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
C1orf127	148345	broad.mit.edu	37	1	11008405	11008405	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11008405C>T	uc010oao.1	-	8	1345	c.1340G>A	c.(1339-1341)CGG>CAG	p.R447Q	C1orf127_uc001arr.1_Missense_Mutation_p.R429Q|C1orf127_uc001ars.1_Missense_Mutation_p.R421Q	NM_173507	NP_775778	B7ZLG7	B7ZLG7_HUMAN	hypothetical protein LOC148345	447										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CAGTGTGGCCCGCCAGGGCCT	0.657													4	74	---	---	---	---	PASS
HSPG2	3339	broad.mit.edu	37	1	22178652	22178652	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22178652C>T	uc001bfj.2	-	53	6839	c.6799G>A	c.(6799-6801)GTG>ATG	p.V2267M	HSPG2_uc009vqd.2_Missense_Mutation_p.V2268M	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	2267	Ig-like C2-type 8.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	CCTGCCACCACGCAGCTCAGA	0.657													21	34	---	---	---	---	PASS
FAM102B	284611	broad.mit.edu	37	1	109143253	109143253	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109143253C>A	uc010ouy.1	+	2	283	c.203C>A	c.(202-204)GCA>GAA	p.A68E		NM_001010883	NP_001010883	Q5T8I3	F102B_HUMAN	hypothetical protein LOC284611	68										large_intestine(1)	1		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)		AAAATGAGTGCAAGTGCTGCC	0.393													4	109	---	---	---	---	PASS
SLC6A17	388662	broad.mit.edu	37	1	110735220	110735220	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110735220A>C	uc009wfq.2	+	8	1660	c.1199A>C	c.(1198-1200)AAG>ACG	p.K400T	SLC6A17_uc001dze.1_5'UTR	NM_001010898	NP_001010898	Q9H1V8	S6A17_HUMAN	solute carrier family 6, member 17	400	Extracellular (Potential).				alanine transport|glycine transport|leucine transport|proline transport	cell junction|integral to plasma membrane|synaptic vesicle membrane	neurotransmitter:sodium symporter activity			ovary(1)|pancreas(1)	2		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		CTGACCACAAAGGACTACATG	0.552													3	78	---	---	---	---	PASS
RNF115	27246	broad.mit.edu	37	1	145684607	145684607	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145684607C>G	uc001eoj.2	+	7	800	c.596C>G	c.(595-597)ACA>AGA	p.T199R	NBPF10_uc001emp.3_Intron|RNF115_uc001eok.2_Missense_Mutation_p.T166R|RNF115_uc009wiy.2_Missense_Mutation_p.T118R	NM_014455	NP_055270	Q9Y4L5	RN115_HUMAN	Rabring 7	199					protein autoubiquitination	cytosol	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1						CTGGAAAACACAGGCCCTCCC	0.433													15	56	---	---	---	---	PASS
SPRR3	6707	broad.mit.edu	37	1	152975813	152975813	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152975813A>G	uc001fax.3	+	3	467	c.317A>G	c.(316-318)TAC>TGC	p.Y106C	SPRR3_uc001faz.3_Missense_Mutation_p.Y106C|SPRR3_uc001fay.2_Missense_Mutation_p.Y98C	NM_005416	NP_005407	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	106	8.|14 X 8 AA approximate tandem repeats.				keratinization|peptide cross-linking|wound healing	cytoplasm	protein binding|structural molecule activity			skin(1)	1	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAGCCAGGCTACACCAAGGTC	0.572													4	75	---	---	---	---	PASS
C1orf110	339512	broad.mit.edu	37	1	162824983	162824983	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162824983C>T	uc001gck.2	-	4	656	c.481G>A	c.(481-483)GAT>AAT	p.D161N	C1orf110_uc009wuw.1_Intron|C1orf110_uc009wux.1_Missense_Mutation_p.D160N	NM_178550	NP_848645	Q86UF4	CA110_HUMAN	hypothetical protein LOC339512	161											0						TTCACAGAATCTTTCTCTTGG	0.468													74	281	---	---	---	---	PASS
SMG7	9887	broad.mit.edu	37	1	183515189	183515189	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183515189A>T	uc001gqg.2	+	17	2581	c.2459A>T	c.(2458-2460)TAC>TTC	p.Y820F	SMG7_uc010pob.1_Missense_Mutation_p.Y803F|SMG7_uc001gqf.2_Missense_Mutation_p.Y774F|SMG7_uc001gqh.2_Missense_Mutation_p.Y774F|SMG7_uc001gqi.2_Missense_Mutation_p.Y732F|SMG7_uc010poc.1_Missense_Mutation_p.Y778F	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1	820	Gln/Pro-rich.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						AAACAGCCCTACTACCTTCAG	0.463													31	81	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235901759	235901759	+	Intron	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235901759C>T	uc001hxj.2	-						LYST_uc001hxi.2_5'Flank|LYST_uc009xga.1_3'UTR	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TAATGGCTTTCCCAAAAACCA	0.428									Chediak-Higashi_syndrome				5	60	---	---	---	---	PASS
OR2W5	441932	broad.mit.edu	37	1	247655186	247655186	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247655186C>T	uc001icz.1	+	1	757	c.757C>T	c.(757-759)CGG>TGG	p.R253W		NM_001004698	NP_001004698	A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W,	253					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|skin(1)	3	all_cancers(71;4.51e-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)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CTCTCTTCTACGGAACCATCA	0.542													5	158	---	---	---	---	PASS
UGT1A4	54657	broad.mit.edu	37	2	234627516	234627516	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234627516T>C	uc002vux.2	+	1	79	c.50T>C	c.(49-51)CTG>CCG	p.L17P	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Intron|UGT1A5_uc002vuw.2_Intron|UGT1A4_uc010zna.1_Missense_Mutation_p.L17P	NM_007120	NP_009051	P22310	UD14_HUMAN	UDP glycosyltransferase 1 family, polypeptide A4	17					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			skin(1)	1		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;3.49e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000504)|Lung(119;0.0026)|LUSC - Lung squamous cell carcinoma(224;0.00624)	Imipramine(DB00458)|Lamotrigine(DB00555)|Paricalcitol(DB00910)|Trifluoperazine(DB00831)	ACAGGACTGCTGCTCCTCCTC	0.657											OREG0003834	type=REGULATORY REGION|Gene=UGT1A4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	25	45	---	---	---	---	PASS
SLC25A20	788	broad.mit.edu	37	3	48929501	48929501	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48929501C>A	uc003cva.3	-	2	285	c.110G>T	c.(109-111)CGA>CTA	p.R37L	SLC25A20_uc011bbw.1_5'UTR|SLC25A20_uc010hkj.2_Missense_Mutation_p.R37L	NM_000387	NP_000378	O43772	MCAT_HUMAN	carnitine/acylcarnitine translocase	37	Solcar 1.|Mitochondrial matrix (Potential).				carnitine shuttle|cellular lipid metabolic process|regulation of fatty acid oxidation	integral to membrane|mitochondrial inner membrane	acyl carnitine transporter activity				0				BRCA - Breast invasive adenocarcinoma(193;0.000168)|Kidney(197;0.00231)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	L-Carnitine(DB00583)	TGTCTGCAGTCGGACCTGAAA	0.498													3	84	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52598158	52598158	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52598158G>T	uc003des.2	-	23	3795	c.3783C>A	c.(3781-3783)TAC>TAA	p.Y1261*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.Y1261*|PBRM1_uc003der.2_Nonsense_Mutation_p.Y1229*|PBRM1_uc003det.2_Nonsense_Mutation_p.Y1276*|PBRM1_uc003deu.2_Nonsense_Mutation_p.Y1276*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.Y1261*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.Y1236*|PBRM1_uc003dey.2_Nonsense_Mutation_p.Y1236*|PBRM1_uc003dez.1_Nonsense_Mutation_p.Y1260*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1261	BAH 2.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CGCTCTCATTGTAGCGGCTCT	0.418			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								45	47	---	---	---	---	PASS
