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
AGTRAP	57085	broad.mit.edu	37	1	11808667	11808667	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11808667G>T	uc001asv.2	+	4	488	c.364G>T	c.(364-366)GGT>TGT	p.G122C	AGTRAP_uc001ast.2_3'UTR|AGTRAP_uc001asu.2_Intron|AGTRAP_uc001asw.2_Intron|AGTRAP_uc001asx.2_Intron	NM_020350	NP_065083	Q6RW13	ATRAP_HUMAN	angiotensin II receptor-associated protein	122	Cytoplasmic (Potential).|Interaction with AGTR1.					cytoplasmic vesicle membrane|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding		AGTRAP/BRAF(2)	stomach(2)	2	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.46e-06)|COAD - Colon adenocarcinoma(227;0.000256)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		GGTCCACACTGGTGAGGCCAC	0.662													12	32	---	---	---	---	PASS
HSPG2	3339	broad.mit.edu	37	1	22163388	22163388	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22163388C>G	uc001bfj.2	-	75	10302	c.10262G>C	c.(10261-10263)TGT>TCT	p.C3421S	HSPG2_uc009vqd.2_Missense_Mutation_p.C3422S	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	3421	Ig-like C2-type 20.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	GGGCACAGCACAGTGGAACTC	0.652													2	7	---	---	---	---	PASS
SPOCD1	90853	broad.mit.edu	37	1	32280096	32280096	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32280096G>A	uc001bts.1	-	2	897	c.839C>T	c.(838-840)TCA>TTA	p.S280L	SPOCD1_uc001btu.2_Missense_Mutation_p.S280L|SPOCD1_uc001btv.2_Intron	NM_144569	NP_653170	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	280					transcription, DNA-dependent					ovary(5)|breast(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		CTCAGTCCCTGAGGCACATCC	0.637													25	85	---	---	---	---	PASS
CYP4B1	1580	broad.mit.edu	37	1	47278168	47278168	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47278168G>A	uc001cqm.3	+	4	452	c.368G>A	c.(367-369)GGG>GAG	p.G123E	CYP4B1_uc009vyl.1_5'UTR|CYP4B1_uc001cqn.3_Missense_Mutation_p.G123E|CYP4B1_uc009vym.2_Missense_Mutation_p.G108E|CYP4B1_uc010omk.1_5'UTR|CYP4B1_uc010oml.1_5'UTR	NM_000779	NP_000770	P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B,	123					xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)					CCTTCCCCAGGGAGAGGCCTG	0.612													26	18	---	---	---	---	PASS
USP24	23358	broad.mit.edu	37	1	55551676	55551676	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55551676C>T	uc001cyg.3	-	53	6224	c.6224G>A	c.(6223-6225)CGA>CAA	p.R2075Q		NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24	2235					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						CACAGCAACTCGTACTTCTCT	0.408													51	40	---	---	---	---	PASS
USP24	23358	broad.mit.edu	37	1	55603512	55603512	+	Silent	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55603512C>A	uc001cyg.3	-	24	2514	c.2514G>T	c.(2512-2514)GTG>GTT	p.V838V		NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24	998					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						GTATATTATCCACAGGAGAGC	0.318													4	17	---	---	---	---	PASS
ITGB3BP	23421	broad.mit.edu	37	1	63919644	63919644	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63919644C>T	uc001dba.1	-	7	460	c.429G>A	c.(427-429)ATG>ATA	p.M143I	ITGB3BP_uc001dbb.1_Missense_Mutation_p.M182I|ITGB3BP_uc001dbc.1_RNA|ITGB3BP_uc001dbd.1_RNA|ITGB3BP_uc009wak.1_Missense_Mutation_p.M165I|ITGB3BP_uc001dbe.1_Missense_Mutation_p.M56I	NM_014288	NP_055103	Q13352	CENPR_HUMAN	integrin beta 3 binding protein	143					apoptosis|cell adhesion|CenH3-containing nucleosome assembly at centromere|induction of apoptosis by extracellular signals|mitotic prometaphase|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome, centromeric region|cytosol|membrane fraction|nucleoplasm	protein C-terminus binding|signal transducer activity				0						TCACTTTTGTCACTAAAAGAA	0.279													26	37	---	---	---	---	PASS
INSL5	10022	broad.mit.edu	37	1	67263691	67263691	+	3'UTR	SNP	T	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67263691T>A	uc001dcw.2	-	2						NM_005478	NP_005469	Q9Y5Q6	INSL5_HUMAN	insulin-like 5 precursor							extracellular region	hormone activity				0						GTATTTGCTCTTGTCTTAGCA	0.373													20	39	---	---	---	---	PASS
LRRC8B	23507	broad.mit.edu	37	1	90049602	90049602	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90049602C>T	uc001dni.2	+	7	1900	c.1393C>T	c.(1393-1395)CTC>TTC	p.L465F	LRRC8B_uc001dnh.2_Missense_Mutation_p.L465F|LRRC8B_uc001dnj.2_Missense_Mutation_p.L465F	NM_001134476	NP_001127948	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member	465	LRR 1.					integral to membrane		p.L465V(1)		ovary(2)	2		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		GCTGGTCAACCTCAAGGAGCT	0.473													48	48	---	---	---	---	PASS
LPPR4	9890	broad.mit.edu	37	1	99753705	99753705	+	Missense_Mutation	SNP	C	G	G	rs145727766		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99753705C>G	uc001dse.2	+	2	513	c.407C>G	c.(406-408)ACG>AGG	p.T136R	LPPR4_uc010oue.1_Missense_Mutation_p.T136R	NM_014839	NP_055654	Q7Z2D5	LPPR4_HUMAN	plasticity related gene 1	136	Helical; (Potential).						phosphatidate phosphatase activity			ovary(3)	3		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		CCTGCAATTACGGTAAGAATT	0.413													47	73	---	---	---	---	PASS
KCNA10	3744	broad.mit.edu	37	1	111059902	111059902	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111059902C>A	uc001dzt.1	-	1	1896	c.1508G>T	c.(1507-1509)GGC>GTC	p.G503V		NM_005549	NP_005540	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related	503						voltage-gated potassium channel complex	intracellular cyclic nucleotide activated cation channel activity|voltage-gated potassium channel activity			ovary(3)|large_intestine(1)	4		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)		TGTGGAACAGCCACCATTGGT	0.358													26	85	---	---	---	---	PASS
KCNA10	3744	broad.mit.edu	37	1	111059903	111059903	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111059903C>T	uc001dzt.1	-	1	1895	c.1507G>A	c.(1507-1509)GGC>AGC	p.G503S		NM_005549	NP_005540	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related	503						voltage-gated potassium channel complex	intracellular cyclic nucleotide activated cation channel activity|voltage-gated potassium channel activity			ovary(3)|large_intestine(1)	4		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)		GTGGAACAGCCACCATTGGTC	0.363													26	85	---	---	---	---	PASS
SELENBP1	8991	broad.mit.edu	37	1	151337064	151337064	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151337064C>T	uc001exx.2	-	12	1421	c.1374G>A	c.(1372-1374)GAG>GAA	p.E458E	SELENBP1_uc010pcy.1_Silent_p.E500E|SELENBP1_uc001exy.2_Silent_p.E355E|SELENBP1_uc001exz.2_Silent_p.E355E|SELENBP1_uc010pcz.1_Silent_p.E396E|SELENBP1_uc009wms.2_Silent_p.E294E|SELENBP1_uc009wmt.2_Silent_p.E355E|SELENBP1_uc001eya.2_Silent_p.E394E|SELENBP1_uc009wmu.2_3'UTR	NM_003944	NP_003935	Q13228	SBP1_HUMAN	selenium binding protein 1	458					protein transport	cytosol|membrane|nucleolus	protein binding|selenium binding				0	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GGTAGCGGAGCTCATGGGCAA	0.567													9	454	---	---	---	---	PASS
SHC1	6464	broad.mit.edu	37	1	154938440	154938440	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154938440G>A	uc001ffv.2	-	10	1587	c.1366C>T	c.(1366-1368)CGG>TGG	p.R456W	SHC1_uc001ffu.2_5'Flank|SHC1_uc001ffz.1_Missense_Mutation_p.R227W|SHC1_uc001ffw.2_Missense_Mutation_p.R457W|SHC1_uc001ffx.2_Missense_Mutation_p.R347W|SHC1_uc001ffy.2_Missense_Mutation_p.R346W	NM_183001	NP_892113	P29353	SHC1_HUMAN	SHC-transforming protein 1 isoform 1	456	Pro-rich.|CH1.				activation of MAPK activity|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|positive regulation of DNA replication|Ras protein signal transduction|regulation of epidermal growth factor receptor activity|regulation of growth	cytosol|mitochondrial matrix|Shc-EGFR complex	epidermal growth factor receptor binding|insulin receptor binding|insulin-like growth factor receptor binding|phospholipid binding|protein binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(1)|skin(1)	2	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			AACAGGTCCCGGGGTGCACTG	0.562													10	330	---	---	---	---	PASS
CD1A	909	broad.mit.edu	37	1	158225133	158225133	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158225133G>A	uc001frt.2	+	2	851	c.318G>A	c.(316-318)CAG>CAA	p.Q106Q		NM_001763	NP_001754	P06126	CD1A_HUMAN	CD1A antigen precursor	106	Extracellular (Potential).				antigen processing and presentation|immune response	endosome membrane|integral to plasma membrane|MHC class I protein complex				pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	ATGAATTGCAGTTTGAATGTG	0.443													22	44	---	---	---	---	PASS
CD1E	913	broad.mit.edu	37	1	158326608	158326608	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158326608G>C	uc001fse.2	+	6	1328	c.1089G>C	c.(1087-1089)CAG>CAC	p.Q363H	CD1E_uc001fsd.2_3'UTR|CD1E_uc001fsk.2_Missense_Mutation_p.Q273H|CD1E_uc001fsj.2_Missense_Mutation_p.Q206H|CD1E_uc001fsc.2_Missense_Mutation_p.Q174H|CD1E_uc010pig.1_RNA|CD1E_uc001fsa.2_Missense_Mutation_p.Q119H|CD1E_uc001fsf.2_Missense_Mutation_p.Q351H|CD1E_uc001fry.2_Missense_Mutation_p.Q296H|CD1E_uc001fsg.2_3'UTR|CD1E_uc001fsh.2_Missense_Mutation_p.Q162H|CD1E_uc001fsi.2_3'UTR|CD1E_uc009wsv.2_Missense_Mutation_p.Q264H|CD1E_uc001frz.2_Missense_Mutation_p.Q261H|CD1E_uc009wsw.2_Missense_Mutation_p.S78T	NM_030893	NP_112155	P15812	CD1E_HUMAN	CD1E antigen isoform a precursor	363					antigen processing and presentation|immune response	early endosome|Golgi membrane|integral to plasma membrane|late endosome|lysosomal lumen				skin(3)	3	all_hematologic(112;0.0378)					CAAGACATCAGTTCTGCTTGG	0.433													26	108	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158650403	158650403	+	Missense_Mutation	SNP	T	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158650403T>G	uc001fst.1	-	5	847	c.648A>C	c.(646-648)GAA>GAC	p.E216D		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	216	Spectrin 3.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					ATTGGTTCACTTCAACAACTC	0.463													86	70	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158650429	158650429	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158650429C>A	uc001fst.1	-	5	821	c.622G>T	c.(622-624)GTA>TTA	p.V208L		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	208	Spectrin 3.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					TCTTTAGCTACCAGCTCCACT	0.478													32	130	---	---	---	---	PASS
OR6K3	391114	broad.mit.edu	37	1	158686969	158686969	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158686969G>T	uc010pip.1	-	1	985	c.985C>A	c.(985-987)CCT>ACT	p.P329T		NM_001005327	NP_001005327	Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K,	329	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(112;0.0378)					TAACCTCCAGGCTTGTTCAAC	0.289													6	176	---	---	---	---	PASS
FCRL6	343413	broad.mit.edu	37	1	159776382	159776382	+	Intron	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159776382G>C	uc001fud.3	+						FCRL6_uc010pix.1_Intron|FCRL6_uc001fuc.2_Intron|FCRL6_uc009wsz.1_Intron|FCRL6_uc009wta.2_Intron	NM_001004310	NP_001004310	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6 precursor							integral to membrane				ovary(2)|skin(1)	3	all_hematologic(112;0.0597)					TTGTTCTCTTGCAGTTCCCTG	0.413													6	493	---	---	---	---	PASS
F5	2153	broad.mit.edu	37	1	169492482	169492482	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169492482G>T	uc001ggg.1	-	21	6146	c.6001C>A	c.(6001-6003)CAG>AAG	p.Q2001K		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	2001	F5/8 type C 1.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	CAGTTGATCTGGTTGGAACTG	0.438													42	111	---	---	---	---	PASS
EDEM3	80267	broad.mit.edu	37	1	184718701	184718701	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184718701G>T	uc010pok.1	-	2	445	c.184C>A	c.(184-186)CAT>AAT	p.H62N	EDEM3_uc010pol.1_RNA|EDEM3_uc010pom.1_Missense_Mutation_p.H62N|EDEM3_uc001gqy.2_Intron	NM_025191	NP_079467	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like	62					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			skin(1)	1						CCATAAGCATGATCAAACATT	0.284													3	28	---	---	---	---	PASS
FAM129A	116496	broad.mit.edu	37	1	184764870	184764870	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184764870G>A	uc001gra.2	-	14	2222	c.2028C>T	c.(2026-2028)CTC>CTT	p.L676L	FAM129A_uc001grb.1_Intron	NM_052966	NP_443198	Q9BZQ8	NIBAN_HUMAN	niban protein isoform 2	676					negative regulation of protein phosphorylation|positive regulation of protein phosphorylation|positive regulation of translation|response to endoplasmic reticulum stress	cytoplasm|nucleus|plasma membrane				ovary(3)|skin(1)	4						ATGTGCCCGGGAGTCCTGCTG	0.577													24	65	---	---	---	---	PASS
F13B	2165	broad.mit.edu	37	1	197009796	197009796	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197009796C>T	uc001gtt.1	-	11	1852	c.1808G>A	c.(1807-1809)AGA>AAA	p.R603K		NM_001994	NP_001985	P05160	F13B_HUMAN	coagulation factor XIII B subunit precursor	603	Sushi 10.				blood coagulation	extracellular region				upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						AATGTGTGGTCTATTGTCAAA	0.299													10	55	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216591901	216591901	+	Silent	SNP	T	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216591901T>G	uc001hku.1	-	3	993	c.606A>C	c.(604-606)ACA>ACC	p.T202T	USH2A_uc001hkv.2_Silent_p.T202T	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	202	Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTCTCCCCAGTGTCATTACTT	0.338										HNSCC(13;0.011)			59	87	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216591902	216591902	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216591902G>T	uc001hku.1	-	3	992	c.605C>A	c.(604-606)ACA>AAA	p.T202K	USH2A_uc001hkv.2_Missense_Mutation_p.T202K	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	202	Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TCTCCCCAGTGTCATTACTTT	0.343										HNSCC(13;0.011)			59	86	---	---	---	---	PASS
C1orf69	200205	broad.mit.edu	37	1	228362381	228362381	+	Intron	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228362381C>G	uc001hsl.3	+						C1orf69_uc010pvw.1_Intron	NM_001010867	NP_001010867	Q5T440	CAF17_HUMAN	hypothetical protein LOC200205 precursor						glycine catabolic process|heme biosynthetic process	mitochondrion	aminomethyltransferase activity				0		Prostate(94;0.0405)				GCCCCTGCCTCTCTCCCTGCA	0.647													6	3	---	---	---	---	PASS
HIST3H2BB	128312	broad.mit.edu	37	1	228645991	228645991	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228645991G>A	uc001hsz.2	+	1	184	c.161G>A	c.(160-162)GGC>GAC	p.G54D	HIST3H2A_uc001hsy.2_5'Flank	NM_175055	NP_778225	Q8N257	H2B3B_HUMAN	histone cluster 3, H2bb	54					nucleosome assembly	nucleosome|nucleus	DNA binding			skin(1)	1		Prostate(94;0.183)				CCCGACACCGGCATCTCGTCC	0.587													4	198	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237664208	237664208	+	Intron	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237664208G>T	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AATAAAGTTAGTATGTCTATG	0.403													37	48	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237670001	237670001	+	Intron	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237670001A>G	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTCTTTTTGTAAATTTTAGAT	0.353													9	20	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237787176	237787176	+	Intron	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237787176G>C	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTGTGGTAAGGTCTTTTTGAT	0.313													9	59	---	---	---	---	PASS
