_001482	NP_001473	P50440	GATM_HUMAN	L-arginine:glycine amidinotransferase precursor						creatine biosynthetic process	mitochondrial inner membrane|mitochondrial intermembrane space	glycine amidinotransferase activity|protein binding				0		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Creatine(DB00148)|Glycine(DB00145)|L-Ornithine(DB00129)	GAGAATGAACCTTGCCCCTAA	0.478													6	24	---	---	---	---	PASS
PIAS1	8554	broad.mit.edu	37	15	68434675	68434675	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68434675G>A	uc002aqz.2	+	4	698	c.602G>A	c.(601-603)AGG>AAG	p.R201K	PIAS1_uc010ujx.1_Missense_Mutation_p.R201K	NM_016166	NP_057250	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	201	PINIT.				androgen receptor signaling pathway|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|positive regulation of protein sumoylation|positive regulation of transcription, DNA-dependent|regulation of interferon-gamma-mediated signaling pathway|transcription, DNA-dependent	nuclear speck	androgen receptor binding|DNA binding|enzyme binding|SUMO ligase activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)	2						GTCCAGTTAAGGTACAGTGCT	0.353													15	41	---	---	---	---	PASS
UACA	55075	broad.mit.edu	37	15	70960389	70960389	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70960389T>G	uc002asr.2	-	16	2738	c.2634A>C	c.(2632-2634)AAA>AAC	p.K878N	UACA_uc010uke.1_Missense_Mutation_p.K769N|UACA_uc002asq.2_Missense_Mutation_p.K865N|UACA_uc010bin.1_Missense_Mutation_p.K853N	NM_018003	NP_060473	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and	878	Potential.					cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4						CTCTGTTAGTTTTGGCTAACG	0.294													9	81	---	---	---	---	PASS
CDH8	1006	broad.mit.edu	37	16	61851427	61851427	+	Silent	SNP	C	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61851427C>A	uc002eog.1	-	7	1485	c.1233G>T	c.(1231-1233)GGG>GGT	p.G411G	CDH8_uc002eoh.2_Silent_p.G180G	NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	411	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CAGTCACTTGCCCAATCACGG	0.423													11	116	---	---	---	---	PASS
ELMO3	79767	broad.mit.edu	37	16	67236410	67236410	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67236410C>T	uc002esa.2	+	14	1574	c.1531C>T	c.(1531-1533)CGG>TGG	p.R511W	ELMO3_uc002esb.2_Missense_Mutation_p.R494W|ELMO3_uc002esc.2_Missense_Mutation_p.R345W|uc010vjf.1_5'Flank|MIR328_hsa-mir-328|MI0000804_5'Flank	NM_024712	NP_078988	Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	458	ELMO.				apoptosis|phagocytosis	cytoplasm|cytoskeleton	SH3 domain binding				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		GAAGGAGATGCGGGCTACACA	0.607													5	151	---	---	---	---	PASS
NUTF2	10204	broad.mit.edu	37	16	67902527	67902527	+	Intron	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67902527G>A	uc002eup.2	+						NUTF2_uc010vkf.1_3'UTR|NUTF2_uc002euq.3_5'Flank	NM_005796	NP_005787	P61970	NTF2_HUMAN	nuclear transport factor 2						protein transport	cytosol|nuclear pore	protein binding|transporter activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00443)|Epithelial(162;0.0199)|all cancers(182;0.129)		ACAGTGGTAGGGAGGGGTGGG	0.552													29	78	---	---	---	---	PASS
EDC4	23644	broad.mit.edu	37	16	67920202	67920202	+	3'UTR	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67920202G>T	uc002eut.1	+	1					NRN1L_uc002euu.2_3'UTR			Q6P2E9	EDC4_HUMAN	Homo sapiens cDNA FLJ43830 fis, clone TESTI4004887, weakly  similar to Homo sapiens autoantigen (RCD-8).						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|central_nervous_system(2)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		CTCCAGCCCTGCTCTGGCGGT	0.597													3	8	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													3	11	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268081	70268081	+	RNA	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268081G>A	uc010cfp.1	-	3		c.334C>T								Homo sapiens cDNA, FLJ98908.																		TCTTACTGTTGGCTAAAAGGC	0.373													3	11	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268158	70268158	+	RNA	SNP	A	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268158A>C	uc010cfp.1	-	3		c.257T>G								Homo sapiens cDNA, FLJ98908.																		TTCTTCATTAAAACAGCTACT	0.333													3	14	---	---	---	---	PASS
SCARF1	8578	broad.mit.edu	37	17	1540047	1540047	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1540047C>T	uc002fsz.1	-	10	1639	c.1589G>A	c.(1588-1590)GGA>GAA	p.G530E	SCARF1_uc002fsy.1_Missense_Mutation_p.E518K|SCARF1_uc002fta.1_RNA|SCARF1_uc010cjv.1_Missense_Mutation_p.G444E	NM_003693	NP_003684	Q14162	SREC_HUMAN	scavenger receptor class F, member 1 isoform 1	530	Pro/Ser-rich.|Cytoplasmic (Potential).				cell adhesion|neuron remodeling|positive regulation of axon regeneration|receptor-mediated endocytosis	integral to membrane	low-density lipoprotein particle binding|scavenger receptor activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ATCTGCCTCTCCAGACTCAGG	0.627													34	120	---	---	---	---	PASS
UNC45B	146862	broad.mit.edu	37	17	33501331	33501331	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33501331G>C	uc002hja.2	+	14	2004	c.1907G>C	c.(1906-1908)TGC>TCC	p.C636S	UNC45B_uc002hjb.2_Missense_Mutation_p.C634S|UNC45B_uc002hjc.2_Missense_Mutation_p.C634S|UNC45B_uc010cto.2_Missense_Mutation_p.C555S	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	636					cell differentiation|muscle organ development	cytosol	binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)				GCCCTGGCTTGCATGGTGAAA	0.572													28	95	---	---	---	---	PASS