APPL1	26060	broad.mit.edu	37	3	57283562	57283562	+	Silent	SNP	T	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57283562T>A	uc003dio.2	+	11	1185	c.1038T>A	c.(1036-1038)TCT>TCA	p.S346S	APPL1_uc010hnb.2_Silent_p.S346S|APPL1_uc011bey.1_Silent_p.S329S	NM_012096	NP_036228	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH	346	Required for RAB5A binding.|PH.				apoptosis|cell cycle|cell proliferation|insulin receptor signaling pathway|regulation of apoptosis|regulation of establishment of protein localization in plasma membrane|regulation of glucose import	cytosol|early endosome membrane|microsome|nucleus|vesicle membrane	protein kinase B binding			breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		AGATCACCTCTTTCGATGGAA	0.368													35	42	---	---	---	---	PASS
TOPBP1	11073	broad.mit.edu	37	3	133342007	133342007	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133342007C>T	uc003eps.2	-	19	3238	c.3106G>A	c.(3106-3108)GTA>ATA	p.V1036I	TOPBP1_uc003ept.1_Missense_Mutation_p.V40I	NM_007027	NP_008958	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1036					DNA repair|response to ionizing radiation	microtubule organizing center|PML body|spindle pole	DNA binding|protein C-terminus binding			ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1)	7						ATATTGTCTACATCATTTTCT	0.284								Other_conserved_DNA_damage_response_genes					11	17	---	---	---	---	PASS
DLG1	1739	broad.mit.edu	37	3	196842954	196842954	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196842954C>G	uc003fxo.3	-	14	1576	c.1386G>C	c.(1384-1386)AGG>AGC	p.R462S	DLG1_uc011bub.1_Missense_Mutation_p.R346S|DLG1_uc011buc.1_Missense_Mutation_p.R346S|DLG1_uc011bud.1_Missense_Mutation_p.R145S|DLG1_uc003fxn.3_Missense_Mutation_p.R462S|DLG1_uc011bue.1_Missense_Mutation_p.R429S|DLG1_uc010ial.2_Missense_Mutation_p.R462S|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_RNA|DLG1_uc010iam.1_Missense_Mutation_p.R429S|DLG1_uc010ian.2_Missense_Mutation_p.R329S	NM_001098424	NP_001091894	Q12959	DLG1_HUMAN	discs, large homolog 1 isoform 1	462					actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		TTCTAGGTTCCCTAAAAATTA	0.318													36	75	---	---	---	---	PASS
HPGD	3248	broad.mit.edu	37	4	175412964	175412964	+	3'UTR	SNP	A	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175412964A>T	uc003itu.2	-	7					HPGD_uc003itt.2_3'UTR|HPGD_uc003itv.2_3'UTR|HPGD_uc011ckf.1_3'UTR|HPGD_uc010irp.2_3'UTR|HPGD_uc010irq.2_3'UTR|HPGD_uc011ckg.1_3'UTR|HPGD_uc011ckh.1_3'UTR	NM_000860	NP_000851	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)						female pregnancy|lipoxygenase pathway|negative regulation of cell cycle|parturition|prostaglandin metabolic process|transforming growth factor beta receptor signaling pathway	cytosol|nucleus	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|NAD+ binding|prostaglandin E receptor activity|protein homodimerization activity				0		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)	NADH(DB00157)	CTTAACTAAAAATTTAGAAAA	0.274													7	11	---	---	---	---	PASS
ARSK	153642	broad.mit.edu	37	5	94918640	94918640	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94918640C>A	uc003kld.2	+	4	595	c.437C>A	c.(436-438)ACA>AAA	p.T146K	ARSK_uc010jbg.2_5'UTR|ARSK_uc011cum.1_RNA	NM_198150	NP_937793	Q6UWY0	ARSK_HUMAN	arylsulfatase K precursor	146						extracellular region	arylsulfatase activity|metal ion binding			pancreas(1)	1		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		GAAGCGTGGACAAGAGATGTT	0.388													79	169	---	---	---	---	PASS
PCDHB8	56128	broad.mit.edu	37	5	140558166	140558166	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140558166G>A	uc011dai.1	+	1	737	c.551G>A	c.(550-552)CGC>CAC	p.R184H	PCDHB16_uc003liv.2_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	184	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTCCTCACCCGCAAACGCAGT	0.483													4	146	---	---	---	---	PASS
DCTN4	51164	broad.mit.edu	37	5	150090663	150090663	+	3'UTR	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150090663G>A	uc003lsv.2	-	13					DCTN4_uc003lsu.2_3'UTR|DCTN4_uc010jhi.2_3'UTR	NM_016221	NP_057305	Q9UJW0	DCTN4_HUMAN	dynactin 4 (p62) isoform b							centrosome|nucleus	protein N-terminus binding			central_nervous_system(1)	1		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTTTAACGCAGGTTTACGGTG	0.473													8	23	---	---	---	---	PASS
CLINT1	9685	broad.mit.edu	37	5	157232985	157232985	+	Silent	SNP	G	C	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157232985G>C	uc003lxj.1	-	7	1021	c.831C>G	c.(829-831)CGC>CGG	p.R277R	CLINT1_uc003lxi.1_Silent_p.R259R|CLINT1_uc011ddv.1_Silent_p.R277R	NM_014666	NP_055481	Q14677	EPN4_HUMAN	epsin 4	277					endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GATTTGCTGTGCGCTTGTGTC	0.473													3	106	---	---	---	---	PASS
HLA-DPA1	3113	broad.mit.edu	37	6	33036365	33036365	+	Intron	SNP	T	C	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33036365T>C	uc003ocs.1	-						HLA-DPA1_uc010juk.2_3'UTR	NM_033554	NP_291032	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to plasma membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity			skin(1)	1						GAATTTTTCCTCCCTTCCTTA	0.408													14	37	---	---	---	---	PASS
UBR2	23304	broad.mit.edu	37	6	42604791	42604791	+	Silent	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42604791C>T	uc011dur.1	+	15	1717	c.1717C>T	c.(1717-1719)CTG>TTG	p.L573L	UBR2_uc011dus.1_Silent_p.L218L|UBR2_uc010jxv.1_Silent_p.L77L|UBR2_uc003osh.2_RNA	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	573					cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TCTCGCTGTACTGATGCAGTG	0.373													30	77	---	---	---	---	PASS
MYCT1	80177	broad.mit.edu	37	6	153043393	153043393	+	Intron	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153043393G>A	uc003qpd.3	+						MYCT1_uc010kjc.1_3'UTR|MYCT1_uc003qpc.3_3'UTR	NM_025107	NP_079383	Q8N699	MYCT1_HUMAN	myc target 1							nucleus				ovary(1)	1		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		TCCTGAGTAGGGTGGCTTTTG	0.443													33	35	---	---	---	---	PASS
MPP6	51678	broad.mit.edu	37	7	24720095	24720095	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24720095C>T	uc003swx.2	+	12	1701	c.1402C>T	c.(1402-1404)CAC>TAC	p.H468Y	MPP6_uc003swy.2_Missense_Mutation_p.H468Y|MPP6_uc010kur.2_Missense_Mutation_p.H136Y	NM_016447	NP_057531	Q9NZW5	MPP6_HUMAN	membrane protein, palmitoylated 6	468	Guanylate kinase-like.				protein complex assembly		protein binding				0						ACGTGCCATGCACAAGGCTGT	0.433													44	98	---	---	---	---	PASS
CDK13	8621	broad.mit.edu	37	7	39991366	39991366	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39991366T>C	uc003thh.3	+	1	1408	c.1126T>C	c.(1126-1128)TAC>CAC	p.Y376H	CDK13_uc003thi.3_Missense_Mutation_p.Y376H	NM_003718	NP_003709	Q14004	CDK13_HUMAN	cell division cycle 2-like 5 isoform 1	376					alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5						CCACAGCTCCTACGAGCGGGG	0.706													18	35	---	---	---	---	PASS