EXO1	9156	broad.mit.edu	37	1	242024807	242024807	+	Intron	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242024807A>G	uc001hzh.2	+						EXO1_uc001hzi.2_Intron|EXO1_uc001hzj.2_Intron|EXO1_uc009xgq.2_Intron	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b						meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			CTGCTATGGTAACGTTTTGAT	0.353								Direct_reversal_of_damage|Editing_and_processing_nucleases					42	39	---	---	---	---	PASS
OR14A16	284532	broad.mit.edu	37	1	247978180	247978180	+	Silent	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247978180G>C	uc001idm.1	-	1	852	c.852C>G	c.(850-852)CCC>CCG	p.P284P		NM_001001966	NP_001001966	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A,	284	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TGTATATAATGGGATTAAAGG	0.408													43	52	---	---	---	---	PASS
ASAP2	8853	broad.mit.edu	37	2	9474862	9474862	+	Intron	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9474862G>A	uc002qzh.2	+						ASAP2_uc002qzi.2_Intron	NM_003887	NP_003878	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0						TCTTTTTCCTGCTAGTTTTTT	0.388													17	67	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32738147	32738147	+	Silent	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32738147A>G	uc010ezu.2	+	54	10628	c.10494A>G	c.(10492-10494)GCA>GCG	p.A3498A		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	3498					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					ACTGTGTAGCAGCCATTCTGT	0.423													30	79	---	---	---	---	PASS
FSHR	2492	broad.mit.edu	37	2	49190942	49190942	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49190942C>T	uc002rww.2	-	10	1092	c.1018G>A	c.(1018-1020)GAA>AAA	p.E340K	FSHR_uc002rwx.2_Missense_Mutation_p.E278K|FSHR_uc010fbn.2_Missense_Mutation_p.E314K	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	340	Extracellular (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)	TCAACCACTTCATTGCATAAG	0.473									Gonadal_Dysgenesis_46_XX				59	159	---	---	---	---	PASS
LRRTM4	80059	broad.mit.edu	37	2	77745749	77745749	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77745749C>A	uc002snr.2	-	3	1661	c.1246G>T	c.(1246-1248)GAG>TAG	p.E416*	LRRTM4_uc002snq.2_Nonsense_Mutation_p.E416*|LRRTM4_uc002sns.2_Nonsense_Mutation_p.E416*|LRRTM4_uc002snt.2_Nonsense_Mutation_p.E417*	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	416	Extracellular (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		TGCTCATACTCTTGCTCTGCG	0.478													22	79	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90260098	90260098	+	RNA	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90260098G>C	uc010fhm.2	+	30		c.4081G>C								Parts of antibodies, mostly variable regions.																		AAGCCCCTGAGCTCCTGATCT	0.507													8	154	---	---	---	---	PASS
STEAP3	55240	broad.mit.edu	37	2	120012355	120012355	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120012355C>T	uc002tlp.2	+	5	1273	c.1116C>T	c.(1114-1116)TCC>TCT	p.S372S	STEAP3_uc002tlq.2_Silent_p.S382S|STEAP3_uc002tlr.2_Silent_p.S372S|STEAP3_uc010fle.2_Silent_p.S372S	NM_018234	NP_060704	Q658P3	STEA3_HUMAN	dudulin 2 isoform b	372	Ferric oxidoreductase.|Helical; (Potential).				apoptosis|cell cycle|cellular iron ion homeostasis|protein secretion|transferrin transport|transmembrane transport	endosome membrane|integral to membrane|multivesicular body	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			central_nervous_system(2)|skin(1)	3						GCACGTTGTCCCTGCTGGCCG	0.592													38	35	---	---	---	---	PASS
LCT	3938	broad.mit.edu	37	2	136570431	136570431	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136570431C>T	uc002tuu.1	-	7	1814	c.1803G>A	c.(1801-1803)CTG>CTA	p.L601L		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	601	Extracellular (Potential).|4 X approximate repeats.|2.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)		AGTCTGAGTTCAGCACAATGC	0.592													15	60	---	---	---	---	PASS
CHRNA1	1134	broad.mit.edu	37	2	175619132	175619132	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175619132C>T	uc002ujd.2	-	6	508	c.430G>A	c.(430-432)GAC>AAC	p.D144N	uc002uiw.2_Intron|CHRNA1_uc002uje.2_Missense_Mutation_p.D119N|CHRNA1_uc002ujf.3_Missense_Mutation_p.D119N	NM_001039523	NP_001034612	P02708	ACHA_HUMAN	nicotinic cholinergic receptor alpha 1 isoform a	144	Extracellular.				muscle cell homeostasis|neuromuscular junction development|neuromuscular process|neuromuscular synaptic transmission|neuron homeostasis|regulation of action potential in neuron|skeletal muscle contraction|skeletal muscle tissue growth	cell junction|cell surface|neuromuscular junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(2)|central_nervous_system(1)|skin(1)	4						ATAGCAAAGTCACCATCTGCA	0.463													34	31	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178098960	178098960	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178098960C>G	uc002ulh.3	-	2	640	c.85G>C	c.(85-87)GAT>CAT	p.D29H	NFE2L2_uc002ulg.3_Missense_Mutation_p.D13H|NFE2L2_uc010zfa.1_Missense_Mutation_p.D13H|NFE2L2_uc002uli.3_Missense_Mutation_p.D13H|NFE2L2_uc010fra.2_Missense_Mutation_p.D13H|NFE2L2_uc010frb.2_Missense_Mutation_p.D13H	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	29					transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ACTCCAAGATCTATATCTTGC	0.363			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			40	34	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179498792	179498792	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179498792A>T	uc010zfg.1	-	180	34954	c.34730T>A	c.(34729-34731)ATG>AAG	p.M11577K	TTN_uc010zfh.1_Missense_Mutation_p.M5272K|TTN_uc010zfi.1_Missense_Mutation_p.M5205K|TTN_uc010zfj.1_Missense_Mutation_p.M5080K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	12504							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGAGGTGACATGAATTTCAG	0.353													21	92	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179501193	179501193	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179501193C>T	uc010zfg.1	-	174	33781	c.33557G>A	c.(33556-33558)GGT>GAT	p.G11186D	TTN_uc010zfh.1_Missense_Mutation_p.G4881D|TTN_uc010zfi.1_Missense_Mutation_p.G4814D|TTN_uc010zfj.1_Missense_Mutation_p.G4689D|TTN_uc010fre.1_Missense_Mutation_p.G1047D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	12113							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTGTATTCACCAGCATCGGA	0.398													18	64	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179526556	179526556	+	Silent	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179526556G>C	uc010zfk.1	-	23	2039	c.1491C>G	c.(1489-1491)CCC>CCG	p.P497P	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron			Q8WZ42	TITIN_HUMAN	SubName: Full=Titin; Flags: Fragment;	11734							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAACTTCTTTGGGAGCCTCTG	0.413													29	36	---	---	---	---	PASS
SATB2	23314	broad.mit.edu	37	2	200193544	200193544	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200193544G>A	uc002uuy.1	-	8	2080	c.1263C>T	c.(1261-1263)TTC>TTT	p.F421F	SATB2_uc010fsq.1_Silent_p.F303F|SATB2_uc002uuz.1_Silent_p.F421F|SATB2_uc002uva.1_Silent_p.F421F	NM_015265	NP_056080	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	421	CUT 1.					cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1						GCAGATTGAGGAAATTCTGCA	0.517													16	70	---	---	---	---	PASS
ALS2CR12	130540	broad.mit.edu	37	2	202213034	202213034	+	Intron	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202213034G>A	uc010ftg.2	-						ALS2CR12_uc002uya.3_Intron|ALS2CR12_uc010fth.2_Intron	NM_139163	NP_631902	Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)						regulation of GTPase activity		protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3						TTCTGCAAGAGAAAGACATGC	0.418													46	57	---	---	---	---	PASS
TRAK2	66008	broad.mit.edu	37	2	202254569	202254569	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202254569C>A	uc002uyb.3	-	11	1594	c.1148G>T	c.(1147-1149)CGT>CTT	p.R383L		NM_015049	NP_055864	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	383	Interaction with HGS (By similarity).			Missing (in Ref. 2).		early endosome|plasma membrane	GABA receptor binding				0						CAGCTTTTTACGCATAGTCCC	0.348													44	187	---	---	---	---	PASS
INO80D	54891	broad.mit.edu	37	2	206869731	206869731	+	Silent	SNP	T	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206869731T>C	uc002vaz.3	-	11	2850	c.2445A>G	c.(2443-2445)CAA>CAG	p.Q815Q		NM_017759	NP_060229	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	815					DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1						CACTGCTGTATTGCTGTCGTG	0.537													66	261	---	---	---	---	PASS
ZDBF2	57683	broad.mit.edu	37	2	207172252	207172252	+	Silent	SNP	A	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207172252A>C	uc002vbp.2	+	5	3250	c.3000A>C	c.(2998-3000)ACA>ACC	p.T1000T		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1000							nucleic acid binding|zinc ion binding			ovary(3)	3						GTTCAAAAACAAGTTTAGATT	0.358													21	80	---	---	---	---	PASS
UGT1A5	54579	broad.mit.edu	37	2	234622111	234622111	+	Silent	SNP	G	A	A	rs147117995	byFrequency	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234622111G>A	uc002vuw.2	+	1	474	c.474G>A	c.(472-474)GCG>GCA	p.A158A	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Silent_p.A158A	NM_019078	NP_061951	P35504	UD15_HUMAN	UDP glycosyltransferase 1 family, polypeptide A5	158					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		ACCTCTGCGCGGCGGTGCTGG	0.493													4	225	---	---	---	---	PASS
CNTN3	5067	broad.mit.edu	37	3	74385786	74385786	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74385786C>G	uc003dpm.1	-	11	1468	c.1388G>C	c.(1387-1389)GGA>GCA	p.G463A		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor	463	Ig-like C2-type 5.				cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		TATTTTGAGTCCTCCATCGTT	0.323													20	40	---	---	---	---	PASS
PROS1	5627	broad.mit.edu	37	3	93624922	93624922	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93624922T>C	uc003drb.3	-	5	753	c.412A>G	c.(412-414)AAA>GAA	p.K138E	PROS1_uc010hoo.2_Missense_Mutation_p.K7E|PROS1_uc003dqz.3_Missense_Mutation_p.K7E	NM_000313	NP_000304	P07225	PROS_HUMAN	protein S, alpha preproprotein	138	EGF-like 1.				leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)	AAAGAAGCTTTTCCATCTTTG	0.418													51	369	---	---	---	---	PASS
PLA1A	51365	broad.mit.edu	37	3	119347676	119347676	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119347676G>A	uc003ecu.2	+	10	1289	c.1250G>A	c.(1249-1251)GGG>GAG	p.G417E	PLA1A_uc003ecv.2_Missense_Mutation_p.G401E|PLA1A_uc003ecw.2_RNA|PLA1A_uc011bjc.1_Missense_Mutation_p.G244E	NM_015900	NP_056984	Q53H76	PLA1A_HUMAN	phospholipase A1 member A precursor	417	Involved in the recognition of diacyl- phospholipids.				lipid catabolic process|phosphatidylserine metabolic process	extracellular region	phospholipase A1 activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						ACCATTATTGGGAAGTTCTGC	0.463													31	226	---	---	---	---	PASS
TMCC1	23023	broad.mit.edu	37	3	129547121	129547121	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129547121A>G	uc003emz.3	-	4	602	c.101T>C	c.(100-102)TTG>TCG	p.L34S	TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	34						integral to membrane				skin(1)	1						CATTTTAGACAATTTTTGTTC	0.483													70	294	---	---	---	---	PASS
EPHB1	2047	broad.mit.edu	37	3	134670776	134670776	+	Silent	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134670776A>G	uc003eqt.2	+	3	907	c.687A>G	c.(685-687)GCA>GCG	p.A229A	EPHB1_uc010htz.1_RNA|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	229	Extracellular (Potential).|Cys-rich.					integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						TCCCCAACGCAGAGGAAGTGG	0.547													393	218	---	---	---	---	PASS
IL20RB	53833	broad.mit.edu	37	3	136710897	136710897	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136710897G>A	uc003eri.1	+	5	898	c.649G>A	c.(649-651)GCC>ACC	p.A217T	IL20RB_uc003erj.1_Intron|IL20RB_uc010hud.1_Missense_Mutation_p.A75T	NM_144717	NP_653318	Q6UXL0	I20RB_HUMAN	interleukin 20 receptor beta precursor	217	Extracellular (Potential).|Fibronectin type-III 2.					integral to membrane	receptor activity			ovary(1)	1						GAGGTACAGCGCCTTCAGCCA	0.572													29	166	---	---	---	---	PASS
MRAS	22808	broad.mit.edu	37	3	138117349	138117349	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138117349A>G	uc003esh.3	+	4	947	c.386A>G	c.(385-387)GAT>GGT	p.D129G	MRAS_uc011bmi.1_Missense_Mutation_p.D53G|MRAS_uc003esi.3_Missense_Mutation_p.D129G|MRAS_uc011bmj.1_Missense_Mutation_p.D53G	NM_012219	NP_036351	O14807	RASM_HUMAN	muscle RAS oncogene homolog precursor	129	GTP (By similarity).				actin cytoskeleton organization|muscle organ development|Ras protein signal transduction	intracellular|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity			lung(2)|upper_aerodigestive_tract(1)|ovary(1)	4						AACAAGGTCGATTTGATGCAC	0.512													5	235	---	---	---	---	PASS
MME	4311	broad.mit.edu	37	3	154834694	154834694	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154834694G>A	uc010hvr.1	+	7	784	c.573G>A	c.(571-573)CTG>CTA	p.L191L	MME_uc003fab.1_Silent_p.L191L|MME_uc003fac.1_Silent_p.L191L|MME_uc003fad.1_Silent_p.L191L|MME_uc003fae.1_Silent_p.L191L	NM_007289	NP_009220	P08473	NEP_HUMAN	membrane metallo-endopeptidase	191	Extracellular (Potential).				cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)	TTGCACAACTGAATTCTAAAT	0.289													159	89	---	---	---	---	PASS
RTP1	132112	broad.mit.edu	37	3	186917714	186917714	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186917714C>T	uc003frg.2	+	2	678	c.648C>T	c.(646-648)ACC>ACT	p.T216T		NM_153708	NP_714919	P59025	RTP1_HUMAN	receptor transporting protein 1	216	Cytoplasmic (Potential).				protein insertion into membrane	cell surface|integral to membrane|plasma membrane	olfactory receptor binding			ovary(2)|breast(1)	3	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		CCACCTACACCTTCTCCCGGG	0.667													4	209	---	---	---	---	PASS
LEPREL1	55214	broad.mit.edu	37	3	189692442	189692442	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189692442C>T	uc011bsk.1	-	9	1745	c.1357G>A	c.(1357-1359)GTC>ATC	p.V453I	LEPREL1_uc003fsg.2_Missense_Mutation_p.V272I	NM_018192	NP_060662	Q8IVL5	P3H2_HUMAN	leprecan-like 1 isoform a	453					collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	GAGTTGTAGACGAATGTGATG	0.537													18	216	---	---	---	---	PASS
SENP5	205564	broad.mit.edu	37	3	196613165	196613165	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196613165G>A	uc003fwz.3	+	2	1362	c.1113G>A	c.(1111-1113)CTG>CTA	p.L371L	SENP5_uc011bty.1_Silent_p.L371L	NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	371					cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		GTACAGAGCTGATTCATGACA	0.438													12	202	---	---	---	---	PASS
ZNF595	152687	broad.mit.edu	37	4	53386	53386	+	Splice_Site	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53386G>T	uc003fzv.1	+	1	159	c.3_splice	c.e1+1	p.M1_splice	ZNF595_uc003fzu.1_Splice_Site|ZNF718_uc003fzt.3_Splice_Site_p.M1_splice|ZNF595_uc010iay.1_Splice_Site|ZNF595_uc011bus.1_Splice_Site|ZNF595_uc011but.1_Splice_Site	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TCGGGAAATGGTGAGTGTGCG	0.642													31	382	---	---	---	---	PASS