COASY	80347	broad.mit.edu	37	17	40717515	40717515	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40717515G>T	uc002hzz.2	+	8	1571	c.1414G>T	c.(1414-1416)GCT>TCT	p.A472S	COASY_uc010cyj.2_Missense_Mutation_p.A501S|COASY_uc002iab.2_Missense_Mutation_p.A177S|COASY_uc002iad.2_Missense_Mutation_p.A472S|COASY_uc002iac.2_Missense_Mutation_p.A472S|COASY_uc002iae.2_Missense_Mutation_p.A267S|MLX_uc002iaf.2_5'Flank|MLX_uc002iag.2_5'Flank|MLX_uc002iah.2_5'Flank	NM_001042529	NP_001035994	Q13057	COASY_HUMAN	coenzyme A synthase isoform a	472	DPCK.				coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial outer membrane	ATP binding|dephospho-CoA kinase activity|pantetheine-phosphate adenylyltransferase activity				0		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		GATTGATGCCGCTGTGTTGCT	0.607													3	73	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630632	44630632	+	3'UTR	SNP	C	T	T	rs142505146	by1000genomes	TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630632C>T	uc002iks.2	-	4					LRRC37A2_uc002ikn.1_Intron|ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Intron	NM_001113738	NP_001107210	Q8IVW1	ARL17_HUMAN	hypothetical protein LOC51326 isoform a						protein transport|vesicle-mediated transport	Golgi apparatus	GTP binding				0						TGTTACACAGCATACAATTCC	0.234													4	49	---	---	---	---	PASS
FBF1	85302	broad.mit.edu	37	17	73934245	73934245	+	5'UTR	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73934245G>A	uc002jqc.2	-	2					FBF1_uc010wsp.1_5'Flank|FBF1_uc002jqd.1_5'UTR	NM_001080542	NP_001074011	Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1												0						CGGCTCTCGGGGGTGCTCTCA	0.498													10	47	---	---	---	---	PASS
PRPSAP1	5635	broad.mit.edu	37	17	74307778	74307778	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74307778C>T	uc010wta.1	-	10	1449	c.1003G>A	c.(1003-1005)GTG>ATG	p.V335M	PRPSAP1_uc010wtb.1_Missense_Mutation_p.V232M	NM_002766	NP_002757	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate	306					nucleotide biosynthetic process		enzyme inhibitor activity|identical protein binding|magnesium ion binding|ribose phosphate diphosphokinase activity			ovary(1)	1						TTCGTCACCACCACCTAGTCA	0.438													25	105	---	---	---	---	PASS
NDC80	10403	broad.mit.edu	37	18	2616501	2616501	+	Silent	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2616501C>T	uc002kli.2	+	17	2039	c.1857C>T	c.(1855-1857)CTC>CTT	p.L619L		NM_006101	NP_006092	O14777	NDC80_HUMAN	kinetochore associated 2	619	Potential.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore|cell division|establishment of mitotic spindle orientation|mitotic prometaphase|mitotic sister chromatid segregation|mitotic spindle organization|phosphatidylinositol-mediated signaling	condensed nuclear chromosome outer kinetochore|cytosol|Ndc80 complex	protein binding			ovary(1)	1						CAGAAGATCTCTCGGAAAATA	0.289													16	126	---	---	---	---	PASS
TAF4B	6875	broad.mit.edu	37	18	23872291	23872291	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23872291G>A	uc002kvu.3	+	8	2161	c.1672G>A	c.(1672-1674)GGA>AGA	p.G558R	TAF4B_uc002kvs.3_RNA|TAF4B_uc002kvt.3_Missense_Mutation_p.G563R	NM_005640	NP_005631	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding	558					transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleolus|transcription factor TFIID complex	DNA binding|NF-kappaB binding|sequence-specific DNA binding transcription factor activity			lung(1)|central_nervous_system(1)|skin(1)	3	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			TCAGAAATGTGGACAGAAGAC	0.438													23	113	---	---	---	---	PASS
MOCOS	55034	broad.mit.edu	37	18	33785102	33785102	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33785102T>A	uc002kzq.3	+	6	1104	c.1081T>A	c.(1081-1083)TCC>ACC	p.S361T		NM_017947	NP_060417	Q96EN8	MOCOS_HUMAN	molybdenum cofactor sulfurase	361					Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	lyase activity|Mo-molybdopterin cofactor sulfurase activity|molybdenum ion binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	CGTGGCCCTGTCCTCTCTCCA	0.478													31	139	---	---	---	---	PASS
ATP8B1	5205	broad.mit.edu	37	18	55319399	55319399	+	Silent	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55319399G>A	uc002lgw.2	-	25	3267	c.3267C>T	c.(3265-3267)GGC>GGT	p.G1089G	uc002lgu.1_Intron|uc002lgv.1_Intron	NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1	1089	Helical; (Potential).				ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(5)|ovary(2)|central_nervous_system(2)|lung(1)	10		Colorectal(73;0.229)				AAGTATCCAAGCCAATCTGTT	0.358									Byler_disease				19	38	---	---	---	---	PASS
DUS3L	56931	broad.mit.edu	37	19	5785681	5785681	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5785681C>A	uc002mdc.2	-	11	1781	c.1684G>T	c.(1684-1686)GGC>TGC	p.G562C	PRR22_uc002mdb.1_5'Flank|PRR22_uc010xiv.1_5'Flank|DUS3L_uc002mdd.2_Missense_Mutation_p.G320C|DUS3L_uc010duk.2_Missense_Mutation_p.G227C	NM_020175	NP_064560	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like isoform 1	562					tRNA processing		flavin adenine dinucleotide binding|nucleic acid binding|tRNA dihydrouridine synthase activity|zinc ion binding				0						GTGTCCGAGCCCCAGTGCTCC	0.682													3	30	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9067149	9067149	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9067149G>A	uc002mkp.2	-	3	20501	c.20297C>T	c.(20296-20298)TCG>TTG	p.S6766L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	6768	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						AGTCGCCATCGAGTGTGTTCC	0.483													68	339	---	---	---	---	PASS
DNMT1	1786	broad.mit.edu	37	19	10262203	10262203	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10262203C>T	uc002mng.2	-	23	2268	c.2088G>A	c.(2086-2088)ATG>ATA	p.M696I	DNMT1_uc010xlc.1_Missense_Mutation_p.M712I|DNMT1_uc002mnh.2_Missense_Mutation_p.M591I|DNMT1_uc010xld.1_Missense_Mutation_p.M696I	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	696	Required for activity.				chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)	CTGCCTCCTTCATGGCCATAT	0.473													59	321	---	---	---	---	PASS
ZNF625	90589	broad.mit.edu	37	19	12256409	12256409	+	Silent	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12256409C>T	uc002mth.2	-	4	974	c.624G>A	c.(622-624)CCG>CCA	p.P208P	ZNF20_uc002mtg.1_Intron|ZNF625_uc010dyn.1_RNA|ZNF625_uc010dyo.1_Silent_p.P242P	NM_145233	NP_660276	Q96I27	ZN625_HUMAN	zinc finger protein 625	208					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TACATTCATACGGCTTCTCCC	0.428													34	135	---	---	---	---	PASS
CCDC105	126402	broad.mit.edu	37	19	15132495	15132495	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15132495A>G	uc002nae.2	+	5	1208	c.1109A>G	c.(1108-1110)GAG>GGG	p.E370G		NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	370					microtubule cytoskeleton organization	microtubule				ovary(1)	1						TATAACCAAGAGTTGTACACC	0.572													13	46	---	---	---	---	PASS