SRRT	51593	broad.mit.edu	37	7	100485932	100485932	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100485932C>A	uc003uwy.2	+	20	2751	c.2483C>A	c.(2482-2484)CCG>CAG	p.P828Q	SRRT_uc010lhl.1_Missense_Mutation_p.P827Q|SRRT_uc003uxa.2_Missense_Mutation_p.P823Q|SRRT_uc003uwz.2_Missense_Mutation_p.P824Q|uc010lhm.1_5'Flank	NM_015908	NP_056992	Q9BXP5	SRRT_HUMAN	arsenate resistance protein 2 isoform a	828	Pro-rich.				cell proliferation|primary miRNA processing|response to arsenic-containing substance	cytoplasm|nucleoplasm	protein binding			ovary(2)	2						CCCCATGCCCCGTATGGTGCT	0.572													3	62	---	---	---	---	PASS
LAMB4	22798	broad.mit.edu	37	7	107706245	107706245	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107706245C>G	uc010ljo.1	-	21	2882	c.2798G>C	c.(2797-2799)AGC>ACC	p.S933T	LAMB4_uc003vey.2_Missense_Mutation_p.S933T|LAMB4_uc010ljp.1_5'Flank	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	933	Laminin EGF-like 9.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						TACATCTGAGCTCCACAGATT	0.423													5	138	---	---	---	---	PASS
HTR5A	3361	broad.mit.edu	37	7	154863136	154863136	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154863136C>A	uc003wlu.1	+	1	591	c.527C>A	c.(526-528)CCG>CAG	p.P176Q	uc011kvt.1_5'UTR|uc003wlt.2_5'UTR	NM_024012	NP_076917	P47898	5HT5A_HUMAN	5-hydroxytryptamine receptor 5A	176	Helical; Name=4; (By similarity).					integral to plasma membrane	serotonin receptor activity			ovary(2)|large_intestine(1)	3	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)		TCTCTGGCCCCGCTGCTTTTT	0.627													3	42	---	---	---	---	PASS
EBF2	64641	broad.mit.edu	37	8	25899690	25899690	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25899690A>G	uc003xes.1	-	2	226	c.209T>C	c.(208-210)GTC>GCC	p.V70A	PPP2R2A_uc003xek.2_Intron|EBF2_uc003xet.1_Missense_Mutation_p.V70A	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2	70					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		GAGCGCCAGGACGAAGTGAAA	0.582													37	72	---	---	---	---	PASS
ZNF395	55893	broad.mit.edu	37	8	28206286	28206286	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28206286A>G	uc003xgq.2	-	10	1580	c.1492T>C	c.(1492-1494)TGG>CGG	p.W498R	ZNF395_uc003xgt.2_Missense_Mutation_p.W498R|ZNF395_uc003xgr.2_Missense_Mutation_p.W498R|ZNF395_uc003xgs.2_Missense_Mutation_p.W498R	NM_018660	NP_061130	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	498					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		GCCGTGCACCACTGGTCCCGG	0.617													23	74	---	---	---	---	PASS
HMBOX1	79618	broad.mit.edu	37	8	28906483	28906483	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28906483T>A	uc003xhd.3	+	9	1385	c.1043T>A	c.(1042-1044)CTG>CAG	p.L348Q	HMBOX1_uc010lvd.2_Missense_Mutation_p.L348Q|HMBOX1_uc003xhc.3_Missense_Mutation_p.L347Q|HMBOX1_uc010lve.2_RNA|HMBOX1_uc003xhe.2_Missense_Mutation_p.L348Q|HMBOX1_uc011lay.1_Missense_Mutation_p.L347Q|HMBOX1_uc003xhf.2_Missense_Mutation_p.L334Q|HMBOX1_uc003xhg.2_Missense_Mutation_p.L335Q	NM_001135726	NP_001129198	Q6NT76	HMBX1_HUMAN	homeobox containing 1	348					negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)		GCAGCAATCCTGGAGAGTCAT	0.448													80	167	---	---	---	---	PASS
GPR124	25960	broad.mit.edu	37	8	37696506	37696506	+	Silent	SNP	C	T	T	rs147055217	byFrequency	TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37696506C>T	uc003xkj.2	+	15	2655	c.2292C>T	c.(2290-2292)GGC>GGT	p.G764G	GPR124_uc010lvy.2_Silent_p.G547G	NM_032777	NP_116166	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124 precursor	764	Extracellular (Potential).				central nervous system development|endothelial cell migration|neuropeptide signaling pathway|regulation of angiogenesis|regulation of chemotaxis|sprouting angiogenesis	integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(2)|ovary(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			AGGTGGGGGGCGCCGGGGCAG	0.662													18	33	---	---	---	---	PASS
KIAA0146	23514	broad.mit.edu	37	8	48353095	48353095	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48353095T>A	uc003xqd.2	+	8	1097	c.1088T>A	c.(1087-1089)TTC>TAC	p.F363Y	KIAA0146_uc011lcz.1_RNA|KIAA0146_uc011lda.1_Missense_Mutation_p.F52Y|KIAA0146_uc011ldb.1_Missense_Mutation_p.F363Y|KIAA0146_uc010lxs.2_5'UTR|KIAA0146_uc011ldc.1_Missense_Mutation_p.F293Y|KIAA0146_uc011ldd.1_Missense_Mutation_p.F303Y|KIAA0146_uc003xqe.2_5'UTR|KIAA0146_uc003xqf.2_RNA|KIAA0146_uc011lde.1_Missense_Mutation_p.F52Y|KIAA0146_uc010lxt.2_Missense_Mutation_p.F52Y	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514	363											0		Lung NSC(58;0.175)				GTCCGGATCTTCCCTCCCTGG	0.517													20	44	---	---	---	---	PASS
OTUD6B	51633	broad.mit.edu	37	8	92082471	92082471	+	5'UTR	SNP	T	C	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92082471T>C	uc003yeu.3	+	1					uc003yet.2_5'Flank|OTUD6B_uc011lgh.1_5'UTR	NM_016023	NP_057107	Q8N6M0	OTU6B_HUMAN	OTU domain containing 6B											ovary(2)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(11;0.0187)			GCAGTGGCTTTGCTTAGATCC	0.652													12	8	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110523161	110523161	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110523161A>G	uc003yne.2	+	71	11655	c.11551A>G	c.(11551-11553)AAG>GAG	p.K3851E		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	3851	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TGATCATAACAAGGTAGGGCA	0.398										HNSCC(38;0.096)			3	145	---	---	---	---	PASS
ENPP2	5168	broad.mit.edu	37	8	120651072	120651072	+	5'UTR	SNP	A	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120651072A>G	uc003yot.1	-	1					ENPP2_uc003yos.1_5'UTR|ENPP2_uc010mdd.1_5'UTR	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	autotaxin isoform 2 preproprotein						cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GCCTTCACGGAGTGCACTGCT	0.502													31	43	---	---	---	---	PASS
TAF1L	138474	broad.mit.edu	37	9	32632433	32632433	+	Missense_Mutation	SNP	G	A	A	rs141135220		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32632433G>A	uc003zrg.1	-	1	3235	c.3145C>T	c.(3145-3147)CGC>TGC	p.R1049C	uc003zrh.1_5'Flank	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1049					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GACATTGTGCGCACCACATCA	0.473													12	290	---	---	---	---	PASS
C9orf125	84302	broad.mit.edu	37	9	104238212	104238212	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104238212A>C	uc004bbm.2	-	2	1485	c.1163T>G	c.(1162-1164)ATC>AGC	p.I388S	uc004bbl.1_5'Flank	NM_032342	NP_115718	Q9BRR3	CI125_HUMAN	hypothetical protein LOC84302	388						integral to membrane					0		Acute lymphoblastic leukemia(62;0.0527)				GAAGAGCCCGATGTGTTTCAC	0.522													19	67	---	---	---	---	PASS
FAM73B	84895	broad.mit.edu	37	9	131832058	131832058	+	Intron	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131832058C>T	uc004bxa.2	+						FAM73B_uc004bwy.2_Intron|FAM73B_uc004bwz.2_Intron|FAM73B_uc004bxb.2_Silent_p.C39C	NM_032809	NP_116198	Q7L4E1	FA73B_HUMAN	hypothetical protein LOC84895							integral to membrane				skin(1)	1						gccctttatgcgacacctggg	0.249													10	21	---	---	---	---	PASS
PPAPDC3	84814	broad.mit.edu	37	9	134165749	134165749	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134165749G>A	uc004cal.2	+	1	669	c.365G>A	c.(364-366)GGC>GAC	p.G122D		NM_032728	NP_116117	Q8NBV4	PPAC3_HUMAN	phosphatidic acid phosphatase type 2 domain	122	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	hydrolase activity			breast(1)	1	all_hematologic(7;0.0119)			OV - Ovarian serous cystadenocarcinoma(145;1.22e-05)|Epithelial(140;0.000173)		ACGGGCCACGGCATCCCCTGG	0.657													4	142	---	---	---	---	PASS