PCDH7	5099	broad.mit.edu	37	4	30724344	30724344	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30724344G>A	uc003gsk.1	+	1	2308	c.1300G>A	c.(1300-1302)GAG>AAG	p.E434K	PCDH7_uc011bxw.1_Missense_Mutation_p.E387K|PCDH7_uc011bxx.1_Missense_Mutation_p.E434K	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	434	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						CAACGTGGCCGAGGACGTTCT	0.627													32	11	---	---	---	---	PASS
GABRG1	2565	broad.mit.edu	37	4	46125865	46125865	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46125865C>T	uc003gxb.2	-	1	218	c.66G>A	c.(64-66)AGG>AGA	p.R22R		NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1	22					gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)		AGAAGACCAACCTCACCCCTC	0.453													22	13	---	---	---	---	PASS
PDGFRA	5156	broad.mit.edu	37	4	55136842	55136842	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55136842C>A	uc003han.3	+	8	1495	c.1164C>A	c.(1162-1164)GAC>GAA	p.D388E	PDGFRA_uc003haa.2_Intron|PDGFRA_uc010igq.1_Missense_Mutation_p.D282E|PDGFRA_uc003ham.2_RNA	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	388	Ig-like C2-type 4.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	AGGAAGAAGACAGTGGCCATT	0.338			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			46	38	---	---	---	---	PASS
SRD5A3	79644	broad.mit.edu	37	4	56212685	56212685	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56212685C>T	uc003hau.2	+	1	277	c.182C>T	c.(181-183)TCG>TTG	p.S61L		NM_024592	NP_078868	Q9H8P0	PORED_HUMAN	steroid 5 alpha-reductase 3	61	Lumenal (Potential).				androgen biosynthetic process|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|polyprenol catabolic process	endoplasmic reticulum membrane|integral to membrane	3-oxo-5-alpha-steroid 4-dehydrogenase activity|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor				0	all_cancers(7;0.0308)|all_lung(4;0.00195)|Lung NSC(11;0.00431)|all_epithelial(27;0.0425)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.0179)			GGGGAGCCGTCGCGCCCCGCC	0.706													15	1	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123230459	123230459	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123230459G>C	uc003ieh.2	+	57	10137	c.10092G>C	c.(10090-10092)TTG>TTC	p.L3364F	KIAA1109_uc003iel.1_Missense_Mutation_p.L1299F	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	3364					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						GTTCTGCTTTGGTATTAACCA	0.353													56	35	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187524342	187524342	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187524342A>T	uc003izf.2	-	19	11526	c.11338T>A	c.(11338-11340)TGT>AGT	p.C3780S		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	3780	Extracellular (Potential).				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						TTGCAGAGACACACCGCTGCC	0.498										HNSCC(5;0.00058)			8	15	---	---	---	---	PASS
TERT	7015	broad.mit.edu	37	5	1253924	1253924	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1253924C>T	uc003jcb.1	-	16	3376	c.3318G>A	c.(3316-3318)AAG>AAA	p.K1106K	TERT_uc003jbz.1_Silent_p.K302K|TERT_uc003jca.1_Silent_p.K1094K|TERT_uc003jcc.1_Silent_p.K1043K|TERT_uc003jcd.1_RNA|TERT_uc003jce.1_RNA	NM_198253	NP_937983	O14746	TERT_HUMAN	telomerase reverse transcriptase isoform 1	1106	CTE.				anti-apoptosis|DNA strand elongation|replicative senescence|telomere formation via telomerase|telomere maintenance via telomerase	cytoplasm|nucleolus|PML body|telomerase holoenzyme complex	protein homodimerization activity|telomeric DNA binding|telomeric RNA binding|telomeric template RNA reverse transcriptase activity			lung(7)|ovary(2)|central_nervous_system(2)|skin(1)	12	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			TCCCCGGGAGCTTCCGACTCA	0.657									TERT_Mutation-Associated_Haematological_Disorders|Congenital_Dyskeratosis|Pulmonary_Fibrosis_Idiopathic				9	12	---	---	---	---	PASS
SEMA5A	9037	broad.mit.edu	37	5	9226976	9226976	+	Intron	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9226976C>T	uc003jek.2	-							NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						AAAAAGAAGCCATACCGAGCG	0.438													24	125	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24511474	24511474	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24511474C>T	uc003jgr.1	-	6	1296	c.964G>A	c.(964-966)GAG>AAG	p.E322K	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	322	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		GTGTCCTTCTCAGTCACGATG	0.413										HNSCC(23;0.051)			128	201	---	---	---	---	PASS
TTC23L	153657	broad.mit.edu	37	5	34863137	34863137	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34863137G>A	uc003jiu.2	+	5	617	c.514G>A	c.(514-516)GTG>ATG	p.V172M	TTC23L_uc003jiv.2_5'Flank|TTC23L_uc010iut.1_5'Flank	NM_144725	NP_653326	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like	172							binding			central_nervous_system(1)	1						CACTCTGGGCGTGGCCTGGCT	0.517													6	189	---	---	---	---	PASS
UGT3A2	167127	broad.mit.edu	37	5	36051998	36051998	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36051998G>T	uc003jjz.1	-	3	378	c.285C>A	c.(283-285)TTC>TTA	p.F95L	UGT3A2_uc011cos.1_Missense_Mutation_p.F61L|UGT3A2_uc011cot.1_5'UTR	NM_174914	NP_777574	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	95	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTTCCAGAAAGAAATCAAAAC	0.308													33	62	---	---	---	---	PASS
OSMR	9180	broad.mit.edu	37	5	38921735	38921735	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38921735G>A	uc003jln.1	+	12	1971	c.1604G>A	c.(1603-1605)AGA>AAA	p.R535K	OSMR_uc011cpj.1_5'UTR	NM_003999	NP_003990	Q99650	OSMR_HUMAN	oncostatin M receptor precursor	535	Fibronectin type-III 3.|Extracellular (Potential).				cell proliferation|positive regulation of cell proliferation	oncostatin-M receptor complex	growth factor binding|oncostatin-M receptor activity			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	all_lung(31;0.000365)					GAGGAAGAAAGAATTGCAGGC	0.398													44	87	---	---	---	---	PASS
HEATR7B2	133558	broad.mit.edu	37	5	41009428	41009428	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41009428A>T	uc003jmj.3	-	32	3864	c.3374T>A	c.(3373-3375)CTG>CAG	p.L1125Q	HEATR7B2_uc003jmi.3_Missense_Mutation_p.L680Q	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	1125	HEAT 12.						binding			ovary(6)|central_nervous_system(2)	8						CTCAGTCTCCAGTTTGTCTAT	0.502													72	112	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127729049	127729049	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127729049C>T	uc003kuu.2	-	10	1683	c.1244G>A	c.(1243-1245)AGA>AAA	p.R415K	FBN2_uc003kuv.2_Missense_Mutation_p.R382K	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	415	TB 2.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CATGCAAAGTCTGCGATATTC	0.478													55	30	---	---	---	---	PASS
TRPC7	57113	broad.mit.edu	37	5	135583342	135583342	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135583342C>A	uc003lbn.1	-	6	1661	c.1658G>T	c.(1657-1659)CGC>CTC	p.R553L	TRPC7_uc010jef.1_Missense_Mutation_p.R490L|TRPC7_uc010jeg.1_RNA|TRPC7_uc010jeh.1_Missense_Mutation_p.R484L|TRPC7_uc010jei.1_Missense_Mutation_p.R429L|TRPC7_uc010jej.1_Missense_Mutation_p.R105L	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,	554	Helical; (Potential).				axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GTATGCAATGCGAGAGAAGCT	0.498													70	32	---	---	---	---	PASS
PCDHA7	56141	broad.mit.edu	37	5	140214080	140214080	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140214080G>A	uc003lhq.2	+	1	112	c.112G>A	c.(112-114)GAG>AAG	p.E38K	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Missense_Mutation_p.E38K	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	38	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTCCCCGAGGAGGCTAAACA	0.617													89	44	---	---	---	---	PASS
PCDH1	5097	broad.mit.edu	37	5	141243253	141243253	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141243253C>A	uc003llq.2	-	3	2760	c.2643G>T	c.(2641-2643)GAG>GAT	p.E881D	PCDH1_uc003llp.2_Missense_Mutation_p.E881D|PCDH1_uc011dbf.1_Missense_Mutation_p.E859D	NM_002587	NP_002578	Q08174	PCDH1_HUMAN	protocadherin 1 isoform 1 precursor	881	Cytoplasmic (Potential).				cell-cell signaling|homophilic cell adhesion|nervous system development	cell-cell junction|integral to plasma membrane	calcium ion binding			ovary(5)	5		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		CACTTTTGGCCTCCCGCTGTC	0.582													200	104	---	---	---	---	PASS
RNF145	153830	broad.mit.edu	37	5	158603839	158603839	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158603839A>G	uc003lxp.2	-	5	735	c.422T>C	c.(421-423)ATG>ACG	p.M141T	RNF145_uc011ddy.1_Missense_Mutation_p.M155T|RNF145_uc003lxo.1_Missense_Mutation_p.M169T|RNF145_uc011ddz.1_Missense_Mutation_p.M158T|RNF145_uc010jiq.1_Missense_Mutation_p.M171T|RNF145_uc011dea.1_Missense_Mutation_p.M157T	NM_144726	NP_653327	Q96MT1	RN145_HUMAN	ring finger protein 145	141	Helical; (Potential).					integral to membrane	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTTTGTTTTCATGACACAGGA	0.363													3	28	---	---	---	---	PASS
FOXI1	2299	broad.mit.edu	37	5	169533492	169533492	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169533492C>T	uc003mai.3	+	1	576	c.531C>T	c.(529-531)CTC>CTT	p.L177L	FOXI1_uc003maj.3_Silent_p.L177L	NM_012188	NP_036320	Q12951	FOXI1_HUMAN	forkhead box I1 isoform a	177	Fork-head.				epidermal cell fate specification|otic placode formation|pattern specification process|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	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 activator activity|transcription factor binding|transcription regulatory region DNA binding			breast(3)|central_nervous_system(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACCTGTCGCTCAACGACTGCT	0.592									Pendred_syndrome				15	13	---	---	---	---	PASS
GCNT2	2651	broad.mit.edu	37	6	10586481	10586481	+	Intron	SNP	C	G	G	rs11966400		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10586481C>G	uc010joo.2	+						GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Intron|GCNT2_uc003mzd.2_Intron|GCNT2_uc003mze.2_Missense_Mutation_p.P87A	NM_145649	NP_663624	Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2,							Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		CATCACAAGTCCCCTGTCGGA	0.448													19	68	---	---	---	---	PASS
TRIM38	10475	broad.mit.edu	37	6	25983831	25983831	+	Silent	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25983831G>T	uc003nfm.2	+	8	1749	c.1314G>T	c.(1312-1314)CCG>CCT	p.P438P	TRIM38_uc003nfn.2_Silent_p.P420P|TRIM38_uc010jqd.2_Silent_p.P74P	NM_006355	NP_006346	O00635	TRI38_HUMAN	tripartite motif-containing 38	438	B30.2/SPRY.				positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular	signal transducer activity|zinc ion binding				0						TTACTTTCCCGAAGGCTTCCT	0.478													47	36	---	---	---	---	PASS
MOCS1	4337	broad.mit.edu	37	6	39874178	39874178	+	Silent	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39874178G>C	uc003opb.2	-	10	2004	c.1866C>G	c.(1864-1866)CTC>CTG	p.L622L	MOCS1_uc003opa.2_3'UTR|MOCS1_uc003opc.2_Silent_p.L606L|MOCS1_uc003opd.2_3'UTR|MOCS1_uc003ope.2_Silent_p.L519L	NM_005942	NP_005933	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis-step 1 protein	622	Molybdenum cofactor biosynthesis protein C.				Mo-molybdopterin cofactor biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding			ovary(1)|liver(1)|central_nervous_system(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					TCTTGCTAATGAGCTTGATCT	0.602													103	59	---	---	---	---	PASS
GPR110	266977	broad.mit.edu	37	6	46977155	46977155	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46977155G>A	uc003oyt.2	-	11	2215	c.2016C>T	c.(2014-2016)TTC>TTT	p.F672F	GPR110_uc011dwl.1_Silent_p.F360F	NM_153840	NP_722582	Q5T601	GP110_HUMAN	G-protein coupled receptor 110 isoform 1	672	Helical; Name=3; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|pancreas(1)	3						GCATCCAGAAGAACAAAGAGA	0.502													18	9	---	---	---	---	PASS
BEND3	57673	broad.mit.edu	37	6	107391717	107391717	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107391717G>A	uc003prs.2	-	5	1328	c.678C>T	c.(676-678)CGC>CGT	p.R226R		NM_001080450	NP_001073919	Q5T5X7	BEND3_HUMAN	BEN domain containing 3	226										ovary(3)	3						GCTTCTTGATGCGGCTCACCT	0.572													46	24	---	---	---	---	PASS
HDAC9	9734	broad.mit.edu	37	7	18674283	18674283	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18674283G>T	uc003suh.2	+	7	862	c.821G>T	c.(820-822)GGT>GTT	p.G274V	HDAC9_uc003sue.2_Missense_Mutation_p.G274V|HDAC9_uc011jyd.1_Missense_Mutation_p.G274V|HDAC9_uc003sui.2_Missense_Mutation_p.G277V|HDAC9_uc003suj.2_Missense_Mutation_p.G233V|HDAC9_uc011jya.1_Missense_Mutation_p.G271V|HDAC9_uc003sua.1_Missense_Mutation_p.G252V|HDAC9_uc011jyb.1_Missense_Mutation_p.G230V|HDAC9_uc003sud.1_Missense_Mutation_p.G274V|HDAC9_uc011jyc.1_Missense_Mutation_p.G233V|HDAC9_uc003suf.1_Missense_Mutation_p.G305V|HDAC9_uc010kud.1_Missense_Mutation_p.G277V|HDAC9_uc011jye.1_Missense_Mutation_p.G246V|HDAC9_uc011jyf.1_Missense_Mutation_p.G197V|HDAC9_uc010kue.1_Missense_Mutation_p.G17V	NM_058176	NP_478056	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 1	274	Interaction with MAPK10 (By similarity).				B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)	CCAGGCTCTGGTCCCAGTTCA	0.423													10	10	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21639577	21639577	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21639577A>T	uc003svc.2	+	15	2871	c.2840A>T	c.(2839-2841)CAA>CTA	p.Q947L		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	947	Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						TTTCAAGCACAAATGATCTTG	0.403									Kartagener_syndrome				15	53	---	---	---	---	PASS
NEUROD6	63974	broad.mit.edu	37	7	31378049	31378049	+	Silent	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31378049G>T	uc003tch.2	-	2	1187	c.834C>A	c.(832-834)ACC>ACA	p.T278T		NM_022728	NP_073565	Q96NK8	NDF6_HUMAN	neurogenic differentiation 6	278					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)	2						CATAGTCCAAGGTTTCTTCTT	0.493													66	66	---	---	---	---	PASS
TBL2	26608	broad.mit.edu	37	7	72985210	72985210	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72985210C>A	uc003tyh.2	-	7	1105	c.971G>T	c.(970-972)GGC>GTC	p.G324V	TBL2_uc011kex.1_Missense_Mutation_p.G288V|TBL2_uc010lbg.2_Missense_Mutation_p.G229V|TBL2_uc003tyi.2_Missense_Mutation_p.G159V|TBL2_uc011key.1_Missense_Mutation_p.G195V|TBL2_uc010lbh.2_Missense_Mutation_p.G229V	NM_012453	NP_036585	Q9Y4P3	TBL2_HUMAN	transducin (beta)-like 2	324											0		Lung NSC(55;0.0659)|all_lung(88;0.152)				TTCAAAGCGGCCTGTCTTCAG	0.582													27	83	---	---	---	---	PASS
GRM3	2913	broad.mit.edu	37	7	86415870	86415870	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86415870G>T	uc003uid.2	+	3	1861	c.762G>T	c.(760-762)AAG>AAT	p.K254N	GRM3_uc010lef.2_Missense_Mutation_p.K252N|GRM3_uc010leg.2_Missense_Mutation_p.K126N|GRM3_uc010leh.2_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	254	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	ACATCCGCAAGTCCTACGACA	0.632													27	41	---	---	---	---	PASS
ZNF804B	219578	broad.mit.edu	37	7	88964707	88964707	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88964707G>T	uc011khi.1	+	4	2949	c.2411G>T	c.(2410-2412)TGC>TTC	p.C804F		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	804						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TATTGTCACTGCAGAGAAAGA	0.358										HNSCC(36;0.09)			34	50	---	---	---	---	PASS
