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
SPEN	23013	broad.mit.edu	37	1	16257994	16257994	+	Silent	SNP	T	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16257994T>C	uc001axk.1	+	11	5463	c.5259T>C	c.(5257-5259)CCT>CCC	p.P1753P	SPEN_uc010obp.1_Silent_p.P1712P	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1753					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		ATCCAGAGCCTGACAGTACCC	0.562													20	98	---	---	---	---	PASS
SPEN	23013	broad.mit.edu	37	1	16257995	16257995	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16257995G>A	uc001axk.1	+	11	5464	c.5260G>A	c.(5260-5262)GAC>AAC	p.D1754N	SPEN_uc010obp.1_Missense_Mutation_p.D1713N	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1754					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TCCAGAGCCTGACAGTACCCA	0.567													18	93	---	---	---	---	PASS
SPEN	23013	broad.mit.edu	37	1	16262076	16262076	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16262076C>G	uc001axk.1	+	11	9545	c.9341C>G	c.(9340-9342)CCA>CGA	p.P3114R	SPEN_uc010obp.1_Missense_Mutation_p.P3073R	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	3114					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		AGCATCCGGCCAGAAGCGCTT	0.652													10	35	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19465596	19465596	+	Silent	SNP	T	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19465596T>C	uc001bbi.2	-	59	8716	c.8712A>G	c.(8710-8712)TCA>TCG	p.S2904S	UBR4_uc001bbk.1_Silent_p.S551S	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	2904					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CGCCAGCCACTGAGTCCACTG	0.612													5	97	---	---	---	---	PASS
BSDC1	55108	broad.mit.edu	37	1	32842063	32842063	+	Missense_Mutation	SNP	A	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32842063A>T	uc001bvh.3	-	9	1003	c.956T>A	c.(955-957)CTG>CAG	p.L319Q	BSDC1_uc010ohg.1_Missense_Mutation_p.L336Q|BSDC1_uc010ohh.1_Missense_Mutation_p.L263Q|BSDC1_uc010ohi.1_Missense_Mutation_p.L224Q|BSDC1_uc001bvg.3_RNA|BSDC1_uc001bvj.2_Missense_Mutation_p.L215Q|BSDC1_uc001bvi.2_Missense_Mutation_p.L336Q	NM_018045	NP_060515	Q9NW68	BSDC1_HUMAN	BSD domain containing 1 isoform b	319							protein binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ATCCACAGCCAGGCCCTGTTC	0.642													22	96	---	---	---	---	PASS
EPHA10	284656	broad.mit.edu	37	1	38192872	38192872	+	Silent	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38192872C>A	uc009vvi.2	-	8	1760	c.1674G>T	c.(1672-1674)GGG>GGT	p.G558G	EPHA10_uc009vvh.1_RNA|EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	558	Extracellular (Potential).					extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(4)|stomach(3)|lung(1)	8	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGTCCCTGGACCCTGAGGCAG	0.632													6	29	---	---	---	---	PASS
FAM73A	374986	broad.mit.edu	37	1	78325069	78325069	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78325069C>A	uc001dhx.2	+	10	1218	c.1186C>A	c.(1186-1188)CAG>AAG	p.Q396K	FAM73A_uc010ork.1_Missense_Mutation_p.Q396K|FAM73A_uc010orl.1_Missense_Mutation_p.Q358K|FAM73A_uc001dhy.1_3'UTR	NM_198549	NP_940951	Q8NAN2	FA73A_HUMAN	hypothetical protein LOC374986	396						integral to membrane				ovary(1)	1				Colorectal(170;0.226)		ACAGGCTTTTCAGGTATTTTT	0.423													17	98	---	---	---	---	PASS
S100A10	6281	broad.mit.edu	37	1	151955649	151955649	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151955649C>A	uc001ezl.2	-	3	792	c.284G>T	c.(283-285)GGA>GTA	p.G95V		NM_002966	NP_002957	P60903	S10AA_HUMAN	S100 calcium binding protein A10	95					signal transduction		calcium ion binding|receptor binding				0	Melanoma(130;0.0648)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			CTACTTCTTTCCCTTCTGCTT	0.483													56	367	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152283060	152283060	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152283060G>T	uc001ezu.1	-	3	4338	c.4302C>A	c.(4300-4302)AGC>AGA	p.S1434R	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1434	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AACGTCCAGAGCTTTCCCCTG	0.557									Ichthyosis				46	331	---	---	---	---	PASS
COPA	1314	broad.mit.edu	37	1	160261217	160261217	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160261217T>C	uc009wti.2	-	31	3722	c.3328A>G	c.(3328-3330)AAT>GAT	p.N1110D	COPA_uc001fvv.3_Missense_Mutation_p.N1119D	NM_004371	NP_004362	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha isoform	1110					COPI coating of Golgi vesicle|intracellular protein transport|pancreatic juice secretion|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|extracellular space|microsome|soluble fraction	hormone activity|structural molecule activity			ovary(1)|skin(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AAGAACAGATTGAGGGCTGTA	0.547											OREG0013929	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	23	90	---	---	---	---	PASS
RFWD2	64326	broad.mit.edu	37	1	176015396	176015396	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176015396A>G	uc001gku.1	-	12	1598	c.1342T>C	c.(1342-1344)TAT>CAT	p.Y448H	RFWD2_uc001gkv.1_Missense_Mutation_p.Y424H|RFWD2_uc001gkw.1_Missense_Mutation_p.Y208H|RFWD2_uc009wwv.2_Missense_Mutation_p.Y247H|RFWD2_uc001gkt.1_Missense_Mutation_p.Y287H	NM_022457	NP_071902	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2 isoform a	448	WD 1.				DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0						TCATATTCATAGACTTTAATC	0.348													6	131	---	---	---	---	PASS
FAM5B	57795	broad.mit.edu	37	1	177199237	177199237	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177199237G>T	uc001glf.2	+	2	537	c.225G>T	c.(223-225)ATG>ATT	p.M75I		NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	75						extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6						CTGACTTCATGGAGCGGTACC	0.617													18	107	---	---	---	---	PASS
LAMC2	3918	broad.mit.edu	37	1	183204764	183204764	+	Nonsense_Mutation	SNP	T	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183204764T>G	uc001gqa.2	+	16	2669	c.2355T>G	c.(2353-2355)TAT>TAG	p.Y785*	LAMC2_uc001gpz.3_Nonsense_Mutation_p.Y785*|LAMC2_uc010poa.1_Nonsense_Mutation_p.Y485*	NM_005562	NP_005553	Q13753	LAMC2_HUMAN	laminin, gamma 2 isoform a precursor	785	Domain II and I.				cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3						CTGAGGACTATTCCAAACAAG	0.517											OREG0014042	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	15	81	---	---	---	---	PASS
PRKD3	23683	broad.mit.edu	37	2	37486752	37486752	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37486752G>T	uc002rqd.2	-	15	2674	c.2119C>A	c.(2119-2121)CTT>ATT	p.L707I	PRKD3_uc002rqe.1_Missense_Mutation_p.L307I	NM_005813	NP_005804	O94806	KPCD3_HUMAN	protein kinase D3	707	Protein kinase.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(2)|ovary(1)|central_nervous_system(1)	4		all_hematologic(82;0.21)				GCTGATGCAAGCAGCACATTT	0.358													10	91	---	---	---	---	PASS
VPS24	51652	broad.mit.edu	37	2	86732851	86732851	+	3'UTR	SNP	G	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86732851G>T	uc002srj.2	-	6					VPS24_uc002srk.2_3'UTR|VPS24_uc002srl.2_3'UTR|VPS24_uc010ytl.1_3'UTR	NM_016079	NP_057163	Q9Y3E7	CHMP3_HUMAN	vacuolar protein sorting 24 isoform 1						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1						CCTCACAACAGAGGTGTAGTG	0.512													22	95	---	---	---	---	PASS
INSIG2	51141	broad.mit.edu	37	2	118854300	118854300	+	Silent	SNP	G	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118854300G>A	uc002tlk.2	+	2	374	c.168G>A	c.(166-168)ACG>ACA	p.T56T	INSIG2_uc010yye.1_Intron	NM_016133	NP_057217	Q9Y5U4	INSI2_HUMAN	insulin induced protein 2	56					ER-nuclear sterol response pathway	SREBP-SCAP-Insig complex				ovary(1)|central_nervous_system(1)	2						GAAATGTGACGCTCTTTCCAC	0.418													15	219	---	---	---	---	PASS
RIF1	55183	broad.mit.edu	37	2	152300220	152300220	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152300220T>G	uc002txm.2	+	18	2113	c.1983T>G	c.(1981-1983)AAT>AAG	p.N661K	RIF1_uc002txl.2_Missense_Mutation_p.N661K|RIF1_uc010fnv.1_Missense_Mutation_p.N625K|RIF1_uc002txn.2_Missense_Mutation_p.N661K|RIF1_uc002txo.2_Missense_Mutation_p.N661K	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1	661					cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)		AATTGATTAATCAGGTATGAA	0.303													22	129	---	---	---	---	PASS
CCDC150	284992	broad.mit.edu	37	2	197531635	197531635	+	Intron	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197531635C>A	uc002utp.1	+						CCDC150_uc002uto.1_Missense_Mutation_p.L319I|CCDC150_uc010zgq.1_Intron|CCDC150_uc010zgr.1_Intron|CCDC150_uc010zgs.1_Intron	NM_001080539	NP_001074008	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150												0						TGGAAAAACTCTTAAGATCCC	0.373													10	57	---	---	---	---	PASS