ZEB1	6935	broad.mit.edu	37	10	31815882	31815882	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31815882C>A	uc001ivs.3	+	9	3128	c.3065C>A	c.(3064-3066)TCG>TAG	p.S1022*	ZEB1_uc001ivr.3_Nonsense_Mutation_p.S804*|ZEB1_uc010qee.1_Nonsense_Mutation_p.S804*|ZEB1_uc010qef.1_Nonsense_Mutation_p.S804*|ZEB1_uc001ivt.3_Nonsense_Mutation_p.S804*|ZEB1_uc001ivu.3_Nonsense_Mutation_p.S1023*|ZEB1_uc001ivv.3_Nonsense_Mutation_p.S1002*|ZEB1_uc010qeh.1_Nonsense_Mutation_p.S955*|ZEB1_uc009xlp.2_Nonsense_Mutation_p.S1006*	NM_030751	NP_110378	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b	1022	Glu-rich (acidic).				cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)				CAGGGCGACTCGGACGAGAGA	0.413													3	54	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	48968566	48968566	+	RNA	SNP	A	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48968566A>G	uc001jgc.1	+	3		c.1234A>G								full-length cDNA clone CS0DI009YC01 of Placenta Cot 25-normalized of Homo sapiens (human).																		ACAGGATAACAAACTGGAAAA	0.284													4	38	---	---	---	---	PASS
PRKG1	5592	broad.mit.edu	37	10	53921672	53921672	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53921672G>A	uc001jjm.2	+	9	1174	c.980G>A	c.(979-981)GGG>GAG	p.G327E	PRKG1_uc001jjo.2_Missense_Mutation_p.G342E|PRKG1_uc009xow.1_Missense_Mutation_p.G45E	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform	327	cGMP 2.				actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTGATTGGAGGGCTGGATGAT	0.328													14	32	---	---	---	---	PASS
SORCS3	22986	broad.mit.edu	37	10	107015522	107015522	+	Silent	SNP	G	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107015522G>T	uc001kyi.1	+	24	3527	c.3300G>T	c.(3298-3300)GGG>GGT	p.G1100G		NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	1100	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity	p.G1100R(1)		ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TGAAGCCGGGGGTACAAGTCA	0.453													19	44	---	---	---	---	PASS
APBB1	322	broad.mit.edu	37	11	6422859	6422859	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6422859C>A	uc001mdb.1	-	9	1548	c.1448G>T	c.(1447-1449)CGC>CTC	p.R483L	APBB1_uc001mcz.1_Missense_Mutation_p.R102L|APBB1_uc001mdd.3_Missense_Mutation_p.R261L|APBB1_uc001mda.2_Missense_Mutation_p.R8L|APBB1_uc001mdc.1_Missense_Mutation_p.R481L|APBB1_uc010rab.1_Missense_Mutation_p.R8L|APBB1_uc010rac.1_RNA|APBB1_uc010rad.1_Missense_Mutation_p.R200L	NM_001164	NP_001155	O00213	APBB1_HUMAN	amyloid beta A4 precursor protein-binding,	483	PID 1.				apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		TGCCTCACAGCGAAACACGTG	0.577													3	70	---	---	---	---	PASS
NDUFS3	4722	broad.mit.edu	37	11	47602127	47602127	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47602127G>T	uc001nga.2	+	3	266	c.184G>T	c.(184-186)GGA>TGA	p.G62*	NDUFS3_uc001nft.3_5'UTR|KBTBD4_uc001nfw.1_5'Flank|KBTBD4_uc001nfx.2_5'Flank|KBTBD4_uc001nfz.2_5'Flank|KBTBD4_uc001nfy.2_5'Flank|NDUFS3_uc010rhn.1_Nonsense_Mutation_p.G62*	NM_004551	NP_004542	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3	62					induction of apoptosis|mitochondrial electron transport, NADH to ubiquinone|negative regulation of cell growth|reactive oxygen species metabolic process|transport	mitochondrial respiratory chain complex I	electron carrier activity|NADH dehydrogenase (ubiquinone) activity|protein binding				0					NADH(DB00157)	CTCAGCTTTTGGAGAGTATGT	0.438													16	58	---	---	---	---	PASS
EEF1G	1937	broad.mit.edu	37	11	62339115	62339115	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62339115G>A	uc001ntm.1	-	4	421	c.275C>T	c.(274-276)GCA>GTA	p.A92V	EEF1G_uc010rlw.1_Missense_Mutation_p.A142V|EEF1G_uc001ntn.1_5'UTR	NM_001404	NP_001395	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1	92	GST C-terminal.				response to virus	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|translation elongation factor activity				0						CACCTGGGCTGCTGCCTCTGG	0.577													3	10	---	---	---	---	PASS
RTN3	10313	broad.mit.edu	37	11	63517659	63517659	+	Silent	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63517659C>A	uc001nxq.2	+	4	2914	c.2727C>A	c.(2725-2727)GGC>GGA	p.G909G	RTN3_uc001nxo.2_Silent_p.G113G|RTN3_uc001nxm.2_Silent_p.G132G|RTN3_uc001nxn.2_Silent_p.G890G|RTN3_uc001nxp.2_Silent_p.G113G|RTN3_uc009yov.2_Silent_p.G797G|RTN3_uc010rmt.1_RNA|RTN3_uc010rmu.1_Silent_p.G113G	NM_201428	NP_958831	O95197	RTN3_HUMAN	reticulon 3 isoform b	909	Reticulon.				apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1						CAGAAGAAGGCCATCCATTCA	0.428													3	31	---	---	---	---	PASS
OR6M1	390261	broad.mit.edu	37	11	123676529	123676529	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123676529C>T	uc010rzz.1	-	1	529	c.529G>A	c.(529-531)GAC>AAC	p.D177N		NM_001005325	NP_001005325	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M,	177	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		GGGGCAATGTCACAGAAGAAA	0.458													4	60	---	---	---	---	PASS
RIMKLB	57494	broad.mit.edu	37	12	8906537	8906537	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8906537A>G	uc001quu.2	+	5	796	c.545A>G	c.(544-546)CAT>CGT	p.H182R	RIMKLB_uc009zgf.1_RNA|RIMKLB_uc001qux.2_Missense_Mutation_p.H182R|RIMKLB_uc010sgl.1_Missense_Mutation_p.H182R|RIMKLB_uc001quw.2_Missense_Mutation_p.H182R	NM_020734	NP_065785	Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family	182	ATP-grasp.|ATP (By similarity).				protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0						GATCTAAGCCATCTTATTCGC	0.438													29	56	---	---	---	---	PASS
BRCA2	675	broad.mit.edu	37	13	32945126	32945126	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32945126T>A	uc001uub.1	+	20	8748	c.8521T>A	c.(8521-8523)TTT>ATT	p.F2841I		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	2841					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		ATTATACATATTTCGCAATGA	0.338			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			38	58	---	---	---	---	PASS
UPF3A	65110	broad.mit.edu	37	13	115057088	115057088	+	Intron	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115057088C>A	uc001vup.2	+						UPF3A_uc001vuq.2_Intron|UPF3A_uc001vus.2_Intron|UPF3A_uc001vur.2_Intron|UPF3A_uc001vut.2_Intron|UPF3A_uc001vuu.2_5'UTR	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A						mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		AGTTTATACACACGCTCTTCC	0.254													27	94	---	---	---	---	PASS
C14orf4	64207	broad.mit.edu	37	14	77492045	77492045	+	Silent	SNP	C	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77492045C>G	uc001xsy.2	-	1	2990	c.2091G>C	c.(2089-2091)GTG>GTC	p.V697V		NM_024496	NP_078772	Q9H1B7	I2BPL_HUMAN	chromosome 14 open reading frame 4	697						nucleus					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.00347)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)		TTTGGGGGTGCACTTGGTCCA	0.637													8	27	---	---	---	---	PASS
WDR93	56964	broad.mit.edu	37	15	90276249	90276249	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90276249G>T	uc002boj.2	+	13	1444	c.1343G>T	c.(1342-1344)GGG>GTG	p.G448V	WDR93_uc010bnr.2_Intron|WDR93_uc010upz.1_Missense_Mutation_p.G165V	NM_020212	NP_064597	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	448	WD.				electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TTCCCTCTTGGGGTCGCTGCT	0.507													58	147	---	---	---	---	PASS