C19orf47	126526	broad.mit.edu	37	19	40827909	40827909	+	Silent	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40827909G>T	uc002oni.3	-	9	1150	c.1149C>A	c.(1147-1149)GTC>GTA	p.V383V	C19orf47_uc002ong.2_Silent_p.V242V|C19orf47_uc002onh.2_Silent_p.V316V	NM_178830	NP_849152	Q8N9M1	CS047_HUMAN	hypothetical protein LOC126526	383										ovary(1)|skin(1)	2			Lung(22;0.000636)			TCTTAATGGTGACCTTGACCT	0.627													6	64	---	---	---	---	PASS
CACNG7	59284	broad.mit.edu	37	19	54445652	54445652	+	3'UTR	SNP	C	A	A	rs59451715	byFrequency	TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54445652C>A	uc002qcr.1	+	5						NM_031896	NP_114102	P62955	CCG7_HUMAN	voltage-dependent calcium channel gamma-7						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(1)	1	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		TCGCTCCCACCCGGAGGAGGC	0.682													8	39	---	---	---	---	PASS
ZSCAN5A	79149	broad.mit.edu	37	19	56735052	56735052	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56735052G>T	uc002qmq.2	-	3	702	c.536C>A	c.(535-537)GCC>GAC	p.A179D	ZSCAN5A_uc010ygi.1_Missense_Mutation_p.A62D|ZSCAN5A_uc002qmr.2_Missense_Mutation_p.A179D|ZSCAN5A_uc002qms.1_Missense_Mutation_p.A179D	NM_024303	NP_077279	Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	179					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3						CTCTCGGTGGGCCTGGCCTTC	0.617													6	93	---	---	---	---	PASS
ZNF530	348327	broad.mit.edu	37	19	58118103	58118103	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58118103G>C	uc002qpk.2	+	3	1430	c.1210G>C	c.(1210-1212)GAA>CAA	p.E404Q	ZNF547_uc002qpm.3_Intron|ZNF530_uc002qpl.2_RNA	NM_020880	NP_065931	Q6P9A1	ZN530_HUMAN	zinc finger protein 530	404					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0443)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TCACACTGGAGAAAGACCTTA	0.423													22	116	---	---	---	---	PASS
ZMYND8	23613	broad.mit.edu	37	20	45905189	45905189	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45905189G>A	uc002xta.1	-	11	1543	c.1289C>T	c.(1288-1290)CCG>CTG	p.P430L	ZMYND8_uc010ghq.1_Missense_Mutation_p.P107L|ZMYND8_uc010ghr.1_Missense_Mutation_p.P405L|ZMYND8_uc002xst.1_Missense_Mutation_p.P405L|ZMYND8_uc002xsu.1_Missense_Mutation_p.P430L|ZMYND8_uc002xsv.1_Missense_Mutation_p.P405L|ZMYND8_uc002xsw.1_Missense_Mutation_p.P182L|ZMYND8_uc002xsx.1_Missense_Mutation_p.P182L|ZMYND8_uc002xsy.1_Missense_Mutation_p.P405L|ZMYND8_uc002xsz.1_Missense_Mutation_p.P367L|ZMYND8_uc010zxy.1_Missense_Mutation_p.P457L|ZMYND8_uc002xtb.1_Missense_Mutation_p.P450L|ZMYND8_uc002xss.2_Missense_Mutation_p.P430L|ZMYND8_uc010zxz.1_Missense_Mutation_p.P425L|ZMYND8_uc002xtc.1_Missense_Mutation_p.P450L|ZMYND8_uc002xtd.1_Missense_Mutation_p.P425L|ZMYND8_uc002xte.1_Missense_Mutation_p.P430L|ZMYND8_uc010zya.1_Missense_Mutation_p.P430L|ZMYND8_uc002xtf.1_Missense_Mutation_p.P450L|ZMYND8_uc002xtg.2_Missense_Mutation_p.P424L|ZMYND8_uc010ghs.1_Missense_Mutation_p.P424L	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b	430							protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			GGGGGAGCGCGGCATATCCGA	0.597													7	135	---	---	---	---	PASS
NCOA3	8202	broad.mit.edu	37	20	46277767	46277767	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46277767C>G	uc002xtk.2	+	19	3770	c.3565C>G	c.(3565-3567)CAG>GAG	p.Q1189E	NCOA3_uc010ght.1_Missense_Mutation_p.Q1184E|NCOA3_uc002xtl.2_Missense_Mutation_p.Q1189E|NCOA3_uc002xtm.2_Missense_Mutation_p.Q1189E|NCOA3_uc002xtn.2_Missense_Mutation_p.Q1189E|NCOA3_uc010zyc.1_Missense_Mutation_p.Q984E	NM_181659	NP_858045	Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3 isoform a	1189	Acetyltransferase.				androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5						TCAGAGCCGACAGGCACTTGA	0.448													26	80	---	---	---	---	PASS
C20orf43	51507	broad.mit.edu	37	20	55049773	55049773	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55049773C>A	uc002xxt.2	+	3	311	c.204C>A	c.(202-204)GAC>GAA	p.D68E	C20orf43_uc010zzf.1_Missense_Mutation_p.D98E|C20orf43_uc002xxu.2_Missense_Mutation_p.D68E|C20orf43_uc002xxv.2_Missense_Mutation_p.D68E	NM_016407	NP_057491	Q9BY42	CT043_HUMAN	hypothetical protein LOC51507	68										ovary(1)	1			Colorectal(105;0.202)			TTCTCTTGGACAAATCTGCAG	0.388													56	250	---	---	---	---	PASS
SYCP2	10388	broad.mit.edu	37	20	58439344	58439344	+	3'UTR	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58439344G>T	uc002yaz.2	-	44						NM_014258	NP_055073	Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2						cell division|meiotic prophase I|synaptonemal complex assembly		DNA binding			ovary(3)|lung(2)	5	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ATTAGATAAAGTATGGTGATA	0.333													9	40	---	---	---	---	PASS
ZGPAT	84619	broad.mit.edu	37	20	62366756	62366756	+	Missense_Mutation	SNP	G	C	C	rs17855481		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62366756G>C	uc002ygk.2	+	6	1475	c.1297G>C	c.(1297-1299)GGG>CGG	p.G433R	ZGPAT_uc002ygi.2_Missense_Mutation_p.G413R|ZGPAT_uc002ygj.2_Missense_Mutation_p.G413R|ZGPAT_uc010gkk.1_5'UTR|ZGPAT_uc010gkl.1_Missense_Mutation_p.G413R|ZGPAT_uc002ygm.2_Missense_Mutation_p.G404R|ZGPAT_uc002ygn.3_RNA|LIME1_uc011abi.1_5'Flank|LIME1_uc002ygp.3_5'Flank	NM_032527	NP_115916	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	433				G -> R (in Ref. 6; AAH19338).	negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					CCTAGAAGCCGGGGCGGCCCC	0.642													5	15	---	---	---	---	PASS
USP25	29761	broad.mit.edu	37	21	17197352	17197352	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17197352C>G	uc002yjy.1	+	12	1493	c.1276C>G	c.(1276-1278)CTC>GTC	p.L426V	USP25_uc011aby.1_Missense_Mutation_p.L426V|USP25_uc002yjz.1_Missense_Mutation_p.L426V|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	426					protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		GAAAGATTACCTCACGGTATT	0.313													20	84	---	---	---	---	PASS