HEPACAM2	253012	broad.mit.edu	37	7	92844914	92844914	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92844914A>G	uc003umm.2	-	3	538	c.515T>C	c.(514-516)GTG>GCG	p.V172A	HEPACAM2_uc003uml.2_Missense_Mutation_p.V160A|HEPACAM2_uc010lff.2_Missense_Mutation_p.V160A|HEPACAM2_uc011khy.1_Missense_Mutation_p.V195A	NM_001039372	NP_001034461	A8MVW5	HECA2_HUMAN	HEPACAM family member 2 isoform 1	172	Ig-like C2-type 1.|Extracellular (Potential).					integral to membrane				ovary(3)|breast(1)|kidney(1)	5						GCCCCCTTCCACATGGCATGT	0.507													48	48	---	---	---	---	PASS
TRRAP	8295	broad.mit.edu	37	7	98546248	98546248	+	Silent	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98546248A>G	uc003upp.2	+	34	4916	c.4707A>G	c.(4705-4707)ACA>ACG	p.T1569T	TRRAP_uc011kis.1_Silent_p.T1551T|TRRAP_uc003upr.2_Silent_p.T1268T	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	1569					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			CCTCGCAGACAGTGGAGCTGT	0.532													41	119	---	---	---	---	PASS
CCDC136	64753	broad.mit.edu	37	7	128446399	128446399	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128446399C>T	uc003vnv.1	+	8	1565	c.1198C>T	c.(1198-1200)CGG>TGG	p.R400W	CCDC136_uc003vnu.1_Intron|CCDC136_uc003vnw.1_Intron|CCDC136_uc003vnx.1_Missense_Mutation_p.R216W|CCDC136_uc010llq.1_5'UTR|CCDC136_uc003vny.1_Missense_Mutation_p.R10W	NM_022742	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	400						integral to membrane	protein binding			ovary(2)	2						GACTGAGCTCCGGCAGCTCAA	0.483													10	11	---	---	---	---	PASS
DGKI	9162	broad.mit.edu	37	7	137237168	137237168	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137237168C>A	uc003vtt.2	-	20	2095	c.2094G>T	c.(2092-2094)CAG>CAT	p.Q698H	DGKI_uc003vtu.2_Missense_Mutation_p.Q398H	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	698					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3						CCATGTTGGCCTGATTCCTCA	0.493													90	97	---	---	---	---	PASS
DGKI	9162	broad.mit.edu	37	7	137266637	137266637	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137266637C>G	uc003vtt.2	-	15	1602	c.1601G>C	c.(1600-1602)GGA>GCA	p.G534A	DGKI_uc003vtu.2_Missense_Mutation_p.G234A	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	534					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3						GGCATCAAATCCAAGGCTGAA	0.443													38	51	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142008567	142008567	+	Intron	SNP	T	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142008567T>C	uc011kro.1	+						uc011krp.1_5'Flank|uc003vxf.3_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		TCTGCTTCTTTCCTTTGCAGG	0.493													13	46	---	---	---	---	PASS
EPHB6	2051	broad.mit.edu	37	7	142561730	142561730	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142561730G>T	uc011kst.1	+	7	959	c.172G>T	c.(172-174)GAG>TAG	p.E58*	EPHB6_uc011ksu.1_Nonsense_Mutation_p.E58*|EPHB6_uc003wbs.2_5'UTR|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_5'UTR	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	58	Extracellular (Potential).					extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19	Melanoma(164;0.059)					GCAGTGGGACGAGGTGAGTGT	0.592													4	299	---	---	---	---	PASS
ZNF786	136051	broad.mit.edu	37	7	148777812	148777812	+	Intron	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148777812G>A	uc003wfh.2	-						ZNF786_uc011kuk.1_Intron|ZNF786_uc003wfi.2_Intron	NM_152411	NP_689624	Q8N393	ZN786_HUMAN	zinc finger protein 786						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|skin(1)	4	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			AGAGGTAGCTGAAATTGTAGA	0.398													30	55	---	---	---	---	PASS
ZNF746	155061	broad.mit.edu	37	7	149172312	149172312	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149172312C>G	uc003wfw.2	-	7	1369	c.1098G>C	c.(1096-1098)GAG>GAC	p.E366D	ZNF746_uc010lpi.2_Missense_Mutation_p.E367D	NM_152557	NP_689770	Q6NUN9	ZN746_HUMAN	zinc finger protein 746 isoform 2	366					negative regulation of transcription, DNA-dependent|neuron death|regulation of cell death|transcription, DNA-dependent	cytoplasm|nucleus	transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|breast(1)	3	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CAGGAGGGGTCTCCTCCTGGG	0.701													23	36	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	4494992	4494992	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4494992G>A	uc011kwk.1	-	2	564	c.174C>T	c.(172-174)TGC>TGT	p.C58C		NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	58	Extracellular (Potential).|CUB 1.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TGATCCAGGTGCAGTTGGCAT	0.478													32	68	---	---	---	---	PASS
MYBL1	4603	broad.mit.edu	37	8	67507919	67507919	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67507919C>T	uc003xwj.2	-	6	993	c.586G>A	c.(586-588)GAT>AAT	p.D196N	MYBL1_uc003xwl.2_Missense_Mutation_p.D196N|MYBL1_uc003xwk.2_Missense_Mutation_p.D196N	NM_001080416	NP_001073885	P10243	MYBA_HUMAN	v-myb myeloblastosis viral oncogene homolog	196					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)	3			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			TTTATTCCATCTTGTAAATAG	0.343													7	11	---	---	---	---	PASS
DCAF4L2	138009	broad.mit.edu	37	8	88885742	88885742	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88885742G>T	uc003ydz.2	-	1	555	c.458C>A	c.(457-459)CCA>CAA	p.P153Q		NM_152418	NP_689631	Q8NA75	DC4L2_HUMAN	WD repeat domain 21C	153										ovary(1)	1						GGCACAGCTTGGAGTATCTGC	0.552													63	37	---	---	---	---	PASS
WDR67	93594	broad.mit.edu	37	8	124157050	124157050	+	Nonsense_Mutation	SNP	G	T	T	rs147130740	byFrequency	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124157050G>T	uc003ypp.1	+	20	3019	c.2929G>T	c.(2929-2931)GAG>TAG	p.E977*	WDR67_uc011lig.1_Nonsense_Mutation_p.E881*|WDR67_uc011lih.1_Nonsense_Mutation_p.E867*|WDR67_uc003ypq.1_RNA|WDR67_uc003yps.1_Nonsense_Mutation_p.E611*|WDR67_uc003ypt.1_Nonsense_Mutation_p.E369*|WDR67_uc003ypu.1_Nonsense_Mutation_p.E369*	NM_145647	NP_663622	Q96DN5	WDR67_HUMAN	WD repeat domain 67 isoform 1	977						centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			TTTAAAGCAAGAGATAAATGC	0.388													46	31	---	---	---	---	PASS
TG	7038	broad.mit.edu	37	8	133899340	133899340	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133899340C>T	uc003ytw.2	+	9	1764	c.1723C>T	c.(1723-1725)CCA>TCA	p.P575S		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	575					hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CCTGGAGCTTCCAGAATTCCT	0.453													6	100	---	---	---	---	PASS
PAX5	5079	broad.mit.edu	37	9	36846876	36846876	+	Missense_Mutation	SNP	T	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36846876T>A	uc003zzo.1	-	9	1511	c.1063A>T	c.(1063-1065)AAC>TAC	p.N355Y	PAX5_uc011lpt.1_Missense_Mutation_p.N151Y|PAX5_uc011lpu.1_RNA|PAX5_uc011lpv.1_Intron|PAX5_uc011lpw.1_Intron|PAX5_uc011lpx.1_Missense_Mutation_p.N255Y|PAX5_uc011lpy.1_Intron|PAX5_uc010mls.1_Intron|PAX5_uc011lpz.1_Missense_Mutation_p.N312Y|PAX5_uc011lqa.1_Missense_Mutation_p.N247Y|PAX5_uc010mlq.1_RNA|PAX5_uc011lqb.1_RNA|PAX5_uc010mlo.1_Missense_Mutation_p.N321Y|PAX5_uc010mlp.1_Intron|PAX5_uc011lqc.1_Intron|PAX5_uc010mlr.1_Silent_p.T277T	NM_016734	NP_057953	Q02548	PAX5_HUMAN	paired box 5	355					cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter	nucleus	DNA binding	p.?(11)|p.N355H(1)	PAX5/JAK2(18)	haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2)	147		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		CAGGAGTCGTTGTACGAGGAA	0.597			T|Mis|D|F|S	IGH@|ETV6|PML|FOXP1|ZNF521|ELN	NHL|ALL|B-ALL								81	50	---	---	---	---	PASS
SVEP1	79987	broad.mit.edu	37	9	113191430	113191430	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113191430C>A	uc010mtz.2	-	35	6137	c.5800G>T	c.(5800-5802)GGA>TGA	p.G1934*	SVEP1_uc010mty.2_Translation_Start_Site	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	1934	Sushi 9.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						TACCTGTATCCTGTATCGCAT	0.308													11	12	---	---	---	---	PASS
ASTN2	23245	broad.mit.edu	37	9	120053768	120053768	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120053768A>G	uc004bjs.1	-	2	568	c.467T>C	c.(466-468)ATC>ACC	p.I156T	ASTN2_uc004bjr.1_Missense_Mutation_p.I156T|ASTN2_uc004bjt.1_Missense_Mutation_p.I156T	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	156	Extracellular (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						CACCAGCGAGATGTCCGCTGC	0.627													22	11	---	---	---	---	PASS
SFMBT2	57713	broad.mit.edu	37	10	7409783	7409783	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7409783C>T	uc009xio.1	-	4	355	c.264G>A	c.(262-264)CCG>CCA	p.P88P	SFMBT2_uc001ijn.1_Silent_p.P88P|SFMBT2_uc010qay.1_Silent_p.P88P|SFMBT2_uc001ijo.1_Silent_p.P88P	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	88	MBT 1.				regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8						AGTACGTGTCCGGGTTGTTCT	0.517													31	14	---	---	---	---	PASS
COL17A1	1308	broad.mit.edu	37	10	105830203	105830203	+	Silent	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105830203C>G	uc001kxr.2	-	9	757	c.588G>C	c.(586-588)GTG>GTC	p.V196V	COL17A1_uc010qqv.1_Silent_p.V180V|COL17A1_uc009xxp.1_Silent_p.V196V	NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	196	Cytoplasmic (Potential).|Nonhelical region (NC16).|Necessary for interaction with DST and for the recruitment of DST to hemidesmosome.				cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		AGCTCGCTGTCACAATTTTGG	0.438													42	21	---	---	---	---	PASS
SEC23IP	11196	broad.mit.edu	37	10	121671669	121671669	+	Silent	SNP	T	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121671669T>C	uc001leu.1	+	6	1377	c.1305T>C	c.(1303-1305)ATT>ATC	p.I435I	SEC23IP_uc010qtc.1_Silent_p.I224I	NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125	435					Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		TTGATGAAATTCCCGACGGTG	0.428													3	153	---	---	---	---	PASS
PSTK	118672	broad.mit.edu	37	10	124746901	124746901	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124746901C>A	uc001lgy.1	+	6	1369	c.929C>A	c.(928-930)GCG>GAG	p.A310E		NM_153336	NP_699167	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	310							ATP binding|kinase activity			liver(1)	1		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		tgggtaagagcgaaccatgca	0.000													43	17	---	---	---	---	PASS
HRAS	3265	broad.mit.edu	37	11	534286	534286	+	Missense_Mutation	SNP	C	G	G	rs104894228		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:534286C>G	uc001lpv.2	-	2	225	c.37G>C	c.(37-39)GGT>CGT	p.G13R	HRAS_uc010qvw.1_Missense_Mutation_p.G13R|HRAS_uc010qvx.1_Missense_Mutation_p.G13R|HRAS_uc010qvy.1_RNA	NM_005343	NP_005334	P01112	RASH_HUMAN	v-Ha-ras Harvey rat sarcoma viral oncogene	13	GTP.		G -> D (in FCSS).|G -> C (in FCSS).		activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding	p.G13R(34)|p.G13V(10)|p.G13D(9)|p.G13S(9)|p.G13C(6)|p.G13G(1)|p.G12_G13insAG(1)		urinary_tract(174)|thyroid(155)|skin(126)|upper_aerodigestive_tract(112)|soft_tissue(37)|prostate(29)|salivary_gland(24)|cervix(23)|stomach(14)|pituitary(10)|lung(9)|haematopoietic_and_lymphoid_tissue(9)|breast(6)|testis(5)|endometrium(4)|bone(3)|large_intestine(2)|oesophagus(2)|penis(2)|kidney(1)|adrenal_gland(1)|thymus(1)	749		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Sulindac(DB00605)	TTGCCCACACCGCCGGCGCCC	0.642		6	Mis		infrequent sarcomas|rare other types	rhadomyosarcoma|ganglioneuroblastoma|bladder			Costello_syndrome	HNSCC(11;0.0054)			16	23	---	---	---	---	PASS
CARS	833	broad.mit.edu	37	11	3039644	3039644	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3039644G>T	uc001lxh.2	-	13	1448	c.1374C>A	c.(1372-1374)TTC>TTA	p.F458L	CARS_uc001lxe.2_Missense_Mutation_p.F448L|CARS_uc001lxf.2_Missense_Mutation_p.F541L|CARS_uc001lxg.2_Missense_Mutation_p.F458L|CARS_uc010qxo.1_Missense_Mutation_p.F541L|CARS_uc010qxp.1_Missense_Mutation_p.F471L	NM_001751	NP_001742	P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase isoform b	458					cysteinyl-tRNA aminoacylation	cytoplasm|cytosol	ATP binding|cysteine-tRNA ligase activity|metal ion binding|protein homodimerization activity|protein homodimerization activity|tRNA binding|tRNA binding		CARS/ALK(5)	soft_tissue(5)|ovary(2)	7		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	TCACATTCAAGAACTTCTCAT	0.592			T	ALK	ALCL								3	19	---	---	---	---	PASS
OR51S1	119692	broad.mit.edu	37	11	4869883	4869883	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4869883A>T	uc010qyo.1	-	1	556	c.556T>A	c.(556-558)TAT>AAT	p.Y186N		NM_001004758	NP_001004758	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S,	186	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGCAAGCAATAAGAATGGGTT	0.562													71	36	---	---	---	---	PASS
PPFIBP2	8495	broad.mit.edu	37	11	7673013	7673013	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7673013G>C	uc001mfj.3	+	23	2762	c.2374G>C	c.(2374-2376)GAG>CAG	p.E792Q	PPFIBP2_uc010rbb.1_Missense_Mutation_p.E715Q|PPFIBP2_uc001mfk.1_Intron|PPFIBP2_uc010rbc.1_Missense_Mutation_p.E726Q|PPFIBP2_uc010rbe.1_Missense_Mutation_p.E680Q|PPFIBP2_uc001mfl.3_Missense_Mutation_p.E649Q|PPFIBP2_uc009yfj.1_Missense_Mutation_p.E436Q	NM_003621	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2	792					cell communication|DNA integration	intracellular	DNA binding|integrase activity|protein binding			ovary(2)|breast(2)	4				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		GGCTGAACAGGAGAAGCGAGA	0.582													60	24	---	---	---	---	PASS
USH1C	10083	broad.mit.edu	37	11	17518319	17518319	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17518319C>A	uc001mnf.2	-	20	1741	c.1632G>T	c.(1630-1632)GAG>GAT	p.E544D	USH1C_uc001mne.2_Missense_Mutation_p.E844D|USH1C_uc009yhb.2_Missense_Mutation_p.E525D|USH1C_uc001mng.2_RNA|USH1C_uc001mnd.2_Missense_Mutation_p.E508D	NM_005709	NP_005700	Q9Y6N9	USH1C_HUMAN	harmonin isoform a	544					equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1						CATCGTCATACTCCTTTGGGG	0.577													42	22	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55136333	55136333	+	Missense_Mutation	SNP	C	A	A	rs149238692	byFrequency	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55136333C>A	uc010rif.1	+	1	974	c.974C>A	c.(973-975)GCC>GAC	p.A325D		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	325	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						ATGAAAAGTGCCATGAGGAAA	0.373													82	68	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55136334	55136334	+	Silent	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55136334C>A	uc010rif.1	+	1	975	c.975C>A	c.(973-975)GCC>GCA	p.A325A		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	325	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						TGAAAAGTGCCATGAGGAAAC	0.373													81	68	---	---	---	---	PASS
PGR	5241	broad.mit.edu	37	11	100933389	100933389	+	Silent	SNP	T	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100933389T>C	uc001pgh.2	-	4	2744	c.2001A>G	c.(1999-2001)CAA>CAG	p.Q667Q	PGR_uc001pgg.2_Silent_p.Q48Q|PGR_uc001pgi.2_Intron|PGR_uc009yww.1_Intron|PGR_uc001pgj.2_RNA|PGR_uc009ywx.1_RNA	NM_000926	NP_000917	P06401	PRGR_HUMAN	progesterone receptor	667					cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			lung(1)|liver(1)|central_nervous_system(1)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)	GGCTTAGGGCTTGGCTTTCAT	0.438													6	156	---	---	---	---	PASS