ITGAX	3687	broad.mit.edu	37	16	31373943	31373943	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31373943G>A	uc002ebu.1	+	12	1295	c.1228G>A	c.(1228-1230)GAG>AAG	p.E410K	ITGAX_uc002ebt.2_Missense_Mutation_p.E410K|ITGAX_uc010vfk.1_Missense_Mutation_p.E60K	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	410	FG-GAP 4.|Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TTACTCCACCGAGCTGGCCCT	0.677													8	13	---	---	---	---	PASS
IRX5	10265	broad.mit.edu	37	16	54967655	54967655	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54967655G>T	uc002ehv.2	+	3	1322	c.1322G>T	c.(1321-1323)GGA>GTA	p.G441V	IRX5_uc002ehw.2_Missense_Mutation_p.G375V	NM_005853	NP_005844	P78411	IRX5_HUMAN	iroquois homeobox protein 5	441					response to stimulus|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|vitamin D binding				0						CATTTCAATGGATTAAACCAG	0.572													29	68	---	---	---	---	PASS
RNF213	57674	broad.mit.edu	37	17	78328249	78328249	+	Silent	SNP	T	C	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78328249T>C	uc002jyh.1	+	11	5177	c.4954T>C	c.(4954-4956)TTG>CTG	p.L1652L	uc002jyi.1_RNA|RNF213_uc010dhw.1_Silent_p.L34L	NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AGCCTCTTTCTTGCGGGTATC	0.547													32	81	---	---	---	---	PASS
TUBB6	84617	broad.mit.edu	37	18	12324969	12324969	+	Intron	SNP	A	C	C			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12324969A>C	uc002kqw.2	+						TUBB6_uc002kqv.2_Intron|TUBB6_uc010dld.2_RNA|TUBB6_uc002kqx.2_Intron|TUBB6_uc002kqy.2_Intron	NM_032525	NP_115914	Q9BUF5	TBB6_HUMAN	tubulin, beta 6						'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0				READ - Rectum adenocarcinoma(1;0.0649)		CTAACAGCACATCATGGAATC	0.547													6	24	---	---	---	---	PASS
HMSD	284293	broad.mit.edu	37	18	61627535	61627535	+	Silent	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61627535C>T	uc010dqj.2	+	4	515	c.366C>T	c.(364-366)TTC>TTT	p.F122F	SERPINB8_uc002ljs.1_Intron	NM_001123366	NP_001116838	A8MTL9	HMSD_HUMAN	histocompatibility (minor) serpin domain	122						extracellular region	serine-type endopeptidase inhibitor activity				0						TATTCTATTTCGATAATATTT	0.299													5	22	---	---	---	---	PASS
SALL3	27164	broad.mit.edu	37	18	76752286	76752286	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76752286C>A	uc002lmt.2	+	2	295	c.295C>A	c.(295-297)CCC>ACC	p.P99T	SALL3_uc010dra.2_5'Flank	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	99					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CGAGCCTTCGCCCGCCAGCTC	0.761													5	5	---	---	---	---	PASS
DOT1L	84444	broad.mit.edu	37	19	2199918	2199918	+	Silent	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2199918G>A	uc002lvb.3	+	8	723	c.687G>A	c.(685-687)AGG>AGA	p.R229R		NM_032482	NP_115871	Q8TEK3	DOT1L_HUMAN	DOT1-like, histone H3 methyltransferase	229						nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGAGTGGAGGGAGCGAATCG	0.672													4	56	---	---	---	---	PASS
ZNF181	339318	broad.mit.edu	37	19	35232767	35232767	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35232767G>A	uc002nvu.3	+	4	1944	c.1481G>A	c.(1480-1482)TGT>TAT	p.C494Y	ZNF181_uc010xsa.1_Missense_Mutation_p.C493Y|ZNF181_uc010xsb.1_Missense_Mutation_p.C493Y|ZNF181_uc010xsc.1_Missense_Mutation_p.C429Y	NM_001029997	NP_001025168	Q2M3W8	ZN181_HUMAN	zinc finger protein 181 isoform 1	494	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TGTATTAAATGTGGGAAGACC	0.393													23	38	---	---	---	---	PASS
FBL	2091	broad.mit.edu	37	19	40330954	40330954	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40330954A>T	uc002omn.2	-	4	411	c.297T>A	c.(295-297)TGT>TGA	p.C99*	FBL_uc002omm.1_Nonsense_Mutation_p.C13*|FBL_uc002omo.2_Nonsense_Mutation_p.C98*|FBL_uc010egr.2_Nonsense_Mutation_p.C99*	NM_001436	NP_001427	P22087	FBRL_HUMAN	fibrillarin	99					rRNA processing|tRNA processing	box C/D snoRNP complex|Cajal body	methyltransferase activity|protein binding|RNA binding			ovary(1)	1	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		CCTTTCCTCGACAAATGAAGA	0.587													36	49	---	---	---	---	PASS
ZNF155	7711	broad.mit.edu	37	19	44501505	44501505	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44501505G>A	uc002oxy.1	+	5	1701	c.1496G>A	c.(1495-1497)CGT>CAT	p.R499H	ZNF155_uc002oxz.1_Missense_Mutation_p.R499H|ZNF155_uc010xwt.1_Missense_Mutation_p.R510H|uc010ejc.1_RNA	NM_003445	NP_003436	Q12901	ZN155_HUMAN	zinc finger protein 155	499	C2H2-type 12; degenerate.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)	2		Prostate(69;0.0352)				AGGACATACCGTAAAGACCAG	0.453													4	124	---	---	---	---	PASS
FAM71E1	112703	broad.mit.edu	37	19	50979507	50979507	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50979507G>A	uc002psh.2	-	1	497	c.139C>T	c.(139-141)CGC>TGC	p.R47C	FAM71E1_uc002psg.2_Missense_Mutation_p.R47C|FAM71E1_uc002psi.2_RNA|C19orf63_uc002psj.2_5'Flank|C19orf63_uc002psk.2_5'Flank|C19orf63_uc002psl.2_5'Flank	NM_138411	NP_612420	Q6IPT2	F71E1_HUMAN	hypothetical protein LOC112703	47										breast(1)	1		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.0077)|GBM - Glioblastoma multiforme(134;0.026)		GGGAGAAAGCGAGGGGGCGGG	0.652													15	46	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29628263	29628263	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29628263A>G	uc010ztl.1	+	3	207	c.175A>G	c.(175-177)ATT>GTT	p.I59V	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Missense_Mutation_p.I11V					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						TAGCTGCTTTATTAGATGCAA	0.363													11	206	---	---	---	---	PASS
PHF20	51230	broad.mit.edu	37	20	34457385	34457385	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34457385G>T	uc002xek.1	+	7	945	c.834G>T	c.(832-834)TTG>TTT	p.L278F	PHF20_uc002xei.1_Missense_Mutation_p.L278F|PHF20_uc010gfo.1_Missense_Mutation_p.L278F|PHF20_uc002xej.1_Missense_Mutation_p.L162F|PHF20_uc002xel.1_Missense_Mutation_p.L140F	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	278					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)					CTCAAACTTTGCAACCAATAA	0.318													26	59	---	---	---	---	PASS
SALL4	57167	broad.mit.edu	37	20	50407915	50407915	+	Silent	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50407915C>A	uc002xwh.3	-	2	1208	c.1107G>T	c.(1105-1107)GTG>GTT	p.V369V	SALL4_uc010gii.2_Silent_p.V369V|SALL4_uc002xwi.3_Intron	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4	369					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						GTTTGACATCCACCGCGGAGA	0.567													32	64	---	---	---	---	PASS
SON	6651	broad.mit.edu	37	21	34922737	34922737	+	Silent	SNP	T	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34922737T>A	uc002yse.1	+	3	1249	c.1200T>A	c.(1198-1200)ACT>ACA	p.T400T	SON_uc002ysb.1_Silent_p.T400T|SON_uc002ysc.2_Silent_p.T400T|SON_uc002ysd.2_5'UTR|SON_uc002ysf.1_Intron|SON_uc002ysg.2_5'Flank	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	400					anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6						CCCCTGTGACTCCAGTGCTGG	0.677													31	58	---	---	---	---	PASS
PCNT	5116	broad.mit.edu	37	21	47841988	47841988	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47841988C>T	uc002zji.3	+	32	7236	c.7129C>T	c.(7129-7131)CCG>TCG	p.P2377S	PCNT_uc002zjj.2_Missense_Mutation_p.P2259S	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	2377					cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					AAGGTTTCAGCCGCTGCCGGA	0.627													4	88	---	---	---	---	PASS