UBE2L3	7332	broad.mit.edu	37	22	21968852	21968852	+	Intron	SNP	C	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21968852C>T	uc002zva.1	+						UBE2L3_uc011aig.1_Intron|UBE2L3_uc002zuz.1_Missense_Mutation_p.S106L|UBE2L3_uc010gti.1_Intron	NM_003347	NP_003338	P68036	UB2L3_HUMAN	ubiquitin-conjugating enzyme E2L 3						cell proliferation|cellular response to glucocorticoid stimulus|protein K11-linked ubiquitination|regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	ATP binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity				0	Colorectal(54;0.105)					ttagaaacttcagcgttccca	0.204													75	442	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22677327	22677327	+	Splice_Site	SNP	A	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22677327A>G	uc011aim.1	+	36		c.3366_splice	c.e36+1							Parts of antibodies, mostly variable regions.												0						GAGTGCTGGCACAGTGCTCCA	0.612													10	26	---	---	---	---	PASS
DDTL	100037417	broad.mit.edu	37	22	24313566	24313566	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24313566G>A	uc002zyy.3	+	3	453	c.376G>A	c.(376-378)GAG>AAG	p.E126K	DDT_uc011ajf.1_Intron|DDT_uc002zyz.3_3'UTR|DDT_uc002zza.3_3'UTR	NM_001084393	NP_001077862	A6NHG4	DDTL_HUMAN	D-dopachrome tautomerase-like	126						cytoplasm	lyase activity				0						ATGTTTGAATGAGGAAGCTCT	0.478													19	96	---	---	---	---	PASS
PKDREJ	10343	broad.mit.edu	37	22	46655753	46655753	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46655753G>A	uc003bhh.2	-	1	3467	c.3467C>T	c.(3466-3468)ACC>ATC	p.T1156I		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	receptor for egg jelly-like protein precursor	1156	Extracellular (Potential).				acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			breast(3)|ovary(2)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CACATAGTGGGTATGCAGGTG	0.517													41	212	---	---	---	---	PASS
MOV10L1	54456	broad.mit.edu	37	22	50555733	50555733	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50555733A>C	uc003bjj.2	+	9	1490	c.1407A>C	c.(1405-1407)CAA>CAC	p.Q469H	MOV10L1_uc003bjk.3_Missense_Mutation_p.Q469H|MOV10L1_uc011arp.1_Missense_Mutation_p.Q449H|MOV10L1_uc011arq.1_Missense_Mutation_p.Q230H|MOV10L1_uc010hao.1_RNA	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1	469					germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		AAAGTTCACAAGCGTTAACAT	0.428													14	78	---	---	---	---	PASS
SFRS17A	8227	broad.mit.edu	37	X	1713017	1713017	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1713017A>G	uc004cqa.2	+	2	858	c.662A>G	c.(661-663)TAC>TGC	p.Y221C	SFRS17A_uc010ncx.1_Missense_Mutation_p.Y221C|SFRS17A_uc004cqb.2_RNA|ASMT_uc004cqd.2_5'Flank	NM_005088	NP_005079	Q02040	AK17A_HUMAN	DNA segment on chromosome X and Y (unique) 155	221	RRM.				B cell activation|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|signal transduction	nuclear speck|spliceosomal complex	nucleotide binding|protein binding|RNA binding				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TATGTGCAGTACCGCGAGTAC	0.607													14	88	---	---	---	---	PASS
ZBED1	9189	broad.mit.edu	37	X	2406675	2406675	+	3'UTR	SNP	G	T	T			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2406675G>T	uc004cqg.2	-	2					DHRSX_uc004cqf.3_Intron|ZBED1_uc004cqh.1_3'UTR	NM_004729	NP_004720	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1							nuclear chromosome	DNA binding|metal ion binding|protein dimerization activity|transposase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACGCTTCCTCGCTACAGGAAG	0.567													3	41	---	---	---	---	PASS
KIF4A	24137	broad.mit.edu	37	X	69622533	69622533	+	Silent	SNP	T	C	C			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69622533T>C	uc004dyg.2	+	23	2734	c.2607T>C	c.(2605-2607)TAT>TAC	p.Y869Y	KIF4A_uc010nkw.2_Silent_p.Y869Y	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	869	Potential.|Interaction with PRC1.				anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4						CCCTGAAATATTTGATTGGAG	0.443													9	10	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	155254735	155254735	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155254735C>G	uc004fnx.3	+	8	1085	c.631C>G	c.(631-633)CTC>GTC	p.L211V		NM_182905	NP_878908			WAS protein family homolog 1																		GATGTCGGATCTCTTCAACAA	0.587													2	2	---	---	---	---	PASS
ACOT7	11332	broad.mit.edu	37	1	6390127	6390128	+	Intron	DEL	GT	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6390127_6390128delGT	uc001ams.2	-						ACOT7_uc010nzq.1_Intron|ACOT7_uc001amt.2_Intron|ACOT7_uc001amu.2_Intron|ACOT7_uc001amv.2_Intron|ACOT7_uc001amq.2_Intron|ACOT7_uc001amr.2_Intron	NM_181864	NP_863654	O00154	BACH_HUMAN	acyl-CoA thioesterase 7 isoform hBACHb							mitochondrion|nucleus	carboxylesterase activity|fatty-acyl-CoA binding|palmitoyl-CoA hydrolase activity				0	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		tgtgtgtgtggtgtgtgtgtgt	0.262													5	4	---	---	---	---	
UBE4B	10277	broad.mit.edu	37	1	10211221	10211221	+	Intron	DEL	A	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10211221delA	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron|UBE4B_uc001aqt.1_Intron	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1						apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		actctgtctcaaaaaaaaaaa	0.219													4	2	---	---	---	---	
FBXO2	26232	broad.mit.edu	37	1	11709029	11709030	+	Intron	INS	-	CAGCC	CAGCC			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11709029_11709030insCAGCC	uc001asj.2	-						FBXO2_uc009vna.2_Intron	NM_012168	NP_036300	Q9UK22	FBX2_HUMAN	F-box only protein 2						glycoprotein catabolic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|endoplasmic reticulum|membrane|microsome|SCF ubiquitin ligase complex	sugar binding|ubiquitin-protein ligase activity				0	Ovarian(185;0.249)	Lung NSC(185;9.37e-06)|all_lung(284;1.39e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|BRCA - Breast invasive adenocarcinoma(304;1.88e-06)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|Lung(427;0.0146)|LUSC - Lung squamous cell carcinoma(448;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		GGTGACTATCTcagcccagccc	0.574													4	2	---	---	---	---	