OR8B3	390271	broad.mit.edu	37	11	124266547	124266547	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124266547C>A	uc010saj.1	-	1	701	c.701G>T	c.(700-702)AGA>ATA	p.R234I	OR8B2_uc001qab.3_Intron	NM_001005467	NP_001005467	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B,	234	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		GGCTTTTGATCTTCCTTGAGT	0.368													67	39	---	---	---	---	PASS
NTM	50863	broad.mit.edu	37	11	132180043	132180043	+	Silent	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132180043C>A	uc001qgp.2	+	5	1363	c.699C>A	c.(697-699)GTC>GTA	p.V233V	NTM_uc001qgm.2_Silent_p.V233V|NTM_uc010sch.1_Silent_p.V224V|NTM_uc010sci.1_Silent_p.V233V|NTM_uc010scj.1_Silent_p.V192V|NTM_uc001qgo.2_Silent_p.V233V|NTM_uc001qgq.2_Silent_p.V233V|NTM_uc001qgr.2_5'UTR	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1	233	Ig-like C2-type 3.				cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						GTACAGGTGTCCCCGTGGGAC	0.448													94	53	---	---	---	---	PASS
CLEC4D	338339	broad.mit.edu	37	12	8673755	8673755	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8673755G>A	uc001qun.2	+	6	729	c.536G>A	c.(535-537)GGA>GAA	p.G179E		NM_080387	NP_525126	Q8WXI8	CLC4D_HUMAN	C-type lectin domain family 4, member D	179	C-type lectin.|Extracellular (Potential).				innate immune response	integral to membrane	sugar binding				0	Lung SC(5;0.184)					AACTCTCAGGGAGAAAACTGT	0.348													30	91	---	---	---	---	PASS
PZP	5858	broad.mit.edu	37	12	9307276	9307276	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9307276G>T	uc001qvl.2	-	29	3739	c.3710C>A	c.(3709-3711)GCA>GAA	p.A1237E	PZP_uc009zgl.2_Missense_Mutation_p.A1023E	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5						AATGTTAGTTGCAGAGGTCAG	0.567													46	59	---	---	---	---	PASS
PPFIBP1	8496	broad.mit.edu	37	12	27820098	27820098	+	Splice_Site	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27820098G>T	uc001ric.1	+	13	1420	c.1043_splice	c.e13-1	p.G348_splice	PPFIBP1_uc010sjr.1_Splice_Site_p.G179_splice|PPFIBP1_uc001rib.1_Splice_Site_p.G331_splice|PPFIBP1_uc001ria.2_Splice_Site_p.G317_splice|PPFIBP1_uc001rid.1_Splice_Site_p.G195_splice	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1						cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)					TCTTTTCCTAGGCAAAGATGG	0.363													39	39	---	---	---	---	PASS
KIF5A	3798	broad.mit.edu	37	12	57963425	57963425	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57963425C>T	uc001sor.1	+	11	1284	c.1076C>T	c.(1075-1077)ACG>ATG	p.T359M	KIF5A_uc010srr.1_Missense_Mutation_p.T270M	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A	359					blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3						cagaaggagaCGATTGCGAAG	0.413													48	22	---	---	---	---	PASS
GRIP1	23426	broad.mit.edu	37	12	66786489	66786489	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66786489G>T	uc001stk.2	-	17	2322	c.2081C>A	c.(2080-2082)ACT>AAT	p.T694N	GRIP1_uc010sta.1_Missense_Mutation_p.T638N|GRIP1_uc001stj.2_Missense_Mutation_p.T476N|GRIP1_uc001stl.1_Missense_Mutation_p.T586N|GRIP1_uc001stm.2_Missense_Mutation_p.T694N	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	746	PDZ 6.				androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		CAAGGTGACAGTCTCTCCTGC	0.428													107	57	---	---	---	---	PASS
C12orf50	160419	broad.mit.edu	37	12	88420378	88420378	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88420378C>A	uc001tam.1	-	3	188	c.20G>T	c.(19-21)TGC>TTC	p.C7F	C12orf50_uc001tan.2_Missense_Mutation_p.C61F	NM_152589	NP_689802	Q8NA57	CL050_HUMAN	hypothetical protein LOC160419	7										skin(2)|ovary(1)	3						TGAAATGCTGCAGTTTTGCTA	0.368													4	52	---	---	---	---	PASS
RB1	5925	broad.mit.edu	37	13	48916852	48916852	+	Splice_Site	SNP	T	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48916852T>G	uc001vcb.2	+	3	546	c.380_splice	c.e3+2	p.S127_splice	RB1_uc010acs.1_Intron	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(4)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AGAAATCAGGTAAAGTTTCTT	0.343		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			49	26	---	---	---	---	PASS
ERCC5	2073	broad.mit.edu	37	13	103514619	103514619	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103514619G>A	uc001vpw.2	+	8	1563	c.1120G>A	c.(1120-1122)GCA>ACA	p.A374T	ERCC5_uc001vpu.1_Missense_Mutation_p.A828T|ERCC5_uc010tjb.1_Missense_Mutation_p.A374T|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_Missense_Mutation_p.A206T	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	374					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)					TGGGAGGAACGCACCTGCTGC	0.522			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				25	56	---	---	---	---	PASS
SHC4	399694	broad.mit.edu	37	15	49254968	49254968	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49254968G>A	uc001zxb.1	-	1	674	c.245C>T	c.(244-246)CCA>CTA	p.P82L		NM_203349	NP_976224	Q6S5L8	SHC4_HUMAN	rai-like protein	82	CH2.				intracellular signal transduction	cell junction|postsynaptic membrane				ovary(3)|pancreas(2)	5		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		GGTGCACAGTGGGGTGGGGCT	0.632													25	112	---	---	---	---	PASS
ETFA	2108	broad.mit.edu	37	15	76588074	76588074	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76588074G>T	uc002bbt.2	-	2	125	c.44C>A	c.(43-45)TCA>TAA	p.S15*	ETFA_uc010bkq.1_Intron|ETFA_uc002bbu.1_Nonsense_Mutation_p.S15*	NM_000126	NP_000117	P13804	ETFA_HUMAN	electron transfer flavoprotein, alpha	15					respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity				0						TCGTAGCAATGAGGCCTAAAA	0.358													48	46	---	---	---	---	PASS
NTRK3	4916	broad.mit.edu	37	15	88472482	88472482	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88472482C>T	uc002bme.1	-	16	2235	c.2073G>A	c.(2071-2073)CTG>CTA	p.L691L	NTRK3_uc002bmh.2_Silent_p.L683L|NTRK3_uc002bmf.1_Silent_p.L691L|NTRK3_uc010upl.1_Silent_p.L593L|NTRK3_uc010bnh.1_Silent_p.L683L	NM_001012338	NP_001012338	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	691	Cytoplasmic (Potential).|Protein kinase.				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	281			BRCA - Breast invasive adenocarcinoma(143;0.211)			TCTTCACTAGCAGATTCGCTC	0.552			T	ETV6	congenital fibrosarcoma|Secretory breast 					TSP Lung(13;0.10)			102	64	---	---	---	---	PASS
ZNF710	374655	broad.mit.edu	37	15	90623046	90623046	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90623046C>A	uc002bov.1	+	5	2103	c.1980C>A	c.(1978-1980)TAC>TAA	p.Y660*		NM_198526	NP_940928	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	660					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			AGATGGCCTACTACAATGTGC	0.632													3	99	---	---	---	---	PASS
LRRK1	79705	broad.mit.edu	37	15	101586211	101586211	+	Missense_Mutation	SNP	T	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101586211T>G	uc002bwr.2	+	21	3308	c.2989T>G	c.(2989-2991)TCT>GCT	p.S997A	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	997					small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TCTCCTTCCATCTAAACCTGG	0.587													47	223	---	---	---	---	PASS
WDR90	197335	broad.mit.edu	37	16	712030	712030	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:712030T>C	uc002cii.1	+	32	4058	c.4004T>C	c.(4003-4005)TTG>TCG	p.L1335S	WDR90_uc002cij.1_Intron|WDR90_uc002cik.1_Missense_Mutation_p.L862S|WDR90_uc002cil.1_RNA|WDR90_uc002cim.1_Missense_Mutation_p.L509S|WDR90_uc002cin.1_5'UTR|WDR90_uc010uul.1_5'Flank|WDR90_uc002cio.1_5'Flank|WDR90_uc010bqx.1_5'Flank	NM_145294	NP_660337	Q96KV7	WDR90_HUMAN	WD repeat domain 90	1335	WD 16.									ovary(1)	1		Hepatocellular(780;0.0218)				CGCTGCTTCTTGTCCTGGGAG	0.662													24	43	---	---	---	---	PASS
FAM86A	196483	broad.mit.edu	37	16	5141863	5141863	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5141863G>T	uc002cyo.2	-	4	323	c.274C>A	c.(274-276)CTG>ATG	p.L92M	FAM86A_uc002cyp.2_Intron	NM_201400	NP_958802	Q96G04	FA86A_HUMAN	hypothetical protein LOC196483 isoform 1	92											0						GCTTCATACAGCTCGTCCAAA	0.527													7	112	---	---	---	---	PASS
C16orf82	162083	broad.mit.edu	37	16	27078353	27078353	+	Missense_Mutation	SNP	G	C	C	rs143151440	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27078353G>C	uc010vcm.1	+	1	135	c.37G>C	c.(37-39)GAG>CAG	p.E13Q		NM_001145545	NP_001139017	Q7Z2V1	TNT_HUMAN	hypothetical protein LOC162083	76											0						CATTTTTCTCGAGGGAGAAAA	0.592													25	27	---	---	---	---	PASS
C16orf54	283897	broad.mit.edu	37	16	29755978	29755978	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29755978C>G	uc002dtp.2	-	2	404	c.295G>C	c.(295-297)GCG>CCG	p.A99P	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|uc002dtq.1_5'Flank	NM_175900	NP_787096	Q6UWD8	CP054_HUMAN	hypothetical protein LOC283897	99						integral to membrane					0						AGGGGGACCGCAGAGCCATAC	0.682													3	4	---	---	---	---	PASS
ZNF48	197407	broad.mit.edu	37	16	30409782	30409782	+	Missense_Mutation	SNP	C	T	T	rs144019727		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30409782C>T	uc002dya.1	+	2	1270	c.1211C>T	c.(1210-1212)CCT>CTT	p.P404L	ZNF48_uc002dxz.1_Missense_Mutation_p.P281L	NM_152652	NP_689865	Q96MX3	ZNF48_HUMAN	zinc finger protein 48	404	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CCACCCCCACCTCCTCTGGGC	0.667													12	40	---	---	---	---	PASS
HSD3B7	80270	broad.mit.edu	37	16	30998034	30998034	+	Intron	SNP	A	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30998034A>T	uc002eaf.2	+						HSD3B7_uc010cac.2_Intron|HSD3B7_uc002eag.2_Intron|HSD3B7_uc002eah.2_Intron	NM_025193	NP_079469	Q9H2F3	3BHS7_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta-						bile acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|cholest-5-ene-3-beta,7-alpha-diol 3-beta-dehydrogenase activity				0						AGGTGAGCCCAGAAAAAGGAG	0.657													15	55	---	---	---	---	PASS
CDH15	1013	broad.mit.edu	37	16	89256738	89256738	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89256738G>C	uc002fmt.2	+	8	1143	c.1066G>C	c.(1066-1068)GAG>CAG	p.E356Q		NM_004933	NP_004924	P55291	CAD15_HUMAN	cadherin 15 preproprotein	356	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	calcium ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0261)		CCTTAGGGCTGAGCGGGGCCA	0.637													10	26	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577548	7577548	+	Missense_Mutation	SNP	C	T	T	rs28934575		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577548C>T	uc002gim.2	-	7	927	c.733G>A	c.(733-735)GGC>AGC	p.G245S	TP53_uc002gig.1_Missense_Mutation_p.G245S|TP53_uc002gih.2_Missense_Mutation_p.G245S|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.G113S|TP53_uc010cng.1_Missense_Mutation_p.G113S|TP53_uc002gii.1_Missense_Mutation_p.G113S|TP53_uc010cnh.1_Missense_Mutation_p.G245S|TP53_uc010cni.1_Missense_Mutation_p.G245S|TP53_uc002gij.2_Missense_Mutation_p.G245S|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.G152S|TP53_uc002gio.2_Missense_Mutation_p.G113S	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	245	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> A (in sporadic cancers; somatic mutation).|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> E (in a sporadic cancer; somatic mutation).|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.G245S(274)|p.G245D(93)|p.G245V(50)|p.G245C(47)|p.G245R(10)|p.G245A(8)|p.0?(7)|p.G245G(3)|p.G245fs*2(3)|p.G245N(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.G245E(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.G245fs*22(1)|p.M243fs*18(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CGGTTCATGCCGCCCATGCAG	0.577	G245S(SKLMS1_SOFT_TISSUE)|G245S(LS1034_LARGE_INTESTINE)|G245S(NUGC2_STOMACH)|G245S(PANC0403_PANCREAS)|G245S(SKMEL2_SKIN)	111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			32	25	---	---	---	---	PASS
AMAC1	146861	broad.mit.edu	37	17	33520323	33520323	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33520323C>T	uc002hjd.2	-	1	1090	c.1004G>A	c.(1003-1005)AGG>AAG	p.R335K		NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1	335						integral to membrane					0				BRCA - Breast invasive adenocarcinoma(366;0.0917)		CTCCTCCACCCTCCCTGTCCT	0.557													4	72	---	---	---	---	PASS
CYB561	1534	broad.mit.edu	37	17	61513431	61513431	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61513431G>A	uc002jap.2	-	2	687	c.285C>T	c.(283-285)CTC>CTT	p.L95L	CYB561_uc002jaq.2_Silent_p.L141L|CYB561_uc002jar.2_Silent_p.L95L|CYB561_uc002jas.2_Silent_p.L95L|CYB561_uc010ddt.2_Silent_p.L95L|CYB561_uc002jat.2_Silent_p.L95L|CYB561_uc010wpf.1_Silent_p.L95L|CYB561_uc010wpg.1_Silent_p.L66L	NM_001915	NP_001906	P49447	CY561_HUMAN	cytochrome b-561	95	Helical; (Potential).|Cytochrome b561.				electron transport chain|transport	integral to plasma membrane	cytochrome-b5 reductase activity|ferric-chelate reductase activity|metal ion binding			ovary(1)	1				READ - Rectum adenocarcinoma(1115;0.0689)		GGGCGATGACGAGCGCAAAGA	0.617													68	15	---	---	---	---	PASS
CD300LB	124599	broad.mit.edu	37	17	72522134	72522134	+	Silent	SNP	T	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72522134T>A	uc002jkx.2	-	2	247	c.234A>T	c.(232-234)GGA>GGT	p.G78G	CD300LB_uc010wqz.1_Silent_p.G78G	NM_174892	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	41	Ig-like V-type.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(1)	1						AGGTCTCCCATCCTTGCTTAT	0.547													268	204	---	---	---	---	PASS
ZNF407	55628	broad.mit.edu	37	18	72343085	72343085	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72343085C>T	uc002llw.2	+	1	167	c.110C>T	c.(109-111)TCT>TTT	p.S37F	ZNF407_uc010xfc.1_Missense_Mutation_p.S37F|ZNF407_uc010dqu.1_Missense_Mutation_p.S37F|ZNF407_uc002llu.2_Missense_Mutation_p.S36F	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1	37					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)		GGGCCTGTATCTGATGTGATA	0.378													13	33	---	---	---	---	PASS
MED16	10025	broad.mit.edu	37	19	875420	875420	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:875420G>A	uc002lqd.1	-	10	1746	c.1595C>T	c.(1594-1596)TCG>TTG	p.S532L	MED16_uc010drw.1_Missense_Mutation_p.S357L|MED16_uc002lqe.2_Missense_Mutation_p.S521L|MED16_uc002lqf.2_Missense_Mutation_p.S521L|MED16_uc010xfv.1_Intron|MED16_uc010xfw.1_Missense_Mutation_p.S452L|MED16_uc010xfx.1_Missense_Mutation_p.S377L|MED16_uc010xfy.1_Intron|MED16_uc010xfz.1_5'Flank	NM_005481	NP_005472	Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	532					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTGCAGAGCGAGGCCTTCAT	0.667													3	54	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	8996458	8996458	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8996458G>T	uc002mkp.2	-	61	41318	c.41114C>A	c.(41113-41115)GCC>GAC	p.A13705D	MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Missense_Mutation_p.A522D|MUC16_uc010xki.1_RNA	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GGTGCAGATGGCATCCACTCC	0.552													9	73	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	8996459	8996459	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8996459C>T	uc002mkp.2	-	61	41317	c.41113G>A	c.(41113-41115)GCC>ACC	p.A13705T	MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Missense_Mutation_p.A522T|MUC16_uc010xki.1_RNA	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GTGCAGATGGCATCCACTCCA	0.547													37	57	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9062192	9062192	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9062192C>T	uc002mkp.2	-	3	25458	c.25254G>A	c.(25252-25254)TTG>TTA	p.L8418L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8420	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGGTCTCCCTCAATCCAGAAG	0.522													29	137	---	---	---	---	PASS