C2orf62	375307	broad.mit.edu	37	2	219232614	219232614	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219232614T>G	uc002vhr.2	+	10	1120	c.1091T>G	c.(1090-1092)TTG>TGG	p.L364W	C2orf62_uc002vhs.2_RNA|uc002vht.2_5'Flank	NM_198559	NP_940961	Q7Z7H3	CB062_HUMAN	hypothetical protein LOC375307	364											0		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCACCGGCCTTGGGCTCCTCC	0.731													10	38	---	---	---	---	PASS
HDLBP	3069	broad.mit.edu	37	2	242179325	242179325	+	Silent	SNP	G	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242179325G>A	uc002waz.2	-	18	2610	c.2382C>T	c.(2380-2382)ATC>ATT	p.I794I	HDLBP_uc002wba.2_Silent_p.I794I|HDLBP_uc002wbb.2_Silent_p.I746I	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	794	KH 9.				cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|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;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		CCAGGTTTTGGATCAAGGCCT	0.582													10	67	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52678806	52678806	+	Splice_Site	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52678806C>T	uc003des.2	-	8	826	c.814_splice	c.e8-1	p.D272_splice	PBRM1_uc003dex.2_Splice_Site|PBRM1_uc003deq.2_Splice_Site_p.D272_splice|PBRM1_uc003der.2_Splice_Site_p.D272_splice|PBRM1_uc003det.2_Splice_Site_p.D272_splice|PBRM1_uc003deu.2_Splice_Site_p.D272_splice|PBRM1_uc003dev.2_Splice_Site|PBRM1_uc003dew.2_Splice_Site_p.D272_splice|PBRM1_uc010hmk.1_Splice_Site_p.D272_splice|PBRM1_uc003dey.2_Splice_Site_p.D272_splice|PBRM1_uc003dez.1_Splice_Site_p.D272_splice|PBRM1_uc003dfb.1_Splice_Site_p.D170_splice	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4						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)		AATTTGCATCCTGTCAAGATA	0.338			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								4	32	---	---	---	---	PASS
LRIG1	26018	broad.mit.edu	37	3	66502055	66502055	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66502055T>C	uc003dmx.2	-	3	307	c.293A>G	c.(292-294)TAC>TGC	p.Y98C	LRIG1_uc010hnz.2_5'UTR|LRIG1_uc010hoa.2_Missense_Mutation_p.Y98C	NM_015541	NP_056356	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like	98	Extracellular (Potential).|LRR 2.					integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		ATTATTGAGGTACCTGTAACA	0.428													8	65	---	---	---	---	PASS
GTF2E1	2960	broad.mit.edu	37	3	120495384	120495384	+	Silent	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120495384C>T	uc003edz.3	+	4	879	c.765C>T	c.(763-765)GTC>GTT	p.V255V		NM_005513	NP_005504	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1,	255					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.159)		AGAATGTTGTCATTAACATGG	0.502													25	122	---	---	---	---	PASS
SPATA16	83893	broad.mit.edu	37	3	172607188	172607188	+	3'UTR	SNP	G	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172607188G>T	uc003fin.3	-	11						NM_031955	NP_114161	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16						cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)|skin(1)	3	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			TGCCAGTTGAGATTAATGAAA	0.348													7	25	---	---	---	---	PASS
ABLIM2	84448	broad.mit.edu	37	4	8009692	8009692	+	Intron	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8009692C>A	uc003gko.2	-						ABLIM2_uc003gkk.2_Intron|ABLIM2_uc003gkl.2_Intron|ABLIM2_uc003gkj.3_Intron|ABLIM2_uc003gkm.3_Intron|ABLIM2_uc003gkp.2_Intron|ABLIM2_uc003gkq.2_Intron|ABLIM2_uc003gkr.2_Intron|ABLIM2_uc003gks.3_3'UTR|MIR95_hsa-mir-95|MI0000097_5'Flank	NM_001130084	NP_001123556	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2						axon guidance|cytoskeleton organization	actin cytoskeleton|cytoplasm|intermediate filament cytoskeleton|nucleus	actin binding|zinc ion binding			pancreas(3)	3						ACAGGCAAGGCTTAGATGTAG	0.502													10	59	---	---	---	---	PASS
NAF1	92345	broad.mit.edu	37	4	164050358	164050358	+	Silent	SNP	A	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164050358A>G	uc003iqj.2	-	8	1370	c.1176T>C	c.(1174-1176)CCT>CCC	p.P392P	NAF1_uc010iqw.1_Intron	NM_138386	NP_612395	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 homolog isoform a	392					rRNA processing|snRNA pseudouridine synthesis	cytoplasm|nucleus|small nucleolar ribonucleoprotein complex	protein binding|snoRNA binding			ovary(2)	2	all_hematologic(180;0.166)	Prostate(90;0.109)				AGAAATGCTGAGGTGGAGGCC	0.458													21	102	---	---	---	---	PASS
SDHAP3	728609	broad.mit.edu	37	5	1593386	1593386	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1593386A>C	uc010itg.1	-	2	151	c.74T>G	c.(73-75)GTG>GGG	p.V25G	SDHAP3_uc011cme.1_RNA					Homo sapiens cDNA clone IMAGE:40127561.												0						CTGGCCATTCACGTGCCTCAG	0.597													3	65	---	---	---	---	PASS
RNASEN	29102	broad.mit.edu	37	5	31468136	31468136	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31468136C>T	uc003jhg.2	-	17	2635	c.2276G>A	c.(2275-2277)CGT>CAT	p.R759H	RNASEN_uc003jhh.2_Missense_Mutation_p.R722H|RNASEN_uc003jhi.2_Missense_Mutation_p.R722H	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1	759	Necessary for interaction with DGCR8 and pri-miRNA processing activity.				gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0						GAACTGTTCACGATCCAGTTG	0.408													3	40	---	---	---	---	PASS
TRIM23	373	broad.mit.edu	37	5	64907630	64907630	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64907630C>G	uc003jty.2	-	4	531	c.445G>C	c.(445-447)GAG>CAG	p.E149Q	TRIM23_uc003jtw.2_Missense_Mutation_p.E149Q|TRIM23_uc003jtx.2_Missense_Mutation_p.E149Q	NM_001656	NP_001647	P36406	TRI23_HUMAN	ADP-ribosylation factor domain protein 1 isoform	149	B box-type; degenerate.				interspecies interaction between organisms|small GTPase mediated signal transduction	Golgi membrane|lysosomal membrane	enzyme activator activity|GDP binding|GTP binding|GTPase activity|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|lung(1)	4		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		TGAGAACACTCAGAGCACAAA	0.408													35	144	---	---	---	---	PASS
PCDHB13	56123	broad.mit.edu	37	5	140594137	140594137	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140594137C>T	uc003lja.1	+	1	629	c.442C>T	c.(442-444)CCT>TCT	p.P148S		NM_018933	NP_061756	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13 precursor	148	Cadherin 2.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGAGAGCAGTCCTCCTGGGAC	0.418													35	221	---	---	---	---	PASS
CAGE1	285782	broad.mit.edu	37	6	7373597	7373597	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7373597C>A	uc003mxi.2	-	4	1768	c.1047G>T	c.(1045-1047)TTG>TTT	p.L349F	CAGE1_uc003mxh.2_RNA|CAGE1_uc003mxj.2_Missense_Mutation_p.L240F|CAGE1_uc003mxk.1_Missense_Mutation_p.L240F	NM_205864	NP_995586	Q8TC20	CAGE1_HUMAN	cancer antigen 1	485	Potential.										0	Ovarian(93;0.0418)					CCTGTAAAGACAAGAACTCTT	0.388													6	59	---	---	---	---	PASS
HIST1H2AM	8336	broad.mit.edu	37	6	27860781	27860781	+	Silent	SNP	C	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27860781C>G	uc003nkb.1	-	1	183	c.147G>C	c.(145-147)CCG>CCC	p.P49P	HIST1H3J_uc003nka.2_5'Flank|HIST1H2BO_uc003nkc.1_5'Flank	NM_003514	NP_003505	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	49					nucleosome assembly	nucleosome|nucleus	DNA binding|enzyme binding			ovary(2)	2						CCAGGTAAACCGGCGCGCCGG	0.657													18	102	---	---	---	---	PASS
VARS2	57176	broad.mit.edu	37	6	30891256	30891256	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30891256C>T	uc003nsc.1	+	24	3072	c.2440C>T	c.(2440-2442)CTT>TTT	p.L814F	VARS2_uc011dmx.1_Missense_Mutation_p.L814F|VARS2_uc011dmy.1_Missense_Mutation_p.L674F|VARS2_uc011dmz.1_Missense_Mutation_p.L844F|VARS2_uc011dna.1_Missense_Mutation_p.L812F|VARS2_uc011dnb.1_RNA|VARS2_uc011dnc.1_RNA|VARS2_uc011dnd.1_Missense_Mutation_p.L252F|VARS2_uc010jsg.1_Missense_Mutation_p.L186F|VARS2_uc010jsh.1_5'UTR	NM_020442	NP_065175	Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	814					valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4						CCACTTCTGGCTTCACAACCT	0.592													7	101	---	---	---	---	PASS
COL12A1	1303	broad.mit.edu	37	6	75814939	75814939	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75814939C>A	uc003phs.2	-	54	8414	c.8248G>T	c.(8248-8250)GGA>TGA	p.G2750*	COL12A1_uc003pht.2_Nonsense_Mutation_p.G1586*	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	2750	Triple-helical region (COL2) with 1 imperfection.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9						CCTGGAGGTCCTGGAGGTCCA	0.388													3	77	---	---	---	---	PASS