EPHA2	1969	broad.mit.edu	37	1	16458076	16458077	+	Intron	INS	-	A	A			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16458076_16458077insA	uc001aya.1	-							NM_004431	NP_004422	P29317	EPHA2_HUMAN	ephrin receptor EphA2 precursor						activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus	focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane	ATP binding|ephrin receptor activity|protein binding			lung(3)|central_nervous_system(3)|stomach(2)|ovary(2)	10		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;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)	actccgtctccaaaaaaaaaaa	0.198													4	2	---	---	---	---	
C1orf177	163747	broad.mit.edu	37	1	55285662	55285665	+	Intron	DEL	TTCT	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55285662_55285665delTTCT	uc001cyb.3	+						C1orf177_uc001cya.3_Intron	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN	hypothetical protein LOC163747 isoform 2												0						tctctctttcttctttctttctcc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	82617156	82617163	+	IGR	DEL	AAGAAAGA	-	-	rs36191171	by1000genomes	TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82617156_82617163delAAGAAAGA								LPHN2 (159050 upstream) : None (None downstream)																							ggaaggaaggaagaaagaaagaaagaaa	0.000													3	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145559919	145559919	+	Intron	DEL	A	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145559919delA	uc001emp.3	+						ANKRD35_uc010oyx.1_Intron|ANKRD35_uc001eob.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		actccgtctcaaaaaaaaaaa	0.204													4	2	---	---	---	---	
GPR161	23432	broad.mit.edu	37	1	168056573	168056574	+	Intron	DEL	GT	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168056573_168056574delGT	uc001gfc.2	-						GPR161_uc001gfb.2_Intron|GPR161_uc010pll.1_Intron|GPR161_uc010plm.1_Intron|GPR161_uc009wvo.2_Intron|GPR161_uc001gfd.2_Intron|GPR161_uc010pln.1_Intron	NM_153832	NP_722561	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161 isoform 2						multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)					ACACgtgtgggtgtgtgtgtgt	0.337													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	226195425	226195425	+	IGR	DEL	A	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226195425delA								C1orf55 (8359 upstream) : H3F3A (54996 downstream)																							aggaaggaagaaaaaaaaaaT	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	236832373	236832374	+	IGR	INS	-	TTCCTTCC	TTCCTTCC	rs71993165		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236832373_236832374insTTCCTTCC								HEATR1 (64559 upstream) : ACTN2 (17396 downstream)																							cctttctttctttccttccttc	0.109													4	5	---	---	---	---	
ZRANB3	84083	broad.mit.edu	37	2	136046444	136046445	+	Intron	DEL	GT	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136046444_136046445delGT	uc002tum.2	-						ZRANB3_uc002tuk.2_Intron|ZRANB3_uc002tul.2_Intron|ZRANB3_uc002tun.1_Intron	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3							intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)		ttcatttatcgtgtgtgtgtgt	0.000													3	3	---	---	---	---	
MBD5	55777	broad.mit.edu	37	2	149204838	149204841	+	Intron	DEL	GAAA	-	-	rs3955149		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149204838_149204841delGAAA	uc002twm.3	+							NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)		aggaaggaaggaaagaaAGTAGAG	0.191													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235453299	235453300	+	IGR	INS	-	GA	GA	rs72118706		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235453299_235453300insGA								ARL4C (47606 upstream) : SH3BP4 (407328 downstream)																							ggaagggaaggagagagggaga	0.109													4	2	---	---	---	---	
COL7A1	1294	broad.mit.edu	37	3	48615598	48615598	+	Intron	DEL	A	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48615598delA	uc003ctz.2	-							NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor						cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		actccatctcaaaaaaaaaaa	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191470816	191470817	+	IGR	DEL	AC	-	-	rs111776778		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191470816_191470817delAC								PYDC2 (291573 upstream) : FGF12 (388867 downstream)																							gcatacgtgtacacacacacac	0.168													4	2	---	---	---	---	
IGJ	3512	broad.mit.edu	37	4	71521932	71521932	+	3'UTR	DEL	A	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71521932delA	uc003hfn.3	-	4					IGJ_uc010ihz.2_3'UTR	NM_144646	NP_653247	P01591	IGJ_HUMAN	immunoglobulin J chain						immune response	extracellular region	antigen binding				0			Lung(101;0.235)			TACATCACCCAAAAAAAAAAA	0.308													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	75751095	75751096	+	IGR	INS	-	CACA	CACA	rs111623943		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75751095_75751096insCACA								BTC (31213 upstream) : PARM1 (107202 downstream)																							TCTCTCTCTTTcacacacacac	0.361													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	117536739	117536742	+	IGR	DEL	GGAA	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117536739_117536742delGGAA								MIR1973 (315815 upstream) : TRAM1L1 (467974 downstream)																							aaggaaggagggaaggaaggaagg	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	183022398	183022405	+	IGR	DEL	AGGGAGGG	-	-	rs142125684	by1000genomes	TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183022398_183022405delAGGGAGGG								None (None upstream) : MGC45800 (37754 downstream)																							gaaggaaagaagggagggaggaaggaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	22995414	22995415	+	IGR	INS	-	TTCC	TTCC			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22995414_22995415insTTCC								CDH12 (141683 upstream) : PRDM9 (512309 downstream)																							tctggttgtttttccttccttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43519922	43519923	+	IGR	DEL	TG	-	-	rs72118305		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43519922_43519923delTG								C5orf34 (4735 upstream) : PAIP1 (6449 downstream)																							TTGGCCAAGTtgtgtgtgtgtg	0.243													4	3	---	---	---	---	