COL5A3	50509	broad.mit.edu	37	19	10088094	10088094	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10088094C>T	uc002mmq.1	-	43	3267	c.3181G>A	c.(3181-3183)GGG>AGG	p.G1061R		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	1061	Triple-helical region.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)			CCCAGAGGCCCCAGGGGCCCT	0.652													28	228	---	---	---	---	PASS
KANK2	25959	broad.mit.edu	37	19	11304017	11304017	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11304017C>T	uc010dxv.2	-	6	1297	c.739G>A	c.(739-741)GAG>AAG	p.E247K	KANK2_uc002mqm.2_Missense_Mutation_p.E247K|KANK2_uc002mqo.3_Missense_Mutation_p.E247K|KANK2_uc002mqp.1_Missense_Mutation_p.E56K|KANK2_uc002mqq.2_Missense_Mutation_p.E247K	NM_015493	NP_056308	Q63ZY3	KANK2_HUMAN	ankyrin repeat domain 25 isoform 1	247											0						AGGCAGAGCTCGCTGCGACCC	0.647													34	43	---	---	---	---	PASS
ZNF439	90594	broad.mit.edu	37	19	11978607	11978607	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11978607G>A	uc002mss.2	+	3	851	c.723G>A	c.(721-723)CCG>CCA	p.P241P	ZNF439_uc002msr.2_Silent_p.P105P	NM_152262	NP_689475	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	241					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						GAGAGAAACCGTATGAATGTA	0.363													97	107	---	---	---	---	PASS
CCDC105	126402	broad.mit.edu	37	19	15131373	15131373	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15131373C>T	uc002nae.2	+	3	875	c.776C>T	c.(775-777)GCC>GTC	p.A259V		NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	259					microtubule cytoskeleton organization	microtubule				ovary(1)	1						CTGGAGCAGGCCAGACGCCAC	0.612													24	37	---	---	---	---	PASS
FAM129C	199786	broad.mit.edu	37	19	17644478	17644478	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17644478G>T	uc010xpr.1	+	5	626	c.488G>T	c.(487-489)CGC>CTC	p.R163L	FAM129C_uc010xpq.1_Missense_Mutation_p.R163L|FAM129C_uc010xps.1_Missense_Mutation_p.R132L|FAM129C_uc010xpt.1_RNA	NM_173544	NP_775815	Q86XR2	NIBL2_HUMAN	B-cell novel protein 1 isoform a	163											0						GAATATCTCCGCCTTTTGGAT	0.438													37	86	---	---	---	---	PASS
ZNF708	7562	broad.mit.edu	37	19	21476637	21476637	+	Silent	SNP	T	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21476637T>A	uc002npq.1	-	4	1329	c.1131A>T	c.(1129-1131)TCA>TCT	p.S377S	ZNF708_uc002npr.1_Silent_p.S313S|ZNF708_uc010ecs.1_Silent_p.S313S	NM_021269	NP_067092	P17019	ZN708_HUMAN	zinc finger protein 708	377	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(4)|skin(2)	6						TAGTAAGGTGTGAGGACCGGT	0.353													44	109	---	---	---	---	PASS
ZNF676	163223	broad.mit.edu	37	19	22363358	22363358	+	Silent	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22363358A>G	uc002nqs.1	-	3	1479	c.1161T>C	c.(1159-1161)CAT>CAC	p.H387H		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	387	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TCTCTTCAGCATGAATTGCCT	0.398													71	112	---	---	---	---	PASS
ZNF676	163223	broad.mit.edu	37	19	22364229	22364229	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22364229C>A	uc002nqs.1	-	3	608	c.290G>T	c.(289-291)GGT>GTT	p.G97V		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	97					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TTTATTATAACCTTCTTTGTG	0.308													65	138	---	---	---	---	PASS
KIRREL2	84063	broad.mit.edu	37	19	36351849	36351849	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36351849G>A	uc002ocb.3	+	8	1179	c.967G>A	c.(967-969)GTG>ATG	p.V323M	KIRREL2_uc002obz.3_Missense_Mutation_p.V323M|KIRREL2_uc002oca.3_Missense_Mutation_p.V273M|KIRREL2_uc002occ.3_Missense_Mutation_p.V270M|KIRREL2_uc002ocd.3_Missense_Mutation_p.V320M	NM_199180	NP_954649	Q6UWL6	KIRR2_HUMAN	kin of IRRE-like 2 isoform c	323	Extracellular (Potential).|Ig-like C2-type 4.				cell adhesion	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)|skin(1)	3	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCCCGTGTCCGTGGACGTGGG	0.667													17	48	---	---	---	---	PASS
SIPA1L3	23094	broad.mit.edu	37	19	38591796	38591796	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38591796C>T	uc002ohk.2	+	6	2468	c.1959C>T	c.(1957-1959)TTC>TTT	p.F653F		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	653	Rap-GAP.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TTGAGGAGTTCCTCTCCCTCA	0.478													5	9	---	---	---	---	PASS
CYP2A6	1548	broad.mit.edu	37	19	41351257	41351257	+	Missense_Mutation	SNP	A	G	G	rs144689858		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41351257A>G	uc002opl.3	-	7	1124	c.1103T>C	c.(1102-1104)ATG>ACG	p.M368T	CYP2A6_uc010ehe.1_Missense_Mutation_p.M164T	NM_000762	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A,	368					coumarin catabolic process|exogenous drug catabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|enzyme binding|heme binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Chlorzoxazone(DB00356)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Formoterol(DB00983)|Halothane(DB01159)|Letrozole(DB01006)|Methoxsalen(DB00553)|Metyrapone(DB01011)|Nicotine(DB00184)|Pilocarpine(DB01085)|Tolbutamide(DB01124)|Tranylcypromine(DB00752)	GGCCAAACTCATGGGGATCAC	0.567													6	244	---	---	---	---	PASS
AXL	558	broad.mit.edu	37	19	41726677	41726677	+	Silent	SNP	G	A	A	rs55690306		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41726677G>A	uc010ehj.2	+	2	412	c.222G>A	c.(220-222)CAG>CAA	p.Q74Q	CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Silent_p.Q74Q|AXL_uc010ehk.2_Silent_p.Q74Q	NM_021913	NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase isoform 1	74	Extracellular (Potential).|Interaction with GAS6.|Ig-like C2-type 1.					integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13						GGGATGGACAGATCCTGGAGC	0.622													22	69	---	---	---	---	PASS
GRLF1	2909	broad.mit.edu	37	19	47491243	47491243	+	Intron	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47491243C>G	uc010ekv.2	+							NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1						axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		TGTTTCTCCTCAGGACTGAGC	0.552													26	31	---	---	---	---	PASS
MIR517C	574492	broad.mit.edu	37	19	54244601	54244601	+	RNA	SNP	A	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54244601A>C	hsa-mir-517c|MI0003174	+			c.35A>C			MIR520H_hsa-mir-520h|MI0003175_5'Flank|uc010yeb.1_5'Flank																	0						AGATGGAAGCACTGTCTGTTG	0.333													24	55	---	---	---	---	PASS
MIR517C	574492	broad.mit.edu	37	19	54244630	54244630	+	RNA	SNP	A	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54244630A>T	hsa-mir-517c|MI0003174	+			c.64A>T			MIR520H_hsa-mir-520h|MI0003175_5'Flank|uc010yeb.1_5'Flank																	0						AAGATCGTGCATCCTTTTAGA	0.403													24	36	---	---	---	---	PASS
NLRP5	126206	broad.mit.edu	37	19	56539488	56539488	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56539488C>A	uc002qmj.2	+	7	1889	c.1889C>A	c.(1888-1890)TCG>TAG	p.S630*	NLRP5_uc002qmi.2_Nonsense_Mutation_p.S611*	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	630						mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CATATCCACTCGCTTTGGATG	0.562													47	34	---	---	---	---	PASS
SIGLEC1	6614	broad.mit.edu	37	20	3670823	3670823	+	Silent	SNP	C	T	T	rs145129138	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3670823C>T	uc002wja.2	-	18	4680	c.4680G>A	c.(4678-4680)CCG>CCA	p.P1560P	SIGLEC1_uc002wjb.1_Silent_p.P199P|SIGLEC1_uc002wiz.3_Silent_p.P1560P	NM_023068	NP_075556	Q9BZZ2	SN_HUMAN	sialoadhesin precursor	1560	Ig-like C2-type 16.|Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding			pancreas(4)|ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	10						GGCTGGCGAGCGGCTCGCTGT	0.657													4	4	---	---	---	---	PASS
SEMG2	6407	broad.mit.edu	37	20	43851856	43851856	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43851856G>T	uc010ggz.2	+	2	1640	c.1583G>T	c.(1582-1584)GGT>GTT	p.G528V	SEMG2_uc002xnk.2_Missense_Mutation_p.G528V|SEMG2_uc002xnl.2_Missense_Mutation_p.G408V	NM_003008	NP_002999	Q02383	SEMG2_HUMAN	semenogelin II precursor	528	Repeat-rich region.|3-2.				sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(1)	1		Myeloproliferative disorder(115;0.0122)				GGAAAGTCTGGTCAATCTGCA	0.383													35	46	---	---	---	---	PASS
TSHZ2	128553	broad.mit.edu	37	20	51872569	51872569	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51872569G>T	uc002xwo.2	+	2	3528	c.2572G>T	c.(2572-2574)GCC>TCC	p.A858S		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	858	Homeobox; atypical.				multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			GATTCTACAAGCCCAGTTTGC	0.493													38	72	---	---	---	---	PASS
DOK5	55816	broad.mit.edu	37	20	53205081	53205081	+	Silent	SNP	T	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53205081T>C	uc002xwy.2	+	3	454	c.234T>C	c.(232-234)CAT>CAC	p.H78H	DOK5_uc010gin.2_5'UTR|DOK5_uc002xwz.2_5'UTR	NM_018431	NP_060901	Q9P104	DOK5_HUMAN	docking protein 5	78	PH.						insulin receptor binding			ovary(1)	1			Colorectal(105;0.202)			CCAAGAAACATGCCATAGGGA	0.418													10	252	---	---	---	---	PASS
MIR1-1	406904	broad.mit.edu	37	20	61151580	61151580	+	RNA	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61151580C>T	hsa-mir-1-1|MI0000651	+			c.68C>T			C20orf200_uc002ycy.2_5'Flank|C20orf200_uc002ycz.1_5'Flank|C20orf166_uc011aaj.1_Intron|uc011aak.1_RNA																	0						AAGTATGTATCTCAGGCCGGG	0.602													65	119	---	---	---	---	PASS
KCNQ2	3785	broad.mit.edu	37	20	62038507	62038507	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62038507C>T	uc002yey.1	-	17	2286	c.2109G>A	c.(2107-2109)GCG>GCA	p.A703A	KCNQ2_uc002yez.1_Silent_p.A672A|KCNQ2_uc002yfa.1_Silent_p.A685A|KCNQ2_uc002yfb.1_Silent_p.A675A	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein	703	Cytoplasmic (Potential).				axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	cggccgggggcgccgAGAAGT	0.602													3	4	---	---	---	---	PASS
KRTAP21-1	337977	broad.mit.edu	37	21	32127623	32127623	+	Missense_Mutation	SNP	C	G	G	rs147233060	byFrequency	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32127623C>G	uc011adi.1	-	1	74	c.74G>C	c.(73-75)GGC>GCC	p.G25A		NM_181619	NP_853650	Q3LI58	KR211_HUMAN	keratin associated protein 21-1	25						intermediate filament				breast(1)	1						acagccacagccagagccaga	0.119													49	63	---	---	---	---	PASS
BACE2	25825	broad.mit.edu	37	21	42613849	42613849	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42613849G>T	uc002yyw.2	+	4	1185	c.722G>T	c.(721-723)GGA>GTA	p.G241V	BACE2_uc002yyx.2_Missense_Mutation_p.G241V|BACE2_uc002yyy.2_Missense_Mutation_p.G241V	NM_012105	NP_036237	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2 isoform A	241	Extracellular (Potential).				membrane protein ectodomain proteolysis|negative regulation of amyloid precursor protein biosynthetic process|peptide hormone processing	cell surface|endoplasmic reticulum|endosome|Golgi apparatus|integral to membrane	aspartic-type endopeptidase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				CCCGTTGCTGGATCTGGGACC	0.478													172	254	---	---	---	---	PASS
LARGE	9215	broad.mit.edu	37	22	34046524	34046524	+	Silent	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34046524G>A	uc003and.3	-	4	816	c.237C>T	c.(235-237)CTC>CTT	p.L79L	LARGE_uc003ane.3_Silent_p.L79L|LARGE_uc010gwp.2_Silent_p.L79L|LARGE_uc011ame.1_Silent_p.L11L|LARGE_uc011amf.1_Silent_p.L79L	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase	79	Lumenal (Potential).|Potential.				glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				GCTGCCTGCGGAGGGCGCGGT	0.692													65	113	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38121247	38121247	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38121247C>T	uc003atr.2	+	7	2955	c.2684C>T	c.(2683-2685)TCA>TTA	p.S895L	TRIOBP_uc003atu.2_Missense_Mutation_p.S723L|TRIOBP_uc003atq.1_Missense_Mutation_p.S895L|TRIOBP_uc003ats.1_Missense_Mutation_p.S723L	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	895					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					CCCAGGAATTCATCTCCCCAT	0.547													133	344	---	---	---	---	PASS
MKL1	57591	broad.mit.edu	37	22	40816474	40816474	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40816474G>A	uc003ayv.1	-	8	1195	c.988C>T	c.(988-990)CGT>TGT	p.R330C	MKL1_uc003ayw.1_Missense_Mutation_p.R330C|MKL1_uc010gye.1_Missense_Mutation_p.R330C|MKL1_uc010gyf.1_Missense_Mutation_p.R280C	NM_020831	NP_065882	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia 1 protein	330					positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						CTGTTCTGACGTGCCAGCCCA	0.657			T	RBM15	acute megakaryocytic leukemia								117	84	---	---	---	---	PASS
TTLL12	23170	broad.mit.edu	37	22	43564146	43564146	+	Silent	SNP	C	T	T	rs142420296	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43564146C>T	uc003bdq.2	-	14	1835	c.1803G>A	c.(1801-1803)CCG>CCA	p.P601P	TTLL12_uc003bdp.2_3'UTR|TTLL12_uc003bdr.1_Silent_p.P601P	NM_015140	NP_055955	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	601	TTL.				protein modification process		tubulin-tyrosine ligase activity			central_nervous_system(1)	1		Ovarian(80;0.221)|Glioma(61;0.222)				CCAGGATCTGCGGCTGCATCA	0.597													51	83	---	---	---	---	PASS
CLCN4	1183	broad.mit.edu	37	X	10163115	10163115	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10163115G>T	uc004csy.3	+	5	839	c.409G>T	c.(409-411)GAG>TAG	p.E137*	CLCN4_uc011mid.1_Nonsense_Mutation_p.E43*	NM_001830	NP_001821	P51793	CLCN4_HUMAN	chloride channel 4	137						early endosome membrane|integral to membrane|late endosome membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						GAAATGGTCGGAGCTGCTGGT	0.557													23	123	---	---	---	---	PASS
TLR7	51284	broad.mit.edu	37	X	12906213	12906213	+	Silent	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12906213C>G	uc004cvc.2	+	3	2725	c.2586C>G	c.(2584-2586)CTC>CTG	p.L862L		NM_016562	NP_057646	Q9NYK1	TLR7_HUMAN	toll-like receptor 7 precursor	862	Cytoplasmic (Potential).				cellular response to mechanical stimulus|defense response to virus|I-kappaB phosphorylation|inflammatory response|innate immune response|positive regulation of chemokine production|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus	early phagosome|endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosome|plasma membrane	double-stranded RNA binding|single-stranded RNA binding|siRNA binding|transmembrane receptor activity			ovary(2)|lung(2)|breast(1)	5					Imiquimod(DB00724)	CAAGTCACCTCTATTTCTGGG	0.398													69	264	---	---	---	---	PASS
ATXN3L	92552	broad.mit.edu	37	X	13337087	13337087	+	Missense_Mutation	SNP	T	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13337087T>C	uc010ned.2	-	1	1432	c.967A>G	c.(967-969)AGT>GGT	p.S323G		NM_001135995	NP_001129467	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	323					protein deubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ubiquitin-specific protease activity			lung(2)|ovary(2)|large_intestine(1)|skin(1)	6						CTGAGATCACTCTCAATTGCT	0.448													51	198	---	---	---	---	PASS
SYTL5	94122	broad.mit.edu	37	X	37984550	37984550	+	Splice_Site	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37984550G>T	uc004ddu.2	+	17	2376	c.1842_splice	c.e17-1	p.G614_splice	SYTL5_uc004ddv.2_Splice_Site_p.G614_splice|SYTL5_uc004ddx.2_Splice_Site_p.G636_splice	NM_001163335	NP_001156807	Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5 isoform 1						intracellular protein transport	membrane	metal ion binding|Rab GTPase binding			skin(1)	1						TTCTCATGCAGCTACCTGCTC	0.408													25	24	---	---	---	---	PASS