AIM1	202	broad.mit.edu	37	6	106975346	106975346	+	Splice_Site	SNP	G	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106975346G>A	uc003prh.2	+	5	3841	c.3354_splice	c.e5+1	p.Q1118_splice		NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1								sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TGTGGTTCAGGTAGGTTGTGG	0.373													21	320	---	---	---	---	PASS
RNF216	54476	broad.mit.edu	37	7	5752486	5752486	+	Silent	SNP	G	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5752486G>T	uc003soy.1	-	12	1861	c.1671C>A	c.(1669-1671)CTC>CTA	p.L557L	RNF216_uc010ksz.1_Silent_p.L179L|RNF216_uc010kta.1_Silent_p.L179L|RNF216_uc011jwj.1_Silent_p.L179L|RNF216_uc003sox.1_Silent_p.L614L	NM_207116	NP_996999	Q9NWF9	RN216_HUMAN	ring finger protein 216 isoform b	557	RING-type 1.				apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		CCATGCAGCTGAGCTCCAACT	0.438													6	38	---	---	---	---	PASS
CCDC129	223075	broad.mit.edu	37	7	31682989	31682989	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31682989A>G	uc003tcj.1	+	11	2998	c.2005A>G	c.(2005-2007)AAA>GAA	p.K669E	CCDC129_uc011kad.1_Missense_Mutation_p.K679E|CCDC129_uc003tci.1_Missense_Mutation_p.K520E|CCDC129_uc011kae.1_Missense_Mutation_p.K695E|CCDC129_uc003tck.1_Missense_Mutation_p.K577E	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	669											0						CCACCTCCATAAACTGCCTGG	0.473													11	74	---	---	---	---	PASS
ZMIZ2	83637	broad.mit.edu	37	7	44801378	44801378	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44801378C>G	uc003tlr.2	+	11	1593	c.1470C>G	c.(1468-1470)AGC>AGG	p.S490R	ZMIZ2_uc003tlq.2_Missense_Mutation_p.S432R|ZMIZ2_uc003tls.2_Missense_Mutation_p.S464R|ZMIZ2_uc003tlt.2_Missense_Mutation_p.S113R|ZMIZ2_uc010kyj.2_Missense_Mutation_p.S12R	NM_031449	NP_113637	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2 isoform 1	490	Interaction with AR.				positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding			ovary(2)|large_intestine(2)|breast(1)	5						TGCAGGTCAGCGTCAATGCCA	0.607													3	21	---	---	---	---	PASS
CFTR	1080	broad.mit.edu	37	7	117199625	117199625	+	Silent	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117199625C>A	uc003vjd.2	+	11	1632	c.1500C>A	c.(1498-1500)GGC>GGA	p.G500G	CFTR_uc011knq.1_5'UTR|CFTR_uc003vje.1_RNA	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	500	Cytoplasmic (Potential).|ABC transporter 1.				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)	TTATGCCTGGCACCATTAAAG	0.378									Cystic_Fibrosis				29	212	---	---	---	---	PASS
HYAL4	23553	broad.mit.edu	37	7	123517219	123517219	+	3'UTR	SNP	G	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123517219G>C	uc003vlc.2	+	5					HYAL4_uc011knz.1_3'UTR	NM_012269	NP_036401	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4						fusion of sperm to egg plasma membrane|glycosaminoglycan catabolic process	integral to membrane	hyalurononglucosaminidase activity			skin(1)	1						AGATAATTGAGTTTAAAGGGA	0.363													23	140	---	---	---	---	PASS
ZNF398	57541	broad.mit.edu	37	7	148876816	148876816	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148876816T>A	uc003wfl.2	+	6	2127	c.1852T>A	c.(1852-1854)TCT>ACT	p.S618T	ZNF398_uc011kul.1_Missense_Mutation_p.S447T|ZNF398_uc011kum.1_Missense_Mutation_p.S623T	NM_170686	NP_733787	Q8TD17	ZN398_HUMAN	zinc finger 398 isoform a	618					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			GCTTGAAACTTCTGGCCTGGG	0.552													6	47	---	---	---	---	PASS
AGAP3	116988	broad.mit.edu	37	7	150784022	150784022	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150784022A>C	uc003wjg.1	+	1	197	c.194A>C	c.(193-195)AAC>ACC	p.N65T	AGAP3_uc003wje.1_Intron|AGAP3_uc003wjf.1_Missense_Mutation_p.N65T|AGAP3_uc010lpy.1_Missense_Mutation_p.N65T	NM_031946	NP_114152	Q96P47	AGAP3_HUMAN	centaurin, gamma 3 isoform a	29					regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3						GCGCTCTCCAACTCCGCGGCC	0.532													7	21	---	---	---	---	PASS
TNKS	8658	broad.mit.edu	37	8	9623811	9623811	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9623811G>A	uc003wss.2	+	25	3621	c.3616G>A	c.(3616-3618)GGA>AGA	p.G1206R	TNKS_uc011kww.1_Missense_Mutation_p.G969R	NM_003747	NP_003738	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related	1206	PARP catalytic.				mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)		ATACATAGGAGGAATGTTTGG	0.403													14	183	---	---	---	---	PASS
CNTNAP3	79937	broad.mit.edu	37	9	39085772	39085772	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39085772A>C	uc004abi.2	-	21	3642	c.3403T>G	c.(3403-3405)TTC>GTC	p.F1135V	CNTNAP3_uc004abj.2_Missense_Mutation_p.F1054V|CNTNAP3_uc011lqr.1_RNA|CNTNAP3_uc004abk.1_3'UTR	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3 precursor	1135	Laminin G-like 4.|Extracellular (Potential).				cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		ACGGCGTTGAATTCTGTCCCT	0.388													49	344	---	---	---	---	PASS
NIPSNAP3A	25934	broad.mit.edu	37	9	107521496	107521496	+	Intron	SNP	G	A	A	rs2297397	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107521496G>A	uc004bch.1	+						NIPSNAP3A_uc011lvt.1_3'UTR|NIPSNAP3A_uc011lvu.1_Intron	NM_015469	NP_056284	Q9UFN0	NPS3A_HUMAN	nipsnap homolog 3A							cytosol					0						GAACAAATGTGTTTCAGTCAG	0.408													4	66	---	---	---	---	PASS
LAMC3	10319	broad.mit.edu	37	9	133911635	133911635	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133911635G>C	uc004caa.1	+	4	990	c.892G>C	c.(892-894)GGC>CGC	p.G298R		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	298	Laminin EGF-like 1.				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)		CAACACCACCGGCACAGACTG	0.677													6	27	---	---	---	---	PASS
GRIN1	2902	broad.mit.edu	37	9	140040311	140040311	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140040311C>T	uc004clk.2	+	3	857	c.527C>T	c.(526-528)GCT>GTT	p.A176V	GRIN1_uc004cli.1_5'UTR|GRIN1_uc004clj.1_Missense_Mutation_p.A173V|GRIN1_uc004cll.2_Missense_Mutation_p.A176V|GRIN1_uc004clm.2_Missense_Mutation_p.A176V|GRIN1_uc004cln.2_Missense_Mutation_p.A173V|GRIN1_uc004clo.2_Missense_Mutation_p.A173V	NM_007327	NP_015566	Q05586	NMDZ1_HUMAN	NMDA receptor 1 isoform NR1-3 precursor	176	Extracellular (Potential).				ionotropic glutamate receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|regulation of excitatory postsynaptic membrane potential|response to ethanol|visual learning	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane|synaptic vesicle|synaptosome	calcium ion binding|calmodulin binding|extracellular-glutamate-gated ion channel activity|glutamate binding|glycine binding			skin(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	L-Glutamic Acid(DB00142)|Orphenadrine(DB01173)	GGCCGGGCGGCTCAGAAACGC	0.677													3	12	---	---	---	---	PASS
DIP2C	22982	broad.mit.edu	37	10	375466	375466	+	Silent	SNP	G	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:375466G>C	uc001ifp.2	-	30	3750	c.3660C>G	c.(3658-3660)GCC>GCG	p.A1220A		NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	1220						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		ACTGACTCACGGCAAGAAGCC	0.562													4	37	---	---	---	---	PASS
NMT2	9397	broad.mit.edu	37	10	15154856	15154856	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15154856T>C	uc001inz.1	-	10	1361	c.1277A>G	c.(1276-1278)AAC>AGC	p.N426S	NMT2_uc001ioa.1_Missense_Mutation_p.N413S|NMT2_uc009xjo.1_Missense_Mutation_p.N426S|NMT2_uc010qbz.1_Missense_Mutation_p.N238S	NM_004808	NP_004799	O60551	NMT2_HUMAN	N-myristoyltransferase 2	426					N-terminal protein myristoylation|protein lipoylation	Golgi apparatus|plasma membrane	glycylpeptide N-tetradecanoyltransferase activity			ovary(1)	1						TGTGTGGATGTTGTAGAATGA	0.547													19	141	---	---	---	---	PASS
OR13A1	79290	broad.mit.edu	37	10	45799058	45799058	+	Silent	SNP	G	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45799058G>T	uc001jcc.1	-	4	1122	c.813C>A	c.(811-813)ACC>ACA	p.T271T	OR13A1_uc001jcd.1_Silent_p.T267T	NM_001004297	NP_001004297	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A,	271	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						AGAAGACAGCGGTGTAATACA	0.572													3	71	---	---	---	---	PASS
PTEN	5728	broad.mit.edu	37	10	89717762	89717762	+	Nonsense_Mutation	SNP	A	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89717762A>T	uc001kfb.2	+	8	1818	c.787A>T	c.(787-789)AAG>TAG	p.K263*		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	263	C2 tensin-type.			KMLKKDK->AAGAADA: Reduces the growth suppression activity and cells show anchorage-independent growth. Reduces binding to phospholipid membranes in vitro. Phosphatase activity towards PtdIns(3,4,5)P3 is not affected.	activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R55fs*1(4)|p.K263*(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.D252_K263>AKE(1)|p.G165_K342del(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		CAAACAGAACAAGATGCTAAA	0.368		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			14	78	---	---	---	---	PASS