PNPLA3	80339	broad.mit.edu	37	22	44322959	44322959	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44322959C>A	uc003bei.1	+	2	505	c.332C>A	c.(331-333)TCC>TAC	p.S111Y	PNPLA3_uc010gzm.1_RNA	NM_025225	NP_079501	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	111	Lumenal (Potential).|Patatin.				triglyceride biosynthetic process|triglyceride catabolic process	integral to membrane	diolein transacylation activity|mono-olein transacylation activity|phospholipase A2 activity|triglyceride lipase activity				0		Ovarian(80;0.024)|all_neural(38;0.0416)				CAGCTCATCTCCGGCAAAATA	0.502													18	42	---	---	---	---	PASS
FBLN1	2192	broad.mit.edu	37	22	45931087	45931087	+	Silent	SNP	C	T	T	rs144704783		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45931087C>T	uc003bgj.1	+	8	939	c.792C>T	c.(790-792)GAC>GAT	p.D264D	FBLN1_uc003bgg.1_Silent_p.D264D|FBLN1_uc003bgh.2_Silent_p.D264D|FBLN1_uc010gzz.2_Silent_p.D302D|FBLN1_uc003bgi.1_Silent_p.D264D	NM_006486	NP_006477	P23142	FBLN1_HUMAN	fibulin 1 isoform D	264	EGF-like 3; calcium-binding (Potential).				interspecies interaction between organisms	extracellular space|soluble fraction	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CAGATATTGACGAGTGTGAGA	0.418													36	107	---	---	---	---	PASS
CXorf38	159013	broad.mit.edu	37	X	40506319	40506319	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40506319A>T	uc004dew.2	-	2	296	c.291T>A	c.(289-291)GAT>GAA	p.D97E	CXorf38_uc011mko.1_Intron|CXorf38_uc004dev.1_5'UTR|CXorf38_uc010nhd.2_RNA	NM_144970	NP_659407	Q8TB03	CX038_HUMAN	hypothetical protein LOC159013	97										ovary(1)	1						CCCAGTGCACATCTCCATTTC	0.632													29	38	---	---	---	---	PASS
UPRT	139596	broad.mit.edu	37	X	74517350	74517350	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74517350T>A	uc004ecb.1	+	4	653	c.524T>A	c.(523-525)TTT>TAT	p.F175Y	UPRT_uc010nlu.1_Missense_Mutation_p.F175Y|UPRT_uc004ecc.1_RNA|UPRT_uc004ecd.1_Missense_Mutation_p.F175Y|UPRT_uc004ece.1_Missense_Mutation_p.F39Y	NM_145052	NP_659489	Q96BW1	UPP_HUMAN	uracil phosphoribosyltransferase (FUR1) homolog	175					nucleoside metabolic process	cytoplasm|nucleus					0						GGAGTGAAATTTGAGAAGGGA	0.368													48	111	---	---	---	---	PASS
ZMAT1	84460	broad.mit.edu	37	X	101153103	101153103	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101153103C>A	uc011mrl.1	-	4	630	c.319G>T	c.(319-321)GAG>TAG	p.E107*	ZMAT1_uc004ein.2_5'UTR|ZMAT1_uc011mrm.1_5'UTR	NM_001011657	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin type 1 isoform 1	Error:Variant_position_missing_in_A7MD47_after_alignment						nucleus	zinc ion binding			ovary(1)	1						TGAAAATTCTCAACATGCATC	0.343													4	102	---	---	---	---	PASS
SPOCD1	90853	broad.mit.edu	37	1	32258806	32258807	+	Intron	DEL	AG	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32258806_32258807delAG	uc001bts.1	-						SPOCD1_uc001btr.1_5'Flank|SPOCD1_uc001btt.2_Intron|SPOCD1_uc001btu.2_Intron|SPOCD1_uc001btv.2_Intron	NM_144569	NP_653170	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1						transcription, DNA-dependent					ovary(5)|breast(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		catgagtGAAAGAGAGAGAGAG	0.376													4	2	---	---	---	---	
USP24	23358	broad.mit.edu	37	1	55545465	55545466	+	Intron	DEL	CT	-	-	rs72019614		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55545465_55545466delCT	uc001cyg.3	-							NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						TACTCACACACTGAGTACTCAC	0.312													5	4	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120612003	120612004	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120612003_120612004delGG	uc001eik.2	-	1	273_274	c.17_18delCC	c.(16-18)CCCfs	p.P6fs	NOTCH2_uc001eil.2_Frame_Shift_Del_p.P6fs|NOTCH2_uc001eim.3_5'UTR	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	6					anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAGCAGAGCGGGGCGCAGGGC	0.663			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				15	8	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148349431	148349432	+	5'Flank	INS	-	G	G	rs67020224		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148349431_148349432insG	uc001eqf.2	-						LOC200030_uc001eqe.2_5'Flank|LOC200030_uc001eqg.2_5'Flank|NBPF14_uc009wkf.1_5'Flank|uc001erd.3_5'Flank|uc001erc.3_5'Flank|uc010paj.1_5'Flank|uc010pav.1_5'Flank|uc010paw.1_5'Flank	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						GGGCTGACACTGGGGGGCCAGA	0.559													5	3	---	---	---	---	
GATAD2B	57459	broad.mit.edu	37	1	153790790	153790790	+	Intron	DEL	C	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153790790delC	uc001fdb.3	-							NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TCAAGGttttctttttttttt	0.189													4	2	---	---	---	---	
CEP170	9859	broad.mit.edu	37	1	243332885	243332886	+	Intron	DEL	AG	-	-	rs140816120		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243332885_243332886delAG	uc001hzs.2	-						CEP170_uc001hzt.2_Intron|CEP170_uc001hzu.2_Intron	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha							centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			aaatggagaaagagaagaaaaa	0.218													2	5	---	---	---	---	
IL1RL2	8808	broad.mit.edu	37	2	102804538	102804539	+	Intron	INS	-	ACC	ACC	rs144678772	by1000genomes	TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102804538_102804539insACC	uc002tbs.2	+						IL1RL2_uc002tbt.2_Intron	NM_003854	NP_003845	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2 precursor						cellular defense response|innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity			ovary(2)	2						GGAAACAGAGAACCAGCTCCAC	0.624													5	5	---	---	---	---	
PASK	23178	broad.mit.edu	37	2	242063236	242063236	+	Intron	DEL	A	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242063236delA	uc002wao.1	-						PASK_uc010zol.1_Intron|PASK_uc010zom.1_Intron|PASK_uc010fzl.1_Intron|PASK_uc010zon.1_Intron|PASK_uc002wap.2_Intron|PASK_uc002waq.2_Intron	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase						regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		tccgtcccagaaaaaaaaaaa	0.204													4	2	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191499	10191499	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191499delG	uc003bvc.2	+	3	705	c.492delG	c.(490-492)CAGfs	p.Q164fs	VHL_uc003bvd.2_Frame_Shift_Del_p.Q123fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	164	Interaction with Elongin BC complex.		Q -> R (in VHLD; type II).|Q -> H (in VHLD).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.Q164*(4)|p.Q164P(3)|p.Q164H(3)|p.Q164fs*9(1)|p.Q164R(1)|p.V165fs*5(1)|p.Q164fs*10(1)|p.Q164L(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GATGCCTCCAGGTTGTCCGGA	0.507		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				25	12	---	---	---	---	
OSBPL10	114884	broad.mit.edu	37	3	32022334	32022335	+	Intron	DEL	CA	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32022334_32022335delCA	uc003cev.2	-						OSBPL10_uc011axf.1_Intron|ZNF860_uc011axg.1_5'Flank	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10						lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)		cacacgcacgcacacacacaca	0.485													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	103257919	103257924	+	IGR	DEL	CTTTTC	-	-	rs142663963	by1000genomes	TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103257919_103257924delCTTTTC								None (None upstream) : None (None downstream)																							TCttttttttcttttctttttttttt	0.301													2	4	---	---	---	---	