GPR82	27197	broad.mit.edu	37	X	41586456	41586456	+	Silent	SNP	T	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41586456T>C	uc004dfs.1	+	3	417	c.177T>C	c.(175-177)ACT>ACC	p.T59T	CASK_uc004dfl.3_Intron|CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron|GPR82_uc004dft.2_Silent_p.T59T|GPR82_uc004dfu.1_RNA	NM_080817	NP_543007	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	59	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2						ACCTTGTGACTGCAAACTTAC	0.378													27	118	---	---	---	---	PASS
GPR82	27197	broad.mit.edu	37	X	41586457	41586457	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41586457G>T	uc004dfs.1	+	3	418	c.178G>T	c.(178-180)GCA>TCA	p.A60S	CASK_uc004dfl.3_Intron|CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron|GPR82_uc004dft.2_Missense_Mutation_p.A60S|GPR82_uc004dfu.1_RNA	NM_080817	NP_543007	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	60	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2						CCTTGTGACTGCAAACTTACT	0.373													25	121	---	---	---	---	PASS
KDM6A	7403	broad.mit.edu	37	X	44870203	44870203	+	Intron	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44870203C>T	uc004dge.3	+						KDM6A_uc010nhk.2_Intron|KDM6A_uc011mkz.1_Intron|KDM6A_uc011mla.1_Intron|KDM6A_uc011mlb.1_Intron|KDM6A_uc011mlc.1_Intron	NM_021140	NP_066963	O15550	KDM6A_HUMAN	ubiquitously transcribed tetratricopeptide						histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	p.?(1)		kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84						CCTTCCTTTACAGAATGCTGC	0.299			D|N|F|S		renal|oesophageal SCC|MM								18	81	---	---	---	---	PASS
TIMM17B	10245	broad.mit.edu	37	X	48752384	48752384	+	Missense_Mutation	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48752384C>G	uc004dlc.1	-	4	276	c.127G>C	c.(127-129)GGA>CGA	p.G43R	PQBP1_uc004dle.2_5'Flank|PQBP1_uc004dlf.2_5'Flank|PQBP1_uc004dlg.2_5'Flank|PQBP1_uc004dld.2_5'Flank|TIMM17B_uc004dla.1_Missense_Mutation_p.G93R|TIMM17B_uc004dlb.1_Missense_Mutation_p.G63R	NM_005834	NP_005825	O60830	TI17B_HUMAN	translocase of inner mitochondrial membrane 17	43					protein targeting to mitochondrion	integral to membrane|microtubule cytoskeleton|mitochondrial inner membrane presequence translocase complex	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1						TGCCGAATTCCCTGGGGAAAG	0.542													4	24	---	---	---	---	PASS
WDR45	11152	broad.mit.edu	37	X	48935748	48935748	+	Nonsense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48935748G>A	uc004dmk.1	-	2	179	c.7C>T	c.(7-9)CAA>TAA	p.Q3*	PRAF2_uc011mmt.1_Nonsense_Mutation_p.Q3*|WDR45_uc004dmj.1_5'Flank|WDR45_uc004dml.1_Nonsense_Mutation_p.Q3*|WDR45_uc004dmm.1_Nonsense_Mutation_p.Q3*|WDR45_uc010nim.1_Nonsense_Mutation_p.Q3*|WDR45_uc004dmn.1_5'UTR|WDR45_uc004dmo.1_Nonsense_Mutation_p.Q25*|WDR45_uc004dmp.1_Nonsense_Mutation_p.Q3*|WDR45_uc011mmu.1_Nonsense_Mutation_p.Q3*	NM_001029896	NP_001025067	Q9Y484	WIPI4_HUMAN	WD repeat domain 45 isoform 2	3					autophagy|response to starvation	organelle membrane	phosphatidylinositol-3,5-bisphosphate binding			ovary(1)	1						AGTGGCTGTTGAGTCATGGTG	0.517													13	47	---	---	---	---	PASS
PPP1R3F	89801	broad.mit.edu	37	X	49143513	49143513	+	Silent	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49143513G>T	uc004dnh.1	+	4	2377	c.2361G>T	c.(2359-2361)CTG>CTT	p.L787L	PPP1R3F_uc011mnd.1_Silent_p.L458L|PPP1R3F_uc004dni.2_Silent_p.L441L|PPP1R3F_uc004dnj.1_Silent_p.L441L	NM_033215	NP_149992	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory (inhibitor)	787	Helical; (Potential).					integral to membrane				ovary(2)|skin(1)	3	Ovarian(276;0.236)					TGTCCCTCCTGGTGCTTGCGC	0.622													18	69	---	---	---	---	PASS
CCNB3	85417	broad.mit.edu	37	X	50053232	50053232	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50053232C>A	uc004dox.3	+	6	2361	c.2063C>A	c.(2062-2064)TCC>TAC	p.S688Y	CCNB3_uc004doy.2_Missense_Mutation_p.S688Y|CCNB3_uc004doz.2_Intron|CCNB3_uc010njq.2_Intron	NM_033031	NP_149020	Q8WWL7	CCNB3_HUMAN	cyclin B3 isoform 3	688					cell division|meiosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	nucleus	protein kinase binding			ovary(4)|lung(3)|large_intestine(1)|pancreas(1)	9	Ovarian(276;0.236)					AAAAGTGGGTCCCTCTTCCAG	0.453													12	25	---	---	---	---	PASS
CCNB3	85417	broad.mit.edu	37	X	50053233	50053233	+	Silent	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50053233C>A	uc004dox.3	+	6	2362	c.2064C>A	c.(2062-2064)TCC>TCA	p.S688S	CCNB3_uc004doy.2_Silent_p.S688S|CCNB3_uc004doz.2_Intron|CCNB3_uc010njq.2_Intron	NM_033031	NP_149020	Q8WWL7	CCNB3_HUMAN	cyclin B3 isoform 3	688					cell division|meiosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	nucleus	protein kinase binding			ovary(4)|lung(3)|large_intestine(1)|pancreas(1)	9	Ovarian(276;0.236)					AAAGTGGGTCCCTCTTCCAGG	0.458													12	25	---	---	---	---	PASS
PHF8	23133	broad.mit.edu	37	X	54022203	54022203	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54022203G>A	uc004dsu.2	-	12	1427	c.1354C>T	c.(1354-1356)CAT>TAT	p.H452Y	PHF8_uc004dst.2_Missense_Mutation_p.H416Y|PHF8_uc004dsv.2_Missense_Mutation_p.H282Y|PHF8_uc004dsw.2_Missense_Mutation_p.H416Y|PHF8_uc004dsx.2_Missense_Mutation_p.H180Y|PHF8_uc004dsy.2_Missense_Mutation_p.H416Y	NM_015107	NP_055922	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	452					brain development|G1/S transition of mitotic cell cycle|negative regulation of chromatin silencing at rDNA|positive regulation of transcription from RNA polymerase I promoter|transcription, DNA-dependent	nucleolus	chromatin binding|histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(3)	3						TCATCCTCATGGTCTGGCAGA	0.368													6	30	---	---	---	---	PASS
HEPH	9843	broad.mit.edu	37	X	65414988	65414988	+	Missense_Mutation	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65414988A>G	uc011moz.1	+	9	1487	c.1427A>G	c.(1426-1428)TAC>TGC	p.Y476C	HEPH_uc004dwn.2_Missense_Mutation_p.Y476C|HEPH_uc004dwo.2_Missense_Mutation_p.Y206C|HEPH_uc010nkr.2_Missense_Mutation_p.Y476C|HEPH_uc011mpa.1_Missense_Mutation_p.Y476C	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	473	Extracellular (Potential).|Plastocyanin-like 3.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9						GTGGTCTTCTACAACCGTGCC	0.507													35	31	---	---	---	---	PASS
NLGN3	54413	broad.mit.edu	37	X	70386935	70386935	+	Missense_Mutation	SNP	T	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70386935T>G	uc004dzd.1	+	6	1188	c.988T>G	c.(988-990)TAC>GAC	p.Y330D	NLGN3_uc010nlb.1_Missense_Mutation_p.Y290D|NLGN3_uc004dzb.2_Missense_Mutation_p.Y310D|NLGN3_uc004dzc.2_Missense_Mutation_p.Y193D|NLGN3_uc011mps.1_Missense_Mutation_p.Y290D|NLGN3_uc004dze.2_Missense_Mutation_p.Y128D	NM_018977	NP_061850	Q9NZ94	NLGN3_HUMAN	neuroligin 3	330	Extracellular (Potential).				neuron cell-cell adhesion|positive regulation of synaptogenesis|receptor-mediated endocytosis|social behavior|synapse assembly	cell surface|endocytic vesicle|integral to plasma membrane|synapse	neurexin binding|receptor activity			ovary(1)	1	Renal(35;0.156)					ACCAGTGAAGTACACCAGCCT	0.537													15	38	---	---	---	---	PASS
CXCR3	2833	broad.mit.edu	37	X	70836522	70836522	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70836522C>A	uc004eaf.2	-	2	868	c.800G>T	c.(799-801)TGC>TTC	p.C267F	BCYRN1_uc011mpt.1_Intron|CXCR3_uc011mpx.1_Missense_Mutation_p.C314F	NM_001504	NP_001495	P49682	CXCR3_HUMAN	chemokine (C-X-C motif) receptor 3 isoform A	267	Helical; Name=6; (Potential).				cell adhesion|cellular component movement|chemotaxis|elevation of cytosolic calcium ion concentration	cytoplasm|integral to plasma membrane	C-X-C chemokine receptor activity			ovary(2)|central_nervous_system(1)	3	Renal(35;0.156)					GGGGGTCCAGCAGAGGGCAAA	0.662													9	28	---	---	---	---	PASS
ZCCHC13	389874	broad.mit.edu	37	X	73524598	73524598	+	Missense_Mutation	SNP	A	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73524598A>T	uc004ebs.3	+	1	574	c.497A>T	c.(496-498)CAG>CTG	p.Q166L		NM_203303	NP_976048	Q8WW36	ZCH13_HUMAN	zinc finger, CCHC domain containing 13	166							nucleic acid binding|zinc ion binding				0						GGAATGTCCCAGTGAGGTTAC	0.517													13	69	---	---	---	---	PASS
MAGEE2	139599	broad.mit.edu	37	X	75003752	75003752	+	Missense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75003752G>T	uc004ecj.1	-	1	1320	c.1135C>A	c.(1135-1137)CTC>ATC	p.L379I		NM_138703	NP_619648	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	379	MAGE 2.									ovary(1)|skin(1)	2						TGGACAAGGAGGTAGATGTGC	0.438													87	91	---	---	---	---	PASS
MAGEE2	139599	broad.mit.edu	37	X	75003753	75003753	+	Nonsense_Mutation	SNP	G	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75003753G>T	uc004ecj.1	-	1	1319	c.1134C>A	c.(1132-1134)TAC>TAA	p.Y378*		NM_138703	NP_619648	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	378	MAGE 2.									ovary(1)|skin(1)	2						GGACAAGGAGGTAGATGTGCT	0.438													87	90	---	---	---	---	PASS
MAGEE1	57692	broad.mit.edu	37	X	75648895	75648895	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75648895C>A	uc004ecm.1	+	1	779	c.572C>A	c.(571-573)ACC>AAC	p.T191N		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	191	Pro-rich.					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6						GTGGTGCCCACCCCTGATGAG	0.692													9	37	---	---	---	---	PASS
PGK1	5230	broad.mit.edu	37	X	77365355	77365355	+	Intron	SNP	C	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77365355C>G	uc004ecz.3	+						PGK1_uc010nlz.2_Intron|PGK1_uc011mqq.1_Intron	NM_000291	NP_000282	P00558	PGK1_HUMAN	phosphoglycerate kinase 1						gluconeogenesis|glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			upper_aerodigestive_tract(1)|ovary(1)	2						TTGCATCTTTCTTTTTTAGAG	0.368													30	98	---	---	---	---	PASS
P2RY10	27334	broad.mit.edu	37	X	78216995	78216995	+	Silent	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78216995C>T	uc004ede.2	+	4	1347	c.978C>T	c.(976-978)TCC>TCT	p.S326S	P2RY10_uc004edf.2_Silent_p.S326S	NM_014499	NP_055314	O00398	P2Y10_HUMAN	G-protein coupled purinergic receptor P2Y10	326	Cytoplasmic (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(2)|lung(2)|breast(1)	5						TGACCCGCTCCCGCCTCATGA	0.428													99	101	---	---	---	---	PASS
CYLC1	1538	broad.mit.edu	37	X	83126587	83126587	+	Intron	SNP	A	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83126587A>T	uc004eei.1	+						CYLC1_uc004eeh.1_Intron	NM_021118	NP_066941	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head						cell differentiation|multicellular organismal development|spermatogenesis	acrosomal matrix|cytoskeletal calyx	structural molecule activity			ovary(4)|skin(1)	5						CTGTAAGTATAGAAAAAGTCA	0.289													37	44	---	---	---	---	PASS
CHM	1121	broad.mit.edu	37	X	85218964	85218964	+	Silent	SNP	A	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85218964A>G	uc004eet.2	-	5	438	c.408T>C	c.(406-408)TCT>TCC	p.S136S	CHM_uc011mqz.1_5'UTR	NM_000390	NP_000381	P24386	RAE1_HUMAN	choroideremia isoform a	136					intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)				GCAGGAAGGCAGAATCTGCAG	0.453													28	103	---	---	---	---	PASS
DACH2	117154	broad.mit.edu	37	X	85994853	85994853	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85994853C>T	uc004eew.2	+	7	1378	c.1208C>T	c.(1207-1209)CCC>CTC	p.P403L	DACH2_uc004eex.2_Missense_Mutation_p.P390L|DACH2_uc010nmq.2_Missense_Mutation_p.P269L|DACH2_uc011mra.1_Missense_Mutation_p.P236L|DACH2_uc010nmr.2_Missense_Mutation_p.P184L|DACH2_uc004eey.2_Missense_Mutation_p.P86L|DACH2_uc004eez.2_Missense_Mutation_p.P86L	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a	403					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5						TCCAGCTCTCCCTCTCAGATG	0.453													8	29	---	---	---	---	PASS
DACH2	117154	broad.mit.edu	37	X	86067939	86067939	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86067939G>A	uc004eew.2	+	8	1491	c.1321G>A	c.(1321-1323)GGA>AGA	p.G441R	DACH2_uc004eex.2_Missense_Mutation_p.G428R|DACH2_uc010nmq.2_Missense_Mutation_p.G307R|DACH2_uc011mra.1_Missense_Mutation_p.G274R|DACH2_uc010nmr.2_Missense_Mutation_p.G222R|DACH2_uc004eey.2_Missense_Mutation_p.G124R|DACH2_uc004eez.2_Missense_Mutation_p.G124R	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a	441					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5						ATTGCCCGCTGGATTCCCTGG	0.413													31	21	---	---	---	---	PASS
KIAA1210	57481	broad.mit.edu	37	X	118219342	118219342	+	Intron	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118219342C>A	uc004era.3	-							NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481											ovary(4)|skin(1)	5						ACCCCAGGTCCTACCTCATAT	0.463													53	78	---	---	---	---	PASS
RNF113A	7737	broad.mit.edu	37	X	119005420	119005420	+	Missense_Mutation	SNP	C	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119005420C>T	uc004esb.2	-	1	372	c.157G>A	c.(157-159)GTG>ATG	p.V53M	NDUFA1_uc004esc.3_5'Flank	NM_006978	NP_008909	O15541	R113A_HUMAN	ring finger protein 113A	53							nucleic acid binding|zinc ion binding			breast(2)	2						GGTCGAACCACAGTGCAGCCT	0.602													69	231	---	---	---	---	PASS
CUL4B	8450	broad.mit.edu	37	X	119671972	119671972	+	Intron	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119671972C>A	uc004esw.2	-						CUL4B_uc010nqq.2_Splice_Site_p.K365_splice|CUL4B_uc004esv.2_Intron	NM_003588	NP_003579	Q13620	CUL4B_HUMAN	cullin 4B isoform 1						cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3						GTTTAACTCACTTTTACCTGT	0.323													26	98	---	---	---	---	PASS
ODZ1	10178	broad.mit.edu	37	X	123556176	123556176	+	Missense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123556176C>A	uc004euj.2	-	23	4460	c.4396G>T	c.(4396-4398)GGT>TGT	p.G1466C	ODZ1_uc011muj.1_Missense_Mutation_p.G1472C|ODZ1_uc010nqy.2_Missense_Mutation_p.G1473C	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	1466	Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23						GTGGGGGCACCAGCGATGATG	0.473													37	145	---	---	---	---	PASS
SMARCA1	6594	broad.mit.edu	37	X	128649954	128649954	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128649954G>A	uc004eun.3	-	4	559	c.446C>T	c.(445-447)ACA>ATA	p.T149I	SMARCA1_uc004eup.3_Missense_Mutation_p.T149I|SMARCA1_uc011muk.1_Missense_Mutation_p.T149I|SMARCA1_uc011mul.1_Missense_Mutation_p.T149I	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	149					ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding			ovary(3)|skin(1)	4						TTCTTGCTCTGTGCGCCTATG	0.373													118	74	---	---	---	---	PASS
MST4	51765	broad.mit.edu	37	X	131188764	131188764	+	Missense_Mutation	SNP	G	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131188764G>A	uc004ewk.1	+	3	449	c.148G>A	c.(148-150)GTT>ATT	p.V50I	MST4_uc004ewl.1_Intron|MST4_uc011mux.1_Missense_Mutation_p.V50I|MST4_uc010nrj.1_Missense_Mutation_p.V50I|MST4_uc004ewm.1_Missense_Mutation_p.V50I	NM_016542	NP_057626	Q9P289	MST4_HUMAN	serine/threonine protein kinase MST4 isoform 1	50	Protein kinase.				cellular component disassembly involved in apoptosis|regulation of apoptosis	cytosol|Golgi membrane	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(3)|stomach(2)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(192;0.000127)					CCAGCAAGTCGTTGCTATTAA	0.398													25	109	---	---	---	---	PASS