B4GALNT4	338707	broad.mit.edu	37	11	372684	372684	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:372684T>C	uc001lpb.2	+	3	287	c.278T>C	c.(277-279)ATG>ACG	p.M93T		NM_178537	NP_848632	Q76KP1	B4GN4_HUMAN	beta	93	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GACCTAGACATGCTGTTTCCT	0.612													5	30	---	---	---	---	PASS
MALAT1	378938	broad.mit.edu	37	11	65268083	65268083	+	RNA	SNP	A	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65268083A>G	uc010roh.1	+	1		c.2851A>G			uc001ody.2_RNA|MALAT1_uc001odz.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0						GCTAGGAAAAAGGATTCCAGG	0.532													18	88	---	---	---	---	PASS
VPS11	55823	broad.mit.edu	37	11	118940211	118940211	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118940211C>G	uc010ryx.1	+	4	438	c.396C>G	c.(394-396)TTC>TTG	p.F132L	VPS11_uc010ryy.1_5'UTR	NM_021729	NP_068375	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11	132					protein transport	endocytic vesicle|HOPS complex|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		CTCGAATCTTCCCTGCTATTC	0.453													16	76	---	---	---	---	PASS
TSPAN31	6302	broad.mit.edu	37	12	58140428	58140428	+	Silent	SNP	G	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58140428G>C	uc001spt.2	+	4	523	c.369G>C	c.(367-369)CTG>CTC	p.L123L	TSPAN31_uc009zqb.2_Intron|TSPAN31_uc010ssa.1_Silent_p.L45L	NM_005981	NP_005972	Q12999	TSN31_HUMAN	sarcoma amplified sequence	123	Extracellular (Potential).				positive regulation of cell proliferation	integral to plasma membrane|membrane fraction					0	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			GGGATGAACTGGAAAGAAGTT	0.448													15	112	---	---	---	---	PASS
CDK8	1024	broad.mit.edu	37	13	26974672	26974672	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26974672C>T	uc001uqr.1	+	10	1042	c.1016C>T	c.(1015-1017)CCA>CTA	p.P339L	CDK8_uc001uqs.1_Missense_Mutation_p.P339L|CDK8_uc001uqt.1_Missense_Mutation_p.P166L	NM_001260	NP_001251	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	339					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mediator complex	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|large_intestine(1)|ovary(1)|skin(1)	5	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		TTAGAAGACCCACTTCCTACA	0.433													32	264	---	---	---	---	PASS
ERCC5	2073	broad.mit.edu	37	13	103474191	103474191	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103474191T>C	uc001vpu.1	+	4	922	c.800T>C	c.(799-801)CTT>CCT	p.L267P	BIVM_uc001vps.2_Missense_Mutation_p.L267P|BIVM_uc010agc.2_Missense_Mutation_p.L38P|BIVM_uc001vpv.2_Missense_Mutation_p.L38P	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	Error:Variant_position_missing_in_P28715_after_alignment					negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					AATACAACACTTATGAGGTAT	0.383			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				34	136	---	---	---	---	PASS
ERCC5	2073	broad.mit.edu	37	13	103474193	103474193	+	Missense_Mutation	SNP	A	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103474193A>T	uc001vpu.1	+	4	924	c.802A>T	c.(802-804)ATG>TTG	p.M268L	BIVM_uc001vps.2_Missense_Mutation_p.M268L|BIVM_uc010agc.2_Missense_Mutation_p.M39L|BIVM_uc001vpv.2_Missense_Mutation_p.M39L	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	Error:Variant_position_missing_in_P28715_after_alignment					negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TACAACACTTATGAGGTATGA	0.388			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				34	135	---	---	---	---	PASS
SALL2	6297	broad.mit.edu	37	14	21992408	21992408	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21992408C>A	uc001wbe.2	-	2	1736	c.1454G>T	c.(1453-1455)AGT>ATT	p.S485I	SALL2_uc010tly.1_Missense_Mutation_p.S483I|SALL2_uc010tlz.1_Missense_Mutation_p.S348I|SALL2_uc001wbf.3_Intron|SALL2_uc010tma.1_Missense_Mutation_p.S350I|SALL2_uc001wbg.1_Intron	NM_005407	NP_005398	Q9Y467	SALL2_HUMAN	sal-like 2	485							DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|large_intestine(1)	3	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		CTCTGTGGCACTGAGTGCTGT	0.587													3	32	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44975274	44975274	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44975274G>T	uc001wvn.2	-	1	1226	c.917C>A	c.(916-918)GCC>GAC	p.A306D		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	306						cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		AACTGCAGTGGCTGCCTCAGC	0.517													18	53	---	---	---	---	PASS
PAPLN	89932	broad.mit.edu	37	14	73732165	73732165	+	Silent	SNP	G	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73732165G>T	uc010ttx.1	+	22	3376	c.3213G>T	c.(3211-3213)CCG>CCT	p.P1071P	PAPLN_uc001xnw.3_Silent_p.P1044P|PAPLN_uc010arl.2_RNA|PAPLN_uc010ttw.1_RNA|PAPLN_uc010tty.1_Silent_p.P1055P|PAPLN_uc010arm.2_Silent_p.P270P|PAPLN_uc010arn.2_Silent_p.P271P	NM_173462	NP_775733	O95428	PPN_HUMAN	papilin	1071	Ig-like C2-type 2.					proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase inhibitor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		AAGGCTTCCCGCCCCCAGCCA	0.627													3	55	---	---	---	---	PASS
SECISBP2L	9728	broad.mit.edu	37	15	49292062	49292062	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49292062C>T	uc001zxe.1	-	16	2505	c.2371G>A	c.(2371-2373)GTA>ATA	p.V791I	SECISBP2L_uc001zxd.1_Missense_Mutation_p.V746I|SECISBP2L_uc010bep.1_Missense_Mutation_p.V553I	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	791										breast(1)|skin(1)	2						ATTCCCACTACGCTAACAGGA	0.448													5	121	---	---	---	---	PASS
NEO1	4756	broad.mit.edu	37	15	73590937	73590937	+	Silent	SNP	T	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73590937T>C	uc002avm.3	+	27	4292	c.4150T>C	c.(4150-4152)TTA>CTA	p.L1384L	NEO1_uc010ukx.1_Silent_p.L1373L|NEO1_uc010uky.1_Silent_p.L1331L|NEO1_uc010ukz.1_Silent_p.L797L|NEO1_uc002avn.3_Silent_p.L1022L	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor	1384	Cytoplasmic (Potential).				axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1						AAGCACACCATTACTGTCCCA	0.582													11	69	---	---	---	---	PASS
LOC645752	645752	broad.mit.edu	37	15	78207541	78207541	+	Silent	SNP	T	G	G	rs56259215	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78207541T>G	uc010bky.2	-	18	2135	c.1371A>C	c.(1369-1371)GTA>GTC	p.V457V	LOC645752_uc010umq.1_Silent_p.V104V|uc002bcw.1_5'Flank|uc002bcx.1_5'Flank	NR_027024				SubName: Full=GOLGA6 protein; Flags: Fragment;												0						TGTCCTGCATTACAGGAGACA	0.567													3	76	---	---	---	---	PASS
BCL2A1	597	broad.mit.edu	37	15	80253472	80253472	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80253472C>T	uc002bfc.3	-	2	647	c.465G>A	c.(463-465)ATG>ATA	p.M155I	BCL2A1_uc002bfd.3_3'UTR	NM_004049	NP_004040	Q16548	B2LA1_HUMAN	BCL2-related protein A1 isoform 1	155					anti-apoptosis|apoptosis	cytoplasm	protein binding			pancreas(1)	1						CTAGAAAAGTCATCCAGCCAG	0.353													14	137	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	102300094	102300094	+	5'Flank	SNP	G	T	T	rs28459357		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102300094G>T	uc002bzk.2	-						uc002bzn.2_5'Flank|uc010uso.1_5'Flank|uc002bzs.2_5'Flank|uc010usv.1_5'Flank|uc002cam.2_RNA|uc010usx.1_5'Flank|uc002cao.2_5'Flank|uc002cap.2_5'Flank|uc002caq.2_5'Flank|uc010usz.1_5'Flank|uc010uta.1_5'Flank|uc002cas.2_5'Flank|uc002cat.1_5'Flank|uc002cau.2_5'Flank|uc010utb.1_5'Flank|uc002cav.2_5'Flank|uc002caw.2_5'Flank|uc002cax.2_5'Flank|uc010utc.1_5'Flank|uc002cay.2_5'Flank|uc002cbb.2_5'Flank|uc002cbc.1_5'Flank|uc002cbd.2_5'Flank|uc002cbe.2_5'Flank|uc002cbg.2_5'Flank|uc002cbh.2_5'Flank|uc002cbi.2_5'Flank|uc002cbk.2_5'Flank|uc002cbl.2_5'Flank|uc010utd.1_5'Flank|uc002cbm.2_5'Flank|uc002cbn.2_5'Flank|uc010ute.1_5'Flank					DQ593627																		GACACTCATGGAGGAGTCGGC	0.582													4	11	---	---	---	---	PASS
FOXC2	2303	broad.mit.edu	37	16	86601069	86601069	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86601069G>A	uc002fjq.2	+	1	213	c.128G>A	c.(127-129)GGC>GAC	p.G43D		NM_005251	NP_005242	Q99958	FOXC2_HUMAN	forkhead box C2	43					anti-apoptosis|artery morphogenesis|blood vessel remodeling|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|embryonic viscerocranium morphogenesis|insulin receptor signaling pathway|lymphangiogenesis|metanephros development|negative regulation of transcription from RNA polymerase II promoter|neural crest cell fate commitment|Notch signaling pathway|ossification|paraxial mesodermal cell fate commitment|patterning of blood vessels|positive regulation of cell adhesion mediated by integrin|positive regulation of cell migration involved in sprouting angiogenesis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of vascular wound healing|regulation of blood vessel size|regulation of organ growth|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|ureteric bud development|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding|transcription regulatory region DNA binding				0						GTCTATTCCGGCCACCCGGAG	0.697									Late-onset_Hereditary_Lymphedema				3	34	---	---	---	---	PASS