MTRR	4552	broad.mit.edu	37	5	7869456	7869456	+	Intron	DEL	C	-	-	rs34828626		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7869456delC	uc003jed.2	+						FASTKD3_uc011cmp.1_5'Flank|FASTKD3_uc003jeb.2_5'Flank|FASTKD3_uc003jec.2_5'Flank|MTRR_uc010itn.1_Intron|MTRR_uc003jee.3_Intron|MTRR_uc003jef.3_Intron|MTRR_uc003jeg.3_Intron|MTRR_uc010ito.2_Intron	NM_024010	NP_076915	Q9UBK8	MTRR_HUMAN	methionine synthase reductase isoform 2						methionine biosynthetic process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	CCTTCGGCCTCCGGGGGTCGC	0.746													2	6	---	---	---	---	
REEP5	7905	broad.mit.edu	37	5	112237914	112237915	+	Intron	DEL	TG	-	-	rs146349247	by1000genomes	TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112237914_112237915delTG	uc003kqe.1	-						REEP5_uc011cvw.1_Intron|REEP5_uc011cvx.1_Intron|REEP5_uc011cvy.1_Intron|REEP5_uc011cvz.1_Intron	NM_005669	NP_005660	Q00765	REEP5_HUMAN	receptor accessory protein 5							integral to membrane	protein binding				0		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		Epithelial(69;1.3e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.26e-08)|all cancers(49;3.56e-07)|Colorectal(14;0.00778)|COAD - Colon adenocarcinoma(37;0.013)		agcATTtttttgtttttgtttt	0.104													6	3	---	---	---	---	
ADAM19	8728	broad.mit.edu	37	5	156847641	156847642	+	Intron	INS	-	A	A	rs13436628		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156847641_156847642insA	uc003lww.1	-									Q9H013	ADA19_HUMAN	SubName: Full=cDNA FLJ34145 fis, clone FCBBF3011867, highly similar to ADAM 19 (EC 3.4.24.-);						proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			atgatcaatttaaaaaaaaaaa	0.168													6	3	---	---	---	---	
PKD1L1	168507	broad.mit.edu	37	7	47857468	47857468	+	Intron	DEL	A	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47857468delA	uc003tny.1	-						C7orf69_uc003tnz.3_Intron|C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_Intron	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						gctctgtctcaaaaaaaaaaT	0.129													4	2	---	---	---	---	
CYP7B1	9420	broad.mit.edu	37	8	65528090	65528091	+	Intron	DEL	AT	-	-	rs4543580		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65528090_65528091delAT	uc003xvj.2	-							NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,						bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				AAAAAAAAAAATATCAATTATA	0.302													4	2	---	---	---	---	
CBWD1	55871	broad.mit.edu	37	9	162575	162575	+	Intron	DEL	A	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:162575delA	uc003zga.3	-						CBWD1_uc010mgs.2_Intron|CBWD1_uc003zgb.3_Intron|CBWD1_uc003zgc.3_Intron|CBWD1_uc011llr.1_Intron	NM_018491	NP_060961	Q9BRT8	CBWD1_HUMAN	COBW domain containing 1 isoform 1								ATP binding|protein binding			ovary(1)	1	all_lung(41;0.218)	all_cancers(5;3.04e-16)|all_epithelial(5;4.68e-12)|all_lung(10;1.94e-10)|Lung NSC(10;3.61e-10)|Acute lymphoblastic leukemia(5;0.00439)|Breast(48;0.0148)|all_hematologic(5;0.024)|Prostate(43;0.122)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		TTCAGTTCACAAATACTACTC	0.274													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	131208284	131208285	+	IGR	DEL	AA	-	-	rs143368600		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131208284_131208285delAA								CERCAM (8657 upstream) : ODF2 (9181 downstream)																							AGTTTGAGACAAGAGGAGAAAA	0.223													4	2	---	---	---	---	
GATA3	2625	broad.mit.edu	37	10	8106259	8106265	+	Intron	DEL	TCTTTTC	-	-	rs60280763		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8106259_8106265delTCTTTTC	uc001ika.2	+						GATA3_uc001ijz.2_Intron	NM_002051	NP_002042	P23771	GATA3_HUMAN	GATA binding protein 3 isoform 2						aortic valve morphogenesis|blood coagulation|canonical Wnt receptor signaling pathway involved in metanephric kidney development|cardiac right ventricle morphogenesis|cell fate determination|cellular response to interferon-alpha|cellular response to interleukin-4|cellular response to tumor necrosis factor|defense response|ear development|lymphocyte migration|male gonad development|mesenchymal to epithelial transition|mesonephros development|negative regulation of cell cycle|negative regulation of cell motility|negative regulation of cell proliferation involved in mesonephros development|negative regulation of endothelial cell apoptosis|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation|negative regulation of inflammatory response|negative regulation of mammary gland epithelial cell proliferation|nephric duct formation|norepinephrine biosynthetic process|pharyngeal system development|phosphatidylinositol 3-kinase cascade|positive regulation of endothelial cell migration|positive regulation of interleukin-13 secretion|positive regulation of interleukin-4 production|positive regulation of interleukin-5 secretion|positive regulation of protein kinase B signaling cascade|positive regulation of T cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription regulatory region DNA binding|positive regulation of ureteric bud formation|regulation of cellular response to X-ray|regulation of cytokine biosynthetic process|regulation of nephron tubule epithelial cell differentiation|response to estrogen stimulus|response to virus|sympathetic nervous system development|T cell receptor signaling pathway|TOR signaling cascade|ureteric bud formation|uterus development|ventricular septum development	nuclear chromatin|nucleolus|nucleoplasm	core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|E-box binding|HMG box domain binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription coactivator activity|transcription factor binding|zinc ion binding			breast(17)|ovary(3)|central_nervous_system(2)	22						tttctttctttcttttcttcttcttct	0.329			F|N|S		breast		HDR syndrome (HYPOPARATHYROIDISM|SENSORINEURAL DEAFNESS|AND RENAL DISEASE)						4	2	---	---	---	---	
DRD4	1815	broad.mit.edu	37	11	639374	639375	+	Intron	INS	-	G	G	rs71738587		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:639374_639375insG	uc001lqp.1	+							NM_000797	NP_000788	P21917	DRD4_HUMAN	dopamine receptor D4						activation of MAPK activity|adult locomotory behavior|arachidonic acid secretion|behavioral fear response|behavioral response to cocaine|behavioral response to ethanol|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cAMP biosynthetic process|negative regulation of protein secretion|positive regulation of sodium:hydrogen antiporter activity|regulation of dopamine metabolic process|regulation of inhibitory postsynaptic membrane potential|response to amphetamine|response to histamine|social behavior	integral to plasma membrane	dopamine D4 receptor activity|drug binding|potassium channel regulator activity|SH3 domain binding				0		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.36e-28)|Epithelial(43;2.59e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Apomorphine(DB00714)|Clozapine(DB00363)|Olanzapine(DB00334)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Ropinirole(DB00268)|Thiethylperazine(DB00372)|Ziprasidone(DB00246)	AGAGTGGGGGCGGGTCACAAGG	0.698													4	3	---	---	---	---	