DDX4	54514	broad.mit.edu	37	5	55111304	55111304	+	Intron	DEL	G	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55111304delG	uc003jqg.3	+						DDX4_uc003jqh.3_Intron|DDX4_uc003jqj.2_Intron	NM_001136034	NP_001129506	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform						multicellular organismal development|sperm motility	perinuclear region of cytoplasm|pi-body|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|skin(1)	2		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				CTTTGTAAATGTTGTGCTTAA	0.318													32	23	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	156507479	156507488	+	IGR	DEL	GCTAGAAAAG	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156507479_156507488delGCTAGAAAAG								HAVCR1 (21349 upstream) : HAVCR2 (5355 downstream)																							ATCTAGTATTGCTAGAAAAGCCTTGCTTAT	0.495													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166471041	166471042	+	IGR	INS	-	GAAG	GAAG	rs13183705		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166471041_166471042insGAAG								None (None upstream) : ODZ2 (240801 downstream)																							TAGTaaggacagaaggaaggaa	0.119													8	4	---	---	---	---	
MBOAT1	154141	broad.mit.edu	37	6	20212200	20212201	+	Intron	INS	-	ACAC	ACAC	rs139229589	by1000genomes	TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20212200_20212201insACAC	uc003ncx.1	-						MBOAT1_uc011dji.1_Intron	NM_001080480	NP_001073949	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain						phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			AAGAAGGGAAAacacacacaca	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	74942086	74942087	+	Intron	DEL	CT	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74942086_74942087delCT	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																		ccctcctttcctcTCTCTCTCT	0.025													4	2	---	---	---	---	
DLL1	28514	broad.mit.edu	37	6	170595891	170595892	+	Intron	DEL	AC	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170595891_170595892delAC	uc003qxm.2	-							NM_005618	NP_005609	O00548	DLL1_HUMAN	delta-like 1 precursor						cell communication|cell fate determination|hemopoiesis|Notch receptor processing|Notch signaling pathway|regulation of cell adhesion	extracellular region|integral to plasma membrane	calcium ion binding|Notch binding			lung(4)|ovary(1)	5		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		CCTCGCGTGTacacacacacac	0.569													4	3	---	---	---	---	
ELFN1	392617	broad.mit.edu	37	7	1786949	1786950	+	3'UTR	INS	-	ACAG	ACAG	rs147894607	by1000genomes	TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1786949_1786950insACAG	uc010ksg.2	+	2						NM_001128636	NP_001122108			extracellular leucine-rich repeat and												0						cacacacacacacacacacaca	0.465													3	3	---	---	---	---	
FAM71F2	346653	broad.mit.edu	37	7	128312704	128312704	+	Intron	DEL	G	-	-	rs10265601		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128312704delG	uc003vnk.3	+						FAM71F2_uc010llm.1_Intron|FAM71F2_uc003vnl.2_Intron|FAM71F2_uc010lln.1_Intron	NM_001012454	NP_001012457	Q6NXP2	F71F2_HUMAN	hypothetical protein LOC346653 isoform a												0						CCCTGGGGGAGGGGGGGGCGG	0.552											OREG0018296	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
CHCHD3	54927	broad.mit.edu	37	7	132719268	132719269	+	Intron	INS	-	TTT	TTT	rs56769155		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132719268_132719269insTTT	uc003vre.2	-						CHCHD3_uc010lmi.2_Intron|CHCHD3_uc003vrf.2_Intron|CHCHD3_uc010lmj.2_Intron|CHCHD3_uc011kpn.1_Intron	NM_017812	NP_060282	Q9NX63	CHCH3_HUMAN	coiled-coil-helix-coiled-coil-helix domain						inner mitochondrial membrane organization|mitochondrial fusion	mitochondrial inner membrane	protein complex scaffold				0						TGGATCCAGTCttttttttttt	0.342													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	9140907	9140910	+	IGR	DEL	CCTT	-	-	rs141660114		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9140907_9140910delCCTT								PPP1R3B (131823 upstream) : TNKS (272535 downstream)																							ccttcccctcccttccttccttcc	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	53358415	53358415	+	IGR	DEL	A	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53358415delA								ST18 (35976 upstream) : FAM150A (88183 downstream)																							TTTTCATTTCAAAAAAAAAAA	0.363													4	2	---	---	---	---	
C8orf83	286144	broad.mit.edu	37	8	93961816	93961819	+	Intron	DEL	GAAA	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93961816_93961819delGAAA	uc003yfk.3	-						C8orf83_uc003yfr.3_Intron|C8orf83_uc010map.2_Intron|C8orf83_uc003yfo.3_Intron|C8orf83_uc003yfn.3_Intron|C8orf83_uc003yfq.3_Intron|C8orf83_uc003yfl.3_Intron|C8orf83_uc003yfm.3_Intron	NR_015339		Q629K1	TRIQK_HUMAN	RecName: Full=UPF0599 protein C8orf83;							endoplasmic reticulum membrane|integral to membrane					0						gaaagagatggaaagaaagaaaga	0.064													4	2	---	---	---	---	
EXD3	54932	broad.mit.edu	37	9	140268130	140268132	+	Intron	DEL	TTT	-	-	rs66959515		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140268130_140268132delTTT	uc004cmp.2	-						C9orf167_uc011mew.1_Intron|EXD3_uc010ncg.1_Intron|EXD3_uc004cmr.2_Intron|EXD3_uc004cms.2_Intron	NM_017820	NP_060290	Q8N9H8	MUT7_HUMAN	exonuclease 3'-5' domain containing 3						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0						CGCAGAGAGGTTTTTTAAAATTT	0.571													3	4	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1266229	1266237	+	Intron	DEL	TGGTGGTGA	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1266229_1266237delTGGTGGTGA	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		atggtgatggtggtggtgatggtggtgat	0.000													4	2	---	---	---	---	
VCL	7414	broad.mit.edu	37	10	75803109	75803110	+	Intron	INS	-	T	T	rs145684984		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75803109_75803110insT	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706	P18206	VINC_HUMAN	vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)					TGACATAATAAttttttttttt	0.099													4	3	---	---	---	---	
NRAP	4892	broad.mit.edu	37	10	115381477	115381477	+	Intron	DEL	C	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115381477delC	uc001laj.2	-						NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Intron	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		AGTTAAACCACTAGCAAAGTA	0.373													5	3	---	---	---	---	