NUP88	4927	broad.mit.edu	37	17	5290385	5290385	+	Silent	SNP	G	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5290385G>A	uc002gbo.1	-	15	1988	c.1962C>T	c.(1960-1962)CTC>CTT	p.L654L	NUP88_uc002gbn.2_5'Flank|NUP88_uc010vsx.1_Silent_p.L670L	NM_002532	NP_002523	Q99567	NUP88_HUMAN	nucleoporin 88kDa	654					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	transporter activity			kidney(1)	1						CACTATCAGAGAGAACTGGGA	0.388													21	122	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10426861	10426861	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10426861C>A	uc010coi.2	-	37	5552	c.5424G>T	c.(5422-5424)CAG>CAT	p.Q1808H	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.Q1808H|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1808	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						TCAGGGCCAGCTGCTCAGCCT	0.552													22	115	---	---	---	---	PASS
NLE1	54475	broad.mit.edu	37	17	33464021	33464021	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33464021T>G	uc002hiy.1	-	7	855	c.827A>C	c.(826-828)GAC>GCC	p.D276A	NLE1_uc010ctn.1_5'UTR|NLE1_uc002hiz.1_5'UTR	NM_018096	NP_060566	Q9NVX2	NLE1_HUMAN	Notchless gene homolog isoform a	276	WD 4.					nucleolus				breast(3)|ovary(1)	4		Ovarian(249;0.17)				AGCACTTACGTCATGAGCTCT	0.542													17	169	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	39296278	39296278	+	RNA	SNP	G	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39296278G>A	uc010cxk.1	-	1		c.426C>T								Homo sapiens partial mRNA for keratin associated protein 4.6 (KRTAP4.6 gene).																		tggattcacagcaagaggggc	0.323													2	0	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630848	44630848	+	3'UTR	SNP	C	T	T	rs139733485	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630848C>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						tttttttcttctcttttgaga	0.154													4	127	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630855	44630855	+	3'UTR	SNP	G	C	C	rs144516284	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630855G>C	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						cttctcttttgagacggagtt	0.139													4	125	---	---	---	---	PASS
SEPT4	5414	broad.mit.edu	37	17	56603081	56603081	+	Silent	SNP	C	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56603081C>A	uc002iwm.1	-	4	641	c.513G>T	c.(511-513)CGG>CGT	p.R171R	SEPT4_uc002iwk.1_Silent_p.R24R|SEPT4_uc010wnw.1_Silent_p.R24R|SEPT4_uc002iwl.1_Silent_p.R24R|SEPT4_uc002iwn.1_Silent_p.R72R|SEPT4_uc002iwo.1_Silent_p.R152R|SEPT4_uc002iwp.1_Silent_p.R152R|SEPT4_uc010wnx.1_Silent_p.R186R|SEPT4_uc010wny.1_Silent_p.R163R|SEPT4_uc010dcy.1_Silent_p.R53R	NM_004574	NP_004565	O43236	SEPT4_HUMAN	septin 4 isoform 1	171					apoptosis|cell cycle|cytokinesis|regulation of apoptosis	cytoskeleton|mitochondrion|nucleus	GTP binding|GTPase activity|protein binding|structural molecule activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GTTTCCGGTCCCGGTACAGAT	0.522													9	75	---	---	---	---	PASS
KIAA0195	9772	broad.mit.edu	37	17	73485346	73485346	+	Splice_Site	SNP	G	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73485346G>A	uc002jnz.3	+	8	1040	c.765_splice	c.e8-1	p.R255_splice	KIAA0195_uc010wsa.1_Splice_Site_p.R265_splice|KIAA0195_uc010wsb.1_5'Flank	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772						ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCTTTCTGCAGATGGTGCCTG	0.562													6	56	---	---	---	---	PASS
CEP192	55125	broad.mit.edu	37	18	13114353	13114353	+	Intron	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13114353C>T	uc010xac.1	+						CEP192_uc010dlf.1_RNA|CEP192_uc010xad.1_Intron|CEP192_uc002kru.2_Intron|CEP192_uc002krv.2_Intron|CEP192_uc002krw.2_Intron|CEP192_uc002krx.2_Intron|CEP192_uc002kry.2_Intron	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa											ovary(4)|pancreas(1)	5						catgtgttaccagcactccaa	0.144													13	53	---	---	---	---	PASS
MYO5B	4645	broad.mit.edu	37	18	47432966	47432966	+	Missense_Mutation	SNP	A	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47432966A>T	uc002leb.2	-	19	2525	c.2237T>A	c.(2236-2238)ATC>AAC	p.I746N		NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	746	Myosin head-like.				protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		TCGAAAGAAGATCTTGGTGCG	0.557													6	75	---	---	---	---	PASS
ZNF407	55628	broad.mit.edu	37	18	72346178	72346178	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72346178A>C	uc002llw.2	+	1	3260	c.3203A>C	c.(3202-3204)GAG>GCG	p.E1068A	ZNF407_uc010xfc.1_Missense_Mutation_p.E1068A|ZNF407_uc010dqu.1_Missense_Mutation_p.E1068A|ZNF407_uc002llu.2_Missense_Mutation_p.E1067A	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1	1068	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GCAGCAACAGAGAAGCACAAA	0.428													24	95	---	---	---	---	PASS
ZNF491	126069	broad.mit.edu	37	19	11917136	11917136	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11917136T>A	uc002mso.1	+	3	653	c.368T>A	c.(367-369)GTA>GAA	p.V123E		NM_152356	NP_689569	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	123	C2H2-type 2; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						AGATATATGGTAACGCACAGT	0.398													27	140	---	---	---	---	PASS
MACROD2	140733	broad.mit.edu	37	20	15967789	15967789	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15967789A>C	uc002wou.2	+	15	1403	c.1139A>C	c.(1138-1140)AAA>ACA	p.K380T	MACROD2_uc002wot.2_Missense_Mutation_p.K380T|MACROD2_uc002woz.2_Missense_Mutation_p.K145T|MACROD2_uc002wpb.2_Missense_Mutation_p.K145T|MACROD2_uc002wpd.2_Missense_Mutation_p.K31T	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1	380	Glu-rich.										0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				CAAGAAGAAAAAGAAGGTGAA	0.383													26	132	---	---	---	---	PASS
MYBL2	4605	broad.mit.edu	37	20	42344673	42344673	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42344673G>T	uc002xlb.1	+	14	2264	c.2049G>T	c.(2047-2049)CAG>CAT	p.Q683H	MYBL2_uc010zwj.1_Missense_Mutation_p.Q659H	NM_002466	NP_002457	P10244	MYBB_HUMAN	MYB-related protein B	683						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(3)|kidney(2)	5		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			AAGCCCGGCAGCTCCTGGGCC	0.602													25	175	---	---	---	---	PASS
LAMA5	3911	broad.mit.edu	37	20	60921136	60921136	+	Splice_Site	SNP	C	T	T	rs112620160		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60921136C>T	uc002ycq.2	-	10	1484	c.1417_splice	c.e10+1	p.P473_splice		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CAGGTGCTCACGGTAGCAGCT	0.652													4	28	---	---	---	---	PASS
EP300	2033	broad.mit.edu	37	22	41574794	41574794	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41574794A>G	uc003azl.3	+	31	7474	c.7079A>G	c.(7078-7080)GAA>GGA	p.E2360G		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	2360					apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						AACCCCATGGAACAAGGGCAT	0.577			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				10	67	---	---	---	---	PASS
SREBF2	6721	broad.mit.edu	37	22	42273293	42273293	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42273293C>T	uc003bbi.2	+	8	1616	c.1447C>T	c.(1447-1449)CTT>TTT	p.L483F	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|SREBF2_uc003bbj.2_RNA	NM_004599	NP_004590	Q12772	SRBP2_HUMAN	sterol regulatory element-binding transcription	483	Interaction with LMNA (By similarity).|Helical; (Potential).				cholesterol metabolic process	ER to Golgi transport vesicle membrane|Golgi membrane|nucleus|SREBP-SCAP-Insig complex	protein C-terminus binding			breast(2)|ovary(1)|central_nervous_system(1)	4						CTCACGGATTCTTCTGTGTGT	0.562													17	160	---	---	---	---	PASS
FBLN1	2192	broad.mit.edu	37	22	45937233	45937233	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45937233G>C	uc003bgj.1	+	9	1194	c.1047G>C	c.(1045-1047)GAG>GAC	p.E349D	FBLN1_uc003bgg.1_Missense_Mutation_p.E349D|FBLN1_uc003bgh.2_Missense_Mutation_p.E349D|FBLN1_uc010gzz.2_Missense_Mutation_p.E387D|FBLN1_uc003bgi.1_Missense_Mutation_p.E349D	NM_006486	NP_006477	P23142	FBLN1_HUMAN	fibulin 1 isoform D	349	EGF-like 4; 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)		ATCTCAACGAGGAGGGAACGC	0.537													16	57	---	---	---	---	PASS