IL18	3606	broad.mit.edu	37	11	112024223	112024223	+	Intron	DEL	T	-	-	rs78854082		TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112024223delT	uc001pnb.1	-						IL18_uc001pna.1_5'Flank|IL18_uc009yym.1_Intron	NM_001562	NP_001553	Q14116	IL18_HUMAN	interleukin 18 proprotein						angiogenesis|cell-cell signaling|chemokine biosynthetic process|granulocyte macrophage colony-stimulating factor biosynthetic process|interferon-gamma biosynthetic process|interleukin-13 biosynthetic process|interleukin-2 biosynthetic process|positive regulation of activated T cell proliferation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma production|positive regulation of interleukin-17 production|positive regulation of natural killer cell proliferation|positive regulation of NK T cell proliferation|regulation of cell adhesion|sleep|T-helper 1 type immune response|type 2 immune response	cytosol|extracellular space	cytokine activity|signal transducer activity				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		ATGAGAACCATTTTTTTTTTT	0.358													4	2	---	---	---	---	
LOC653113	653113	broad.mit.edu	37	12	8386701	8386702	+	Intron	INS	-	C	C	rs11612306	by1000genomes	TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8386701_8386702insC	uc010sgk.1	-							NR_024254				Homo sapiens family with sequence similarity 86, member A pseudogene (LOC653113), non-coding RNA.												0						CTGCCGCAAGACCCCATGCCCC	0.520													5	3	---	---	---	---	
USP30	84749	broad.mit.edu	37	12	109490426	109490427	+	5'UTR	INS	-	CGGCGG	CGGCGG	rs140371213	by1000genomes	TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109490426_109490427insCGGCGG	uc010sxi.1	+	1					USP30_uc001tnu.3_Intron	NM_032663	NP_116052	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30						ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial outer membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(1)	1						ATCCCTCGGTCcggcggcggcg	0.589													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	110072325	110072327	+	IGR	DEL	ACT	-	-	rs147833484	by1000genomes	TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110072325_110072327delACT								MVK (37255 upstream) : C12orf34 (79863 downstream)																							caccaccaccactaccaccacca	0.020													3	3	---	---	---	---	
SLC15A1	6564	broad.mit.edu	37	13	99361816	99361824	+	Splice_Site	DEL	CGTCACCTA	-	-	rs141678981	by1000genomes	TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99361816_99361824delCGTCACCTA	uc001vno.2	-	14	1144	c.1067_splice	c.e14+1	p.T356_splice		NM_005073	NP_005064	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide						digestion|protein transport	integral to plasma membrane|membrane fraction	peptide:hydrogen symporter activity			ovary(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Cefadroxil(DB01140)|Ceftibuten(DB01415)|Cyclacillin(DB01000)	CCAACCCACCCGTCACCTACGTGAAATTG	0.574													12	8	---	---	---	---	
CCPG1	9236	broad.mit.edu	37	15	55726958	55726958	+	Intron	DEL	A	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55726958delA	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Intron|DYX1C1_uc002adc.2_Intron|DYX1C1_uc002add.2_Intron	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)		AAAATCAGTTAAAAAAAAAAA	0.289													4	2	---	---	---	---	
LITAF	9516	broad.mit.edu	37	16	11650629	11650630	+	Intron	INS	-	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11650629_11650630insT	uc002daz.2	-						LITAF_uc002dba.2_Intron|LITAF_uc002dbb.2_Intron|LITAF_uc002dbc.2_Intron|LITAF_uc002dbd.2_Intron|LITAF_uc002dbe.3_Intron	NM_004862	NP_004853	Q99732	LITAF_HUMAN	lipopolysaccharide-induced TNF-alpha factor						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|lysosomal membrane	signal transducer activity|WW domain binding			liver(1)	1						AAGAAATTCAGTTGATCTCTCC	0.441													24	12	---	---	---	---	
COG7	91949	broad.mit.edu	37	16	23456979	23456980	+	Intron	INS	-	A	A			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23456979_23456980insA	uc002dlo.2	-							NM_153603	NP_705831	P83436	COG7_HUMAN	component of oligomeric golgi complex 7						intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)		cactctgtctcaaaaaaaaaaG	0.243													4	2	---	---	---	---	
TMEM219	124446	broad.mit.edu	37	16	29982567	29982567	+	Intron	DEL	A	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29982567delA	uc002duw.2	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TMEM219_uc002duy.2_Intron|TMEM219_uc010bzk.1_Intron|TMEM219_uc002duz.2_Intron|TMEM219_uc010bzl.1_Intron|TAOK2_uc002dva.1_5'Flank|TAOK2_uc002dvb.1_5'Flank|TAOK2_uc002dvc.1_5'Flank	NM_194280	NP_919256	Q86XT9	TM219_HUMAN	transmembrane protein 219							integral to membrane					0						actccatctcaaaaaaaaaaa	0.184													5	4	---	---	---	---	
NFATC3	4775	broad.mit.edu	37	16	68243424	68243424	+	Intron	DEL	G	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68243424delG	uc002evo.1	+						NFATC3_uc010vkm.1_Intron|NFATC3_uc010vkn.1_Intron|NFATC3_uc010vkp.1_Intron|NFATC3_uc010vkq.1_Intron|NFATC3_uc002evm.1_Intron|NFATC3_uc002evn.1_Intron|NFATC3_uc010vks.1_Intron|NFATC3_uc010vkt.1_Intron|NFATC3_uc010vkv.1_Intron|NFATC3_uc010vkw.1_Intron|NFATC3_uc010vky.1_Intron|NFATC3_uc010vkz.1_Intron|NFATC3_uc010vlb.1_Intron|NFATC3_uc010vlc.1_Intron	NM_173165	NP_775188	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells,						inflammatory response|transcription from RNA polymerase II promoter	nucleolus|plasma membrane	DNA binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		CTTTACAAGAGGTGTTGAAGA	0.512													3	4	---	---	---	---	
SMG6	23293	broad.mit.edu	37	17	2202012	2202012	+	Intron	DEL	A	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2202012delA	uc002fub.1	-							NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4						actccgtcttaaaaaaaaaaa	0.169													4	2	---	---	---	---	
CCDC144C	348254	broad.mit.edu	37	17	20279654	20279655	+	Intron	INS	-	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20279654_20279655insT	uc010cqy.1	+							NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0						atctgtctctcttttttttttt	0.119													5	5	---	---	---	---	
MED1	5469	broad.mit.edu	37	17	37597110	37597110	+	Intron	DEL	A	-	-			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37597110delA	uc002hrv.3	-						MED1_uc010wee.1_Intron|MED1_uc002hru.2_Intron	NM_004774	NP_004765	Q15648	MED1_HUMAN	mediator complex subunit 1						androgen biosynthetic process|androgen receptor signaling pathway|cellular lipid metabolic process|fat cell differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|estrogen receptor binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|receptor activity|retinoic acid receptor binding|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			lung(2)|ovary(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	8		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		ACTAAAGGTCAAAAAAAAAAG	0.343										HNSCC(31;0.082)			4	3	---	---	---	---	
MIR518B	574474	broad.mit.edu	37	19	54204650	54204651	+	5'Flank	INS	-	T	T			TCGA-CZ-5982-01A-11D-1669-08	TCGA-CZ-5982-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54204650_54204651insT	hsa-mir-518b|MI0003156	+																							0						ctgtttttttgttttttttttt	0.188													4	2	---	---	---	---	