TDRD1	56165	broad.mit.edu	37	10	115985616	115985616	+	Intron	DEL	A	-	-	rs74608976		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115985616delA	uc001lbg.1	+						TDRD1_uc001lbf.2_Intron|TDRD1_uc001lbh.1_Intron|TDRD1_uc001lbi.1_Intron|TDRD1_uc010qsc.1_Intron|TDRD1_uc001lbj.2_Intron	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1						DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		accctgtctcaaaaaaaaaaa	0.114													6	4	---	---	---	---	
KNDC1	85442	broad.mit.edu	37	10	135032032	135032032	+	Intron	DEL	G	-	-	rs66904615		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135032032delG	uc001llz.1	+							NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GAAGCTGCCTGGGGAGGTGCA	0.557													3	3	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133312622	133312623	+	Intron	DEL	GT	-	-	rs67138081		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133312622_133312623delGT	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		ATATTTAAACgtgtgtgtgtgt	0.218													3	3	---	---	---	---	
CACNA2D4	93589	broad.mit.edu	37	12	2016939	2016951	+	Intron	DEL	GCCTGGTGAGTAT	-	-	rs113797488		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2016939_2016951delGCCTGGTGAGTAT	uc001qjp.2	-						CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		TGGTGGGCCAGCCTGGTGAGTATGCCTGGTGGG	0.662													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16966790	16966790	+	IGR	DEL	C	-	-	rs56049732		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16966790delC								LMO3 (204032 upstream) : None (None downstream)																							ttccttccttcctttctctct	0.000													4	2	---	---	---	---	
BAZ2A	11176	broad.mit.edu	37	12	56999208	56999208	+	Intron	DEL	T	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56999208delT	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc009zov.1_5'Flank|BAZ2A_uc009zow.1_Intron	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A						chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0						TTTTATGTAAttttttttttt	0.174													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80722386	80722386	+	IGR	DEL	T	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80722386delT								PPP1R12A (393151 upstream) : PTPRQ (115740 downstream)																							AATGTAGTCCTTTTTTTTTTG	0.338													9	4	---	---	---	---	
POLR3B	55703	broad.mit.edu	37	12	106852804	106852805	+	Intron	DEL	TG	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106852804_106852805delTG	uc001tlp.2	+						POLR3B_uc001tlq.2_Intron	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2						TAGACTATGAtgtgtgtgtgtg	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115769911	115769912	+	IGR	DEL	AC	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115769911_115769912delAC								TBX3 (647942 upstream) : MED13L (626471 downstream)																							acacacacaaacacacacacac	0.045													3	3	---	---	---	---	
MAP1LC3B2	643246	broad.mit.edu	37	12	117013990	117013990	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117013990delG	uc009zwk.1	+	2	397	c.243delG	c.(241-243)CTGfs	p.L81fs		NM_001085481	NP_001078950	A6NCE7	MP3B2_HUMAN	microtubule-associated protein 1 light chain 3	81					autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule					0						CCTTCTTCCTGTTGGTGAACG	0.453													116	52	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20138377	20138377	+	IGR	DEL	A	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20138377delA								P704P (118105 upstream) : OR4Q3 (77210 downstream)																							CAaaagaaagaaagaaagaaa	0.214													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	36463290	36463291	+	IGR	INS	-	TCCT	TCCT	rs66569553		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36463290_36463291insTCCT								BRMS1L (122122 upstream) : MBIP (304473 downstream)																							GACCATATTTAtccttccttcc	0.158													4	2	---	---	---	---	
SLC25A21	89874	broad.mit.edu	37	14	37203617	37203618	+	Intron	INS	-	TA	TA	rs149858951	by1000genomes	TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37203617_37203618insTA	uc001wtz.1	-							NM_030631	NP_085134	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial						lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		TTTTAGTGCTTTATATATAATT	0.297													4	2	---	---	---	---	
MTFMT	123263	broad.mit.edu	37	15	65295300	65295301	+	3'UTR	INS	-	A	A	rs140680377		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65295300_65295301insA	uc002aof.3	-	9						NM_139242	NP_640335	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase							mitochondrion	methionyl-tRNA formyltransferase activity|methyltransferase activity			ovary(2)	2					Tetrahydrofolic acid(DB00116)	gactctgtctcaaaaaaaaaaa	0.099													5	3	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14700252	14700252	+	Intron	DEL	G	-	-	rs62037478		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14700252delG	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						aagaccctgagggaaaaaaaa	0.139													6	3	---	---	---	---	
CMIP	80790	broad.mit.edu	37	16	81533874	81533877	+	Intron	DEL	TCCG	-	-	rs143054986	by1000genomes	TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81533874_81533877delTCCG	uc002fgp.2	+						CMIP_uc002fgq.1_Intron	NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0						cttccttccttccgtccttccttc	0.137													4	3	---	---	---	---	
TTYH2	94015	broad.mit.edu	37	17	72218928	72218929	+	Intron	DEL	TT	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72218928_72218929delTT	uc002jkc.2	+						TTYH2_uc010wqw.1_Intron	NM_032646	NP_116035	Q9BSA4	TTYH2_HUMAN	tweety 2 isoform 1							chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4						ATGTTGTCCCTTTTTTTTTTTT	0.520													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	44353873	44353874	+	IGR	INS	-	AC	AC	rs5824637		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44353873_44353874insAC								ST8SIA5 (16834 upstream) : PIAS2 (38187 downstream)																							tctctctgtctacacacacaca	0.030													4	2	---	---	---	---	