SBF1	6305	broad.mit.edu	37	22	50903272	50903272	+	Silent	SNP	T	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50903272T>C	uc003blh.2	-	13	1602	c.1407A>G	c.(1405-1407)GAA>GAG	p.E469E	SBF1_uc011arx.1_Silent_p.E133E|SBF1_uc003bli.2_Silent_p.E470E	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	469					protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GCTCTGCCAGTTCCTGGACGT	0.657													6	85	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	24814163	24814163	+	IGR	DEL	G	-	-	rs28829106		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24814163delG								NIPAL3 (14691 upstream) : RCAN3 (15224 downstream)																							agggaaggaagggaaggaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31128133	31128135	+	IGR	DEL	TGA	-	-	rs148324120	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31128133_31128135delTGA								None (None upstream) : MATN1 (55991 downstream)																							gtggtggtggtgatggtggtggt	0.000													6	3	---	---	---	---	
MFSD2A	84879	broad.mit.edu	37	1	40429116	40429116	+	Intron	DEL	A	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40429116delA	uc001cev.2	+						MFSD2A_uc010ojb.1_Intron|MFSD2A_uc001ceu.2_Intron|MFSD2A_uc010ojc.1_Intron|MFSD2A_uc009vvy.2_Intron	NM_001136493	NP_001129965	Q8NA29	MFS2A_HUMAN	major facilitator superfamily domain containing						transmembrane transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)|pancreas(1)	2						TAAGCCTGTTAAAAAAAAAAT	0.224													4	2	---	---	---	---	
NOL10	79954	broad.mit.edu	37	2	10795333	10795333	+	Intron	DEL	A	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10795333delA	uc002raq.2	-						NOL10_uc010yje.1_Intron|NOL10_uc010yjf.1_Intron|NOL10_uc002rap.2_Intron|NOL10_uc002rar.2_Intron	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10							nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		gattctgcccaaaaaaaaaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12293377	12293378	+	Intron	INS	-	TCCT	TCCT	rs67700339		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12293377_12293378insTCCT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		ccttccttccctccttccttcc	0.000													4	2	---	---	---	---	
CAPN13	92291	broad.mit.edu	37	2	30986096	30986097	+	Intron	INS	-	C	C	rs141861649	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30986096_30986097insC	uc002rnn.2	-						CAPN13_uc002rnp.1_Intron	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					CACAGTCCAAACAGCCACTGAG	0.475													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92121304	92121307	+	IGR	DEL	ACAC	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92121304_92121307delACAC								GGT8P (151151 upstream) : FKSG73 (7852 downstream)																							gcaaagccatacacacacacacac	0.015													4	2	---	---	---	---	
LYG2	254773	broad.mit.edu	37	2	99861574	99861575	+	Intron	INS	-	A	A	rs5832869		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99861574_99861575insA	uc002szw.1	-						MRPL30_uc002szl.1_Intron|LYG2_uc010fip.1_Intron|LYG2_uc002szx.1_Intron	NM_175735	NP_783862	Q86SG7	LYG2_HUMAN	lysozyme G-like 2 precursor						cell wall macromolecule catabolic process|peptidoglycan catabolic process	extracellular region	lysozyme activity			ovary(1)	1						aactccatctcaaaaaaaaaaa	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	127274053	127274054	+	IGR	DEL	TG	-	-	rs72011578		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127274053_127274054delTG								None (None upstream) : GYPC (139630 downstream)																							tgtctatgcatgtgtgtgtgtg	0.079													2	4	---	---	---	---	
SLC25A12	8604	broad.mit.edu	37	2	172693471	172693474	+	Intron	DEL	CACA	-	-	rs3836020		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172693471_172693474delCACA	uc002uhh.2	-						SLC25A12_uc010fqh.2_Intron|SLC25A12_uc010zdv.1_Intron	NM_003705	NP_003696	O75746	CMC1_HUMAN	solute carrier family 25, member 12						gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	cacacacatgcacacacacacaca	0.284													3	3	---	---	---	---	
INPP5D	3635	broad.mit.edu	37	2	234079896	234079896	+	Intron	DEL	A	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234079896delA	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		TCCATTAGGCAAAAAAAAAAG	0.438													4	2	---	---	---	---	
GBE1	2632	broad.mit.edu	37	3	81662300	81662300	+	Intron	DEL	T	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81662300delT	uc003dqg.2	-						GBE1_uc011bgm.1_Intron	NM_000158	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		AGCTGCAGTCTTTTTTTTTTT	0.328									Glycogen_Storage_Disease_type_IV				10	5	---	---	---	---	
WWTR1	25937	broad.mit.edu	37	3	149374552	149374553	+	Intron	DEL	TC	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149374552_149374553delTC	uc003exe.2	-						WWTR1_uc003exf.2_Intron|WWTR1_uc011bns.1_Intron|WWTR1_uc003exh.2_Intron|uc010hvg.1_5'Flank|uc003exi.1_5'Flank	NM_015472	NP_056287	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1						hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity			breast(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			tctctctctttctctctctctc	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	172992494	172992494	+	IGR	DEL	C	-	-	rs79222726		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172992494delC								SPATA16 (133462 upstream) : NLGN1 (123750 downstream)																							aacaaacaaacaaaaacatgt	0.000													4	2	---	---	---	---	
CHIC2	26511	broad.mit.edu	37	4	54876121	54876122	+	3'UTR	INS	-	A	A	rs145864126	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54876121_54876122insA	uc003haj.1	-	6					PDGFRA_uc003haa.2_Intron	NM_012110	NP_036242	Q9UKJ5	CHIC2_HUMAN	cysteine-rich hydrophobic domain 2							plasma membrane	protein binding			central_nervous_system(1)	1	all_cancers(7;0.0193)|all_neural(26;0.0209)|Lung NSC(11;0.0281)|Glioma(25;0.08)		LUSC - Lung squamous cell carcinoma(32;0.00216)			TGCGGTTATTTaaaaaaaaaac	0.317			T	ETV6	AML								5	3	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21344713	21344713	+	Intron	DEL	T	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21344713delT	uc011cnn.1	+											Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						ccttccttcctttccttcctt	0.000													3	6	---	---	---	---	
SLC30A5	64924	broad.mit.edu	37	5	68414628	68414628	+	Intron	DEL	C	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68414628delC	uc003jvh.2	+						SLC30A5_uc003jvj.2_Intron|SLC30A5_uc003jvk.2_Intron|SLC30A5_uc003jvi.2_Intron	NM_022902	NP_075053	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter),						cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity			central_nervous_system(1)	1		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TAGAAAttctctttttttttt	0.144													6	3	---	---	---	---	
HSPA9	3313	broad.mit.edu	37	5	137897633	137897634	+	Intron	INS	-	T	T	rs112918142		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137897633_137897634insT	uc003ldf.2	-						HSPA9_uc011cyw.1_Intron|SNORD63_uc003ldg.2_5'Flank	NM_004134	NP_004125	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 precursor						anti-apoptosis|protein folding	cell surface|mitochondrial nucleoid	ATP binding|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACCAAGAATACttttttttttt	0.173													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151727616	151727617	+	IGR	DEL	AC	-	-	rs112050420		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151727616_151727617delAC								GLRA1 (423219 upstream) : NMUR2 (43485 downstream)																							GTGTACCTAAacacacacacac	0.277													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172631919	172631922	+	IGR	DEL	TCCC	-	-	rs10069842		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172631919_172631922delTCCC								BNIP1 (40530 upstream) : NKX2-5 (27216 downstream)																							catccttccttccctccttccatc	0.059													4	2	---	---	---	---	