GALR1	2587	broad.mit.edu	37	18	74964874	74964879	+	Intron	DEL	CACCAT	-	-	rs5826510		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74964874_74964879delCACCAT	uc002lms.3	+							NM_001480	NP_001471	P47211	GALR1_HUMAN	galanin receptor 1						digestion|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity			lung(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		ccaccaccaccaccatcaccaccacc	0.000													4	2	---	---	---	---	
JAK3	3718	broad.mit.edu	37	19	17950547	17950547	+	Intron	DEL	C	-	-	rs10685173		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17950547delC	uc002nhn.3	-						JAK3_uc010ebh.2_Intron|JAK3_uc002nho.2_Intron|JAK3_uc010xpx.1_Intron	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3						B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	56						CCttttttttctttttttttt	0.249		2	Mis		acute megakaryocytic leukemia|								4	2	---	---	---	---	
NLRP12	91662	broad.mit.edu	37	19	54304349	54304349	+	Intron	DEL	A	-	-	rs35326804		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54304349delA	uc002qch.3	-						NLRP12_uc010eqw.2_Intron|NLRP12_uc002qci.3_Intron|NLRP12_uc002qcj.3_Intron|NLRP12_uc002qck.3_Intron|NLRP12_uc010eqx.2_Intron	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform						negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		tgggagtctCAAAAAAAAAAA	0.244													5	4	---	---	---	---	
CCDC106	29903	broad.mit.edu	37	19	56163653	56163655	+	Intron	DEL	TGT	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56163653_56163655delTGT	uc002qlr.2	+						CCDC106_uc002qls.2_Intron|U2AF2_uc002qlt.2_5'Flank|U2AF2_uc002qlu.2_5'Flank	NM_013301	NP_037433	Q9BWC9	CC106_HUMAN	coiled-coil domain containing 106							nucleus					0		Colorectal(82;0.00403)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)		CTTCCTTGCCTGTTGTTCTCCGT	0.606													3	3	---	---	---	---	
FKBP1A	2280	broad.mit.edu	37	20	1332941	1332942	+	Intron	INS	-	T	T	rs35712372		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1332941_1332942insT	uc010gac.2	-						uc002wew.2_Intron|uc002wex.2_Intron			P62942	FKB1A_HUMAN	Homo sapiens FKBP12-Exip2 mRNA for FK506 binding protein12, complete cds.						'de novo' protein folding|beta-amyloid formation|fibril organization|heart trabecula formation|negative regulation of protein phosphatase type 2B activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of protein binding|positive regulation of protein ubiquitination|protein maturation by protein folding|protein refolding|regulation of activin receptor signaling pathway|regulation of immune response|regulation of ryanodine-sensitive calcium-release channel activity|SMAD protein complex assembly|T cell activation|ventricular cardiac muscle tissue morphogenesis	axon|cytosol|sarcoplasmic reticulum membrane|terminal cisterna	activin binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity|signal transducer activity|SMAD binding|type I transforming growth factor beta receptor binding				0					Pimecrolimus(DB00337)|Sirolimus(DB00877)|Tacrolimus(DB00864)	tccttccttccttccttccttc	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	21925407	21925408	+	IGR	DEL	TG	-	-	rs143652318		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21925407_21925408delTG								None (None upstream) : C21orf131 (189506 downstream)																							CATATGTTTAtgtgtgtgtgtg	0.282													4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37313520	37313521	+	Intron	INS	-	T	T	rs35309977		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37313520_37313521insT	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						gtgtgtgtgtggtgtgtgtgtg	0.257			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
ERG	2078	broad.mit.edu	37	21	39774635	39774636	+	Intron	DEL	AA	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39774635_39774636delAA	uc010gnw.2	-						ERG_uc002yxa.2_Intron|ERG_uc011aek.1_Intron|ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc011aem.1_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gny.1_Intron	NM_001136155	NP_001129627	P11308	ERG_HUMAN	ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)				CCTTTCTTACaaaaaaaaaaaa	0.312													5	3	---	---	---	---	
ABCG1	9619	broad.mit.edu	37	21	43663556	43663563	+	Intron	DEL	GCGTGTGT	-	-	rs691748		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43663556_43663563delGCGTGTGT	uc002zaq.2	+						ABCG1_uc002zan.2_Intron|ABCG1_uc002zam.2_Intron|ABCG1_uc002zao.2_Intron|ABCG1_uc002zap.2_Intron|ABCG1_uc002zar.2_Intron|ABCG1_uc011aev.1_Intron	NM_004915	NP_004906	P45844	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1						amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|recycling endosome	ADP binding|ATP binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)|central_nervous_system(1)	3					Adenosine triphosphate(DB00171)	gtgtgtgtgcgcgtgtgtgtgtgtgtgt	0.236													4	2	---	---	---	---	
MYH9	4627	broad.mit.edu	37	22	36744885	36744886	+	Intron	INS	-	G	G	rs113389460		TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36744885_36744886insG	uc003apg.2	-						MYH9_uc003api.1_Intron	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11						TGGGAAGACCCGCCCCCCCCCC	0.619			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				5	3	---	---	---	---	
SUN2	25777	broad.mit.edu	37	22	39138154	39138154	+	Intron	DEL	A	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39138154delA	uc003awh.1	-						SUN2_uc011anz.1_Intron|SUN2_uc011aoa.1_Intron|SUN2_uc003awi.1_Intron|SUN2_uc010gxq.1_Intron|SUN2_uc010gxr.1_Intron|SUN2_uc010gxs.1_Intron	NM_015374	NP_056189	Q9UH99	SUN2_HUMAN	unc-84 homolog B						centrosome localization|cytoskeletal anchoring at nuclear membrane|mitotic spindle organization|nuclear envelope organization|nuclear matrix anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	endosome membrane|integral to membrane|nuclear inner membrane|SUN-KASH complex	lamin binding|microtubule binding			large_intestine(1)|skin(1)	2						tctcaaaaagaaaaaaaaaaa	0.194													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	135917837	135917840	+	IGR	DEL	AGGA	-	-			TCGA-B0-5095-01A-01D-1421-08	TCGA-B0-5095-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135917837_135917840delAGGA								ARHGEF6 (54334 upstream) : RBMX (33513 downstream)																							ggagggagggaggaaggaaggaag	0.000													5	3	---	---	---	---	