BTNL8	79908	broad.mit.edu	37	5	180365545	180365545	+	Intron	DEL	T	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180365545delT	uc003mmp.2	+						BTNL8_uc003mmq.2_Intron|BTNL8_uc011dhg.1_Intron|BTNL8_uc010jll.2_Intron|BTNL8_uc010jlm.2_Intron|BTNL8_uc011dhh.1_Intron	NM_001040462	NP_001035552	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8 isoform 2 precursor							integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			cctttctttcttttttttttt	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26213271	26213272	+	IGR	DEL	TG	-	-	rs35127949		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26213271_26213272delTG								HIST1H4E (8023 upstream) : HIST1H2BG (3156 downstream)																							TAAAACTATAtgtgtgtgtgtg	0.262													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27410560	27410561	+	IGR	INS	-	GAAAGGAA	GAAAGGAA			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27410560_27410561insGAAAGGAA								ZNF391 (41333 upstream) : ZNF184 (7961 downstream)																							aaggaaggaaggaaaggaagaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	32210328	32210331	+	IGR	DEL	TTCT	-	-	rs71811489		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32210328_32210331delTTCT								NOTCH4 (18484 upstream) : C6orf10 (45972 downstream)																							ccttccttccttctttccttcctt	0.064													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	139383236	139383251	+	IGR	DEL	AAGGGAGAAAGGAAGC	-	-	rs12665587		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139383236_139383251delAAGGGAGAAAGGAAGC								C6orf115 (18797 upstream) : HECA (72998 downstream)																							gggagggaggaagggagaaaggaagcaaggaaggaa	0.009													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	151546286	151546289	+	Intron	DEL	CTTT	-	-	rs71814049	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151546286_151546289delCTTT	uc003qod.2	-											Homo sapiens cDNA clone IMAGE:4838370.																		tccttccttcctttctttctttcc	0.000													5	3	---	---	---	---	
USP42	84132	broad.mit.edu	37	7	6175634	6175634	+	Intron	DEL	T	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6175634delT	uc011jwo.1	+						USP42_uc011jwn.1_Intron|USP42_uc010kth.1_Intron|USP42_uc011jwp.1_Intron|USP42_uc011jwq.1_Intron|USP42_uc011jwr.1_Intron	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42						cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		CTAGTTATACttttttttttt	0.154													5	3	---	---	---	---	
USP42	84132	broad.mit.edu	37	7	6185692	6185693	+	Intron	INS	-	A	A			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6185692_6185693insA	uc011jwo.1	+						USP42_uc010kth.1_Intron|USP42_uc011jwp.1_Intron|USP42_uc011jwq.1_Intron|USP42_uc011jwr.1_Intron	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42						cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		gactccatctcaaaaaaaaaga	0.139													4	2	---	---	---	---	
TRA2A	29896	broad.mit.edu	37	7	23552393	23552393	+	Intron	DEL	A	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23552393delA	uc003swi.2	-						TRA2A_uc011jzb.1_Intron|TRA2A_uc011jzc.1_Intron|TRA2A_uc011jzd.1_Intron	NM_013293	NP_037425	Q13595	TRA2A_HUMAN	transformer-2 alpha						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1						tcctatctttaaaaaaaaaaa	0.104													11	5	---	---	---	---	
GLI3	2737	broad.mit.edu	37	7	42102312	42102313	+	Intron	DEL	AC	-	-	rs72131354		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42102312_42102313delAC	uc011kbh.1	-						GLI3_uc011kbg.1_Intron	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						acacacacagacacacacacac	0.287									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	49500824	49500825	+	IGR	INS	-	A	A	rs11407899		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49500824_49500825insA								CDC14C (533775 upstream) : VWC2 (312432 downstream)																							CCAAAGACTTTAAAAAAAAAAA	0.094													6	3	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90742138	90742139	+	Intron	DEL	GT	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90742138_90742139delGT	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						TGCATTACAGgtgtgtgtgtgt	0.272													4	2	---	---	---	---	
NUP205	23165	broad.mit.edu	37	7	135287861	135287861	+	Intron	DEL	T	-	-	rs145569473		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135287861delT	uc003vsw.2	+							NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						CTCAttttacttttttttttt	0.144													6	3	---	---	---	---	
TRIM24	8805	broad.mit.edu	37	7	138255390	138255390	+	Intron	DEL	T	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138255390delT	uc003vuc.2	+						TRIM24_uc003vub.2_Intron	NM_015905	NP_056989	O15164	TIF1A_HUMAN	transcriptional intermediary factor 1 alpha						cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1)	8						ACTGTTTTGGTTTTTTTTTTT	0.308													4	3	---	---	---	---	
MCPH1	79648	broad.mit.edu	37	8	6272541	6272541	+	Intron	DEL	G	-	-	rs3214738		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6272541delG	uc003wqi.2	+						MCPH1_uc003wqh.2_Intron|MCPH1_uc011kwl.1_Intron	NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin							microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		CTAGTAATTTGAAATCCTCCA	0.408													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	9140901	9140902	+	IGR	INS	-	CCCT	CCCT	rs147858248	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9140901_9140902insCCCT								PPP1R3B (131817 upstream) : TNKS (272543 downstream)																							tcctttccttcccctcccttcc	0.064													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	40266001	40266002	+	IGR	INS	-	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40266001_40266002insT								C8orf4 (253180 upstream) : ZMAT4 (122114 downstream)																							ttctttctttctccttccttac	0.000													4	2	---	---	---	---	
NSMCE2	286053	broad.mit.edu	37	8	126317202	126317203	+	Intron	INS	-	AAG	AAG	rs35212928		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126317202_126317203insAAG	uc003yrw.2	+							NM_173685	NP_775956	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			aggaaggaagaaagaaagaaaa	0.054													7	7	---	---	---	---	
RFX3	5991	broad.mit.edu	37	9	3356156	3356159	+	Intron	DEL	GGAA	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3356156_3356159delGGAA	uc003zhr.2	-						RFX3_uc010mhd.2_Intron|RFX3_uc003zhs.1_Intron|RFX3_uc003zht.1_Intron|RFX3_uc010mhe.1_Intron	NM_134428	NP_602304	P48380	RFX3_HUMAN	regulatory factor X3 isoform b						cell maturation|ciliary cell motility|cilium assembly|cilium movement involved in determination of left/right asymmetry|endocrine pancreas development|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|regulation of insulin secretion	nuclear chromatin	protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		tagaataagtggaaggaaggaagg	0.000													4	2	---	---	---	---	
C9orf11	54586	broad.mit.edu	37	9	27285128	27285131	+	Intron	DEL	TTCC	-	-	rs67807368		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27285128_27285131delTTCC	uc003zql.2	-						NCRNA00032_uc010mjd.1_5'Flank|C9orf11_uc011lnq.1_Intron	NM_020641	NP_065692	Q9NQ60	AFAF_HUMAN	Acr formation associated factor isoform 1							acrosomal membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(39;7.39e-08)|Lung(218;1.26e-05)|LUSC - Lung squamous cell carcinoma(38;0.000106)		TTCTTTTCTTTTCCtttttttttt	0.132													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68413605	68413606	+	RNA	DEL	CT	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68413605_68413606delCT	uc004aex.2	+	1		c.160_161delCT								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		TTTGCTGAAACTCTGGGGTTGA	0.609													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93814522	93814523	+	IGR	DEL	AC	-	-	rs149398704		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93814522_93814523delAC								SYK (153689 upstream) : AUH (161576 downstream)																							cctaaagactacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102150493	102150494	+	IGR	INS	-	CTTCCTTC	CTTCCTTC			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102150493_102150494insCTTCCTTC								SEC61B (157593 upstream) : NR4A3 (433643 downstream)																							ATTTGCCCTGTcttccttcctt	0.050													6	4	---	---	---	---	
PPP6C	5537	broad.mit.edu	37	9	127911822	127911822	+	3'UTR	DEL	A	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127911822delA	uc004bpg.3	-	7					PPP6C_uc010mwv.2_3'UTR|PPP6C_uc010mww.2_3'UTR|PPP6C_uc011lzr.1_3'UTR	NM_002721	NP_002712	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2						tttaaaatttaaaaaaaaaaa	0.348													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64528276	64528277	+	IGR	DEL	AC	-	-	rs34106245		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64528276_64528277delAC								ZNF365 (96505 upstream) : ADO (36239 downstream)																							acacacacatacacacacacac	0.356													4	2	---	---	---	---	
MIR606	693191	broad.mit.edu	37	10	77312184	77312184	+	5'Flank	DEL	C	-	-	rs1367290		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77312184delC	hsa-mir-606|MI0003619	+																							0						ttttttttttcccccccctct	0.000													2	4	---	---	---	---	
KCNMA1	3778	broad.mit.edu	37	10	79196716	79196717	+	Intron	DEL	AC	-	-	rs147446936		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79196716_79196717delAC	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)	TTCTTTCTTTacacacacacac	0.351													4	2	---	---	---	---	
SAA1	6288	broad.mit.edu	37	11	18291027	18291028	+	Intron	INS	-	G	G			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18291027_18291028insG	uc010rda.1	+						SAA1_uc010rdb.1_Intron	NM_000331	NP_000322	P02735	SAA_HUMAN	serum amyloid A1 preproprotein						acute-phase response|elevation of cytosolic calcium ion concentration|innate immune response|lymphocyte chemotaxis|macrophage chemotaxis|negative regulation of inflammatory response|neutrophil chemotaxis|platelet activation|positive regulation of cell adhesion|positive regulation of interleukin-1 secretion	high-density lipoprotein particle	G-protein-coupled receptor binding				0					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	GCTCAGTGTGAGGTCTGAGTGG	0.604													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39135798	39135799	+	IGR	DEL	TG	-	-	rs71982060		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39135798_39135799delTG								None (None upstream) : LRRC4C (999954 downstream)																							TTCTAACTGCtgtgtgtgtgtg	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	19566538	19566539	+	IGR	DEL	AA	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19566538_19566539delAA								PLEKHA5 (37207 upstream) : AEBP2 (26069 downstream)																							gaaataaaagaatggctattcc	0.089													1	6	---	---	---	---	
KRT1	3848	broad.mit.edu	37	12	53071751	53071752	+	Intron	INS	-	C	C			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53071751_53071752insC	uc001sau.1	-						KRT1_uc001sav.1_Intron	NM_006121	NP_006112	P04264	K2C1_HUMAN	keratin 1						complement activation, lectin pathway|epidermis development|fibrinolysis|regulation of angiogenesis|response to oxidative stress	plasma membrane	protein binding|receptor activity|structural constituent of cytoskeleton|sugar binding			ovary(1)|skin(1)	2						ACTATGTAAGGTGCTGGGAAAT	0.510													5	3	---	---	---	---	
OSBPL8	114882	broad.mit.edu	37	12	76796328	76796329	+	Intron	DEL	TA	-	-	rs140413265		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76796328_76796329delTA	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron|OSBPL8_uc001syh.1_Intron	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1						taacattttctatgtgtgccTG	0.163													4	2	---	---	---	---	
POC1B	282809	broad.mit.edu	37	12	89866188	89866189	+	Intron	DEL	AT	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89866188_89866189delAT	uc001tbc.2	-						POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc010sun.1_Intron|POC1B_uc009zsp.2_Intron|POC1B_uc009zsq.2_Intron	NM_172240	NP_758440	Q8TC44	POC1B_HUMAN	WD repeat domain 51B						cell projection organization	centriole|microtubule basal body				ovary(1)	1						CAGTAAAGTCATATTCTGCAGC	0.396													2	4	---	---	---	---	
GOLGA3	2802	broad.mit.edu	37	12	133352759	133352765	+	Intron	DEL	CTGTAGC	-	-	rs149066138	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133352759_133352765delCTGTAGC	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GCAGCAGCTGCTGTAGCCCCTCCAGCT	0.657													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	64527974	64527974	+	IGR	DEL	T	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64527974delT								OR7E156P (211273 upstream) : None (None downstream)																							ccttccttccttccttccttc	0.000													4	2	---	---	---	---	
DAPK2	23604	broad.mit.edu	37	15	64217874	64217875	+	Intron	INS	-	GCGC	GCGC	rs147933961	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64217874_64217875insGCGC	uc002amr.2	-						DAPK2_uc010uim.1_Intron	NM_014326	NP_055141	Q9UIK4	DAPK2_HUMAN	death-associated kinase 2						apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)		GCTGACTTGTAGCGcacacaca	0.327													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	14992250	14992251	+	IGR	DEL	TG	-	-	rs150570686		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14992250_14992251delTG								NOMO1 (2237 upstream) : NPIP (28813 downstream)																							tgtgtgtgtttgtgtgtgtgtg	0.366													5	3	---	---	---	---	
GDE1	51573	broad.mit.edu	37	16	19522426	19522426	+	Intron	DEL	T	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19522426delT	uc002dgh.2	-						GDE1_uc002dgi.2_Intron	NM_016641	NP_057725	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1						glycerol metabolic process|lipid metabolic process	cytoplasm|integral to membrane	glycerophosphodiester phosphodiesterase activity|glycerophosphoinositol glycerophosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3						TACTTTAAGAttttttttttt	0.164													5	5	---	---	---	---	
TMEM102	284114	broad.mit.edu	37	17	7340786	7340786	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7340786delG	uc002ggx.1	+	3	1761	c.1488delG	c.(1486-1488)AAGfs	p.K496fs	FGF11_uc010vtw.1_Intron|TMEM102_uc002ggy.1_Frame_Shift_Del_p.K496fs|FGF11_uc010cmh.1_5'Flank|FGF11_uc010cmi.2_5'Flank|FGF11_uc002ggz.2_5'Flank	NM_178518	NP_848613	Q8N9M5	TM102_HUMAN	transmembrane protein 102	496	Cytoplasmic (Potential).				regulation of apoptosis|response to cytokine stimulus|signal transduction	cell surface|integral to membrane|intracellular	protein binding				0		Prostate(122;0.173)				TGGCCCGCAAGGGGGGCGGTT	0.736													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13679923	13679924	+	IGR	INS	-	AC	AC	rs138209312	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13679923_13679924insAC								HS3ST3A1 (174679 upstream) : CDRT15P (247891 downstream)																							cacacacacagacacacacaca	0.337													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	65772750	65772750	+	IGR	DEL	G	-	-			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65772750delG								NOL11 (32484 upstream) : BPTF (49030 downstream)																							aaaaaaaaaagaaGACGTGGC	0.274													4	2	---	---	---	---	
FOXK2	3607	broad.mit.edu	37	17	80544375	80544375	+	Intron	DEL	C	-	-	rs72318042		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80544375delC	uc002kfn.2	+						FOXK2_uc002kfm.1_Intron|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			caaaggtgggccgggggggaa	0.095													4	2	---	---	---	---	
LOC644669	644669	broad.mit.edu	37	18	15323229	15323230	+	Intron	INS	-	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15323229_15323230insT	uc002ktd.1	-							NR_027417				Homo sapiens cDNA FLJ40312 fis, clone TESTI2029880.												0						CTACTCAAGTGTTTTTTAATAA	0.243													6	5	---	---	---	---	
KIAA1328	57536	broad.mit.edu	37	18	34683767	34683770	+	Intron	DEL	ACAC	-	-	rs145289192		TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34683767_34683770delACAC	uc002kzz.2	+						KIAA1328_uc002lab.2_Intron|KIAA1328_uc002lac.1_Intron|KIAA1328_uc010dnc.1_Intron	NM_020776	NP_065827	Q86T90	K1328_HUMAN	hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)		aatagcaaatacacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29310867	29310868	+	IGR	DEL	TG	-	-	rs67572574	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29310867_29310868delTG								None (None upstream) : LOC148145 (145172 downstream)																							tgtgtgtgtatgtgtgtgtgtg	0.000													3	4	---	---	---	---	
COX7A1	1346	broad.mit.edu	37	19	36642561	36642562	+	Intron	INS	-	C	C	rs150771533	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36642561_36642562insC	uc002odm.1	-							NM_001864	NP_001855	P24310	CX7A1_HUMAN	cytochrome c oxidase subunit VIIa polypeptide 1						generation of precursor metabolites and energy	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CACCCCCCCCGACCCCCCACCT	0.698													6	5	---	---	---	---	
RELB	5971	broad.mit.edu	37	19	45526689	45526692	+	Intron	DEL	TCCG	-	-	rs148255845	by1000genomes	TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45526689_45526692delTCCG	uc002paj.1	+							NM_006509	NP_006500	Q01201	RELB_HUMAN	reticuloendotheliosis viral oncogene homolog B							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00986)		cttccttccttccgtccttctttc	0.000													6	4	---	---	---	---	
GART	2618	broad.mit.edu	37	21	34906682	34906683	+	Intron	INS	-	T	T			TCGA-B8-5158-01A-01D-1421-08	TCGA-B8-5158-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34906682_34906683insT	uc002yrx.2	-						GART_uc002yrz.2_Intron|GART_uc010gmd.2_Intron|GART_uc002yry.2_Intron|GART_uc002ysa.2_Intron	NM_000819	NP_000810	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase,						'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|metal ion binding|methyltransferase activity|phosphoribosylamine-glycine ligase activity|phosphoribosylformylglycinamidine cyclo-ligase activity|phosphoribosylglycinamide formyltransferase activity|protein binding			ovary(1)	1					Pemetrexed(DB00642)	tcatgcccggcttttttttttc	0.000													4	2	---	---	---	---	