GPC3	2719	broad.mit.edu	37	X	132887631	132887631	+	Nonsense_Mutation	SNP	C	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132887631C>A	uc004exe.1	-	3	1100	c.910G>T	c.(910-912)GAA>TAA	p.E304*	GPC3_uc004exd.1_Nonsense_Mutation_p.E176*|GPC3_uc010nrn.1_Nonsense_Mutation_p.E304*|GPC3_uc011mvh.1_Nonsense_Mutation_p.E288*|GPC3_uc010nro.1_Nonsense_Mutation_p.E250*|GPC3_uc010nrp.1_Nonsense_Mutation_p.E176*	NM_004484	NP_004475	P51654	GPC3_HUMAN	glypican 3 isoform 2 precursor	304						extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)					ACAAGTTCTTCAAGGGACAGA	0.443			T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				48	181	---	---	---	---	PASS
FHL1	2273	broad.mit.edu	37	X	135290627	135290627	+	Missense_Mutation	SNP	G	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135290627G>C	uc004ezo.2	+	5	615	c.515G>C	c.(514-516)GGA>GCA	p.G172A	FHL1_uc010nrz.2_Missense_Mutation_p.G172A|FHL1_uc004ezm.2_RNA|FHL1_uc004ezl.2_Missense_Mutation_p.G172A|FHL1_uc004ezq.2_Intron|FHL1_uc011mvy.1_Missense_Mutation_p.G172A|FHL1_uc011mvz.1_Missense_Mutation_p.G172A|FHL1_uc004ezn.2_Missense_Mutation_p.G172A|FHL1_uc011mwa.1_Missense_Mutation_p.G201A|FHL1_uc011mwb.1_RNA|FHL1_uc004ezp.2_Missense_Mutation_p.G188A|FHL1_uc004ezr.2_5'UTR	NM_001159702	NP_001153174	Q13642	FHL1_HUMAN	four and a half LIM domains 1 isoform 1	172	LIM zinc-binding 3.				cell differentiation|cell growth|muscle organ development|organ morphogenesis	cytosol|nucleus|plasma membrane	protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(192;0.000127)					ATCACATCTGGAGGAATCACT	0.408													137	147	---	---	---	---	PASS
RBP7	116362	broad.mit.edu	37	1	10068112	10068112	+	Intron	DEL	A	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10068112delA	uc001aqq.2	+						RBP7_uc009vms.2_Intron	NM_052960	NP_443192	Q96R05	RET7_HUMAN	retinol binding protein 7, cellular							cytoplasm	retinal binding|retinol binding|transporter activity				0		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|BRCA - Breast invasive adenocarcinoma(304;0.000302)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00856)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	actccatctcaaaaaaaaaaa	0.189													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	19314274	19314277	+	IGR	DEL	GAAA	-	-	rs72498264		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19314274_19314277delGAAA								IFFO2 (31448 upstream) : UBR4 (84327 downstream)																							aggaaggaaggaaagaaggaagga	0.191													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	41730645	41730645	+	IGR	DEL	T	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41730645delT								SCMH1 (22857 upstream) : EDN2 (213804 downstream)																							TCTGAGCTGCttttttttttt	0.214													4	2	---	---	---	---	
FCRL1	115350	broad.mit.edu	37	1	157767580	157767580	+	Intron	DEL	C	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157767580delC	uc001frg.2	-						FCRL1_uc001frf.2_RNA|FCRL1_uc001frh.2_Intron|FCRL1_uc001fri.2_Frame_Shift_Del_p.G343fs|FCRL1_uc001frj.2_Intron	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor							integral to membrane|plasma membrane	receptor activity			skin(4)|ovary(3)	7	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			CTGTTGTCTGCCATGCACAGC	0.507													25	15	---	---	---	---	
XCL1	6375	broad.mit.edu	37	1	168545684	168545685	+	5'Flank	INS	-	A	A	rs149424364	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168545684_168545685insA	uc001gfo.1	+							NM_002995	NP_002986	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1						CD4-positive, alpha-beta T cell proliferation|CD8-positive, alpha-beta T cell proliferation|cell-cell signaling|cellular response to interleukin-4|cellular response to transforming growth factor beta stimulus|immunoglobulin production in mucosal tissue|lymphocyte chemotaxis|negative regulation of interferon-gamma production|negative regulation of interleukin-2 production|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of T cell cytokine production|negative regulation of T-helper 1 cell activation|negative regulation of transcription, DNA-dependent|neutrophil chemotaxis|positive regulation of activated T cell proliferation|positive regulation of B cell chemotaxis|positive regulation of granzyme A production|positive regulation of granzyme B production|positive regulation of interleukin-10 production|positive regulation of natural killer cell chemotaxis|positive regulation of neutrophil chemotaxis|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of T cell chemotaxis|positive regulation of T cell cytokine production|positive regulation of T cell mediated cytotoxicity|positive regulation of thymocyte migration|positive regulation of transforming growth factor-beta production|regulation of inflammatory response|release of sequestered calcium ion into cytosol|response to virus|T-helper 1 cell cytokine production|T-helper 2 cell cytokine production	extracellular space	chemokine activity|protein homodimerization activity				0	all_hematologic(923;0.208)					TATGAACAGGGAAAGGGACttt	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	170055842	170055857	+	IGR	DEL	TTCCTTCCTTCCTTCC	-	-	rs71772416	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170055842_170055857delTTCCTTCCTTCCTTCC								KIFAP3 (11963 upstream) : METTL11B (59331 downstream)																							cccttttttattccttccttccttccttccttcctt	0.083													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	190792573	190792576	+	IGR	DEL	GAAG	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190792573_190792576delGAAG								FAM5C (345814 upstream) : None (None downstream)																							aagaaagagagaaggaaggaagga	0.000													4	2	---	---	---	---	
GRHL1	29841	broad.mit.edu	37	2	10131062	10131062	+	Intron	DEL	G	-	-	rs71391182		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10131062delG	uc002raa.2	+						GRHL1_uc002rab.2_Intron|GRHL1_uc002rad.2_Intron|GRHL1_uc010yjb.1_Intron	NM_198182	NP_937825	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1						cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		CTCAGCGGGAGGGGTTTTCCT	0.527													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23968281	23968287	+	IGR	DEL	AGGAAGG	-	-	rs72082221	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23968281_23968287delAGGAAGG								KLHL29 (36800 upstream) : ATAD2B (3254 downstream)																							gaaggaaggaaggaaggaaggaaaggg	0.087													5	6	---	---	---	---	
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48807594	48807594	+	5'Flank	DEL	T	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48807594delT	uc010yol.1	+						STON1_uc002rwo.3_Intron|STON1_uc010fbm.2_Intron|STON1-GTF2A1L_uc002rwp.1_Intron|STON1_uc002rwr.2_5'Flank|STON1_uc002rwq.2_5'Flank	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ttggatcatgtttttttttta	0.100													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57275459	57275460	+	IGR	INS	-	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57275459_57275460insT								CCDC85A (662151 upstream) : VRK2 (859326 downstream)																							TCACAGCATGCTTTGCAAAATC	0.426													15	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	101043078	101043079	+	IGR	INS	-	C	C			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101043078_101043079insC								CHST10 (8987 upstream) : NMS (43865 downstream)																							CAGGCAAGAAGCCGGCAAAGCC	0.599													4	6	---	---	---	---	
PLEKHB2	55041	broad.mit.edu	37	2	132109442	132109446	+	Intron	DEL	TTTTG	-	-	rs70994755		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132109442_132109446delTTTTG	uc002tsh.2	+									Q96CS7	PKHB2_HUMAN	SubName: Full=Putative uncharacterized protein PLEKHB2;							membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)		attttcttTCTTTTGTTTTGTTTTA	0.234													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	165178446	165178447	+	IGR	INS	-	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165178446_165178447insT								FIGN (585933 upstream) : GRB14 (170886 downstream)																							TATGTATAATGTTGTAGGGACA	0.361													6	3	---	---	---	---	
SP140	11262	broad.mit.edu	37	2	231175997	231175997	+	Intron	DEL	C	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231175997delC	uc002vql.2	+						SP140_uc010zma.1_Intron|SP140_uc002vqn.2_Intron|SP140_uc002vqm.2_Intron|SP140_uc010fxl.2_Intron	NM_007237	NP_009168	Q13342	LY10_HUMAN	SP140 nuclear body protein isoform 1						defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CATTACCTGACCCTGAAATGG	0.443													25	18	---	---	---	---	
RHOA	387	broad.mit.edu	37	3	49412693	49412694	+	Intron	INS	-	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49412693_49412694insA	uc003cwu.2	-						RHOA_uc010hku.2_Intron	NM_001664	NP_001655	P61586	RHOA_HUMAN	ras homolog gene family, member A precursor						axon guidance|interspecies interaction between organisms|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of axonogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of neuron differentiation|positive regulation of NF-kappaB import into nucleus|positive regulation of stress fiber assembly|regulation of cell migration|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|spindle assembly involved in mitosis	cytoskeleton|cytosol|plasma membrane	GTP binding|GTPase activity|myosin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	Atorvastatin(DB01076)|Simvastatin(DB00641)	actccgtctccaaaaaaaaaaa	0.149													4	3	---	---	---	---	
NCK1	4690	broad.mit.edu	37	3	136586021	136586022	+	Intron	DEL	TC	-	-	rs55659307		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136586021_136586022delTC	uc003erh.2	+							NM_006153	NP_006144	P16333	NCK1_HUMAN	NCK adaptor protein 1						axon guidance|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of translation|signal complex assembly|T cell activation|T cell receptor signaling pathway	cytosol|endoplasmic reticulum|nucleus	cytoskeletal adaptor activity|receptor binding|receptor signaling complex scaffold activity			pancreas(1)	1						cttccttccttctttctttctt	0.030													4	3	---	---	---	---	
WWTR1	25937	broad.mit.edu	37	3	149374544	149374551	+	Intron	DEL	TCTCTCTT	-	-	rs10665547		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149374544_149374551delTCTCTCTT	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)			ACGCACCAtctctctctttctctctctc	0.365													6	3	---	---	---	---	
PLCH1	23007	broad.mit.edu	37	3	155314368	155314368	+	Intron	DEL	A	-	-	rs62708860		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155314368delA	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TTACTAACAGAAAAAAAAAAA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	156329918	156329921	+	IGR	DEL	TCCT	-	-	rs11275550		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156329918_156329921delTCCT								SSR3 (56983 upstream) : LOC100287227 (61043 downstream)																							tctgtattaAtccttccttccttc	0.025													7	4	---	---	---	---	
OTOL1	131149	broad.mit.edu	37	3	161221119	161221119	+	Frame_Shift_Del	DEL	G	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161221119delG	uc011bpb.1	+	4	823	c.823delG	c.(823-825)GGCfs	p.G275fs		NM_001080440	NP_001073909	A6NHN0	OTOL1_HUMAN	otolin-1 precursor	275						collagen					0						TGGAATGGAAGGCAAAAGCGG	0.527													20	20	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166465727	166465727	+	IGR	DEL	T	-	-	rs11328706		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166465727delT								BCHE (910474 upstream) : ZBBX (492354 downstream)																							tttacttttcttttttttttt	0.020													5	3	---	---	---	---	
EIF4G1	1981	broad.mit.edu	37	3	184049982	184049985	+	Intron	DEL	AGAG	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184049982_184049985delAGAG	uc003fnp.2	+						EIF4G1_uc003fnt.2_Intron|EIF4G1_uc003fnq.2_Intron|EIF4G1_uc003fnr.2_Intron|EIF4G1_uc010hxx.2_Intron|EIF4G1_uc003fns.2_Intron|EIF4G1_uc010hxy.2_Intron|EIF4G1_uc003fnv.3_Intron|EIF4G1_uc003fnu.3_Intron|EIF4G1_uc003fnw.2_Intron|EIF4G1_uc003fny.3_Intron|EIF4G1_uc003foa.2_Intron	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4						insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGTAGTCATTAGAGAGCAAAATGC	0.495													42	26	---	---	---	---	
ZDHHC19	131540	broad.mit.edu	37	3	195937314	195937315	+	Intron	INS	-	TAAAGAAAAG	TAAAGAAAAG	rs59406858		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195937314_195937315insTAAAGAAAAG	uc003fwc.2	-						ZDHHC19_uc010hzz.2_Intron|ZDHHC19_uc010iaa.2_Intron|ZDHHC19_uc010iab.2_Intron	NM_001039617	NP_001034706	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC domain containing 19							integral to membrane	acyltransferase activity|zinc ion binding			ovary(3)	3	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		agagaaagaaagaaagaaaaga	0.233													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3938947	3938948	+	IGR	INS	-	G	G			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3938947_3938948insG								ADRA2C (168696 upstream) : LOC348926 (4722 downstream)																							cagagtctgtcggaaaaaaaaa	0.144													9	5	---	---	---	---	
CCNG2	901	broad.mit.edu	37	4	78081697	78081697	+	Intron	DEL	A	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78081697delA	uc003hkq.3	+						CCNG2_uc003hkn.3_Intron|CCNG2_uc011ccc.1_Intron|CCNG2_uc003hkp.3_Intron	NM_004354	NP_004345	Q16589	CCNG2_HUMAN	cyclin G2						cell cycle checkpoint|cell division|mitosis	cytoplasm				ovary(2)|lung(1)	3						GGGGGGGGGGAGGTCGAGAAC	0.249													9	4	---	---	---	---	
RPS3A	6189	broad.mit.edu	37	4	152025591	152025592	+	Intron	INS	-	TTT	TTT	rs13111229		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152025591_152025592insTTT	uc003ilz.2	+							NM_001006	NP_000997	P61247	RS3A_HUMAN	ribosomal protein S3a						cell differentiation|endocrine pancreas development|induction of apoptosis|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_hematologic(180;0.093)					CAGttttttggttttttttttt	0.401													5	4	---	---	---	---	
MTMR12	54545	broad.mit.edu	37	5	32268614	32268615	+	Intron	INS	-	A	A	rs72294899		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32268614_32268615insA	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1						actccatctttaaaaaaaaaaa	0.158													5	3	---	---	---	---	
CEP120	153241	broad.mit.edu	37	5	122751561	122751562	+	Intron	INS	-	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122751561_122751562insA	uc003ktk.2	-						CEP120_uc011cwq.1_Intron|CEP120_uc010jcz.1_Intron	NM_153223	NP_694955	Q8N960	CE120_HUMAN	coiled-coil domain containing 100							centrosome				ovary(1)	1						gactccgtctcaaaaaaaaaaa	0.158													4	2	---	---	---	---	
PCDHA11	56138	broad.mit.edu	37	5	140250029	140250029	+	Frame_Shift_Del	DEL	G	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140250029delG	uc003lia.2	+	1	2199	c.1341delG	c.(1339-1341)GTGfs	p.V447fs	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Frame_Shift_Del_p.V447fs	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	447	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGCCGACGTGAACGACAATG	0.637													61	137	---	---	---	---	
DSP	1832	broad.mit.edu	37	6	7581127	7581142	+	Frame_Shift_Del	DEL	GCAGAAGCAGAAGGTG	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7581127_7581142delGCAGAAGCAGAAGGTG	uc003mxp.1	+	23	4983_4998	c.4704_4719delGCAGAAGCAGAAGGTG	c.(4702-4719)CTGCAGAAGCAGAAGGTGfs	p.L1568fs	DSP_uc003mxq.1_Intron	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	1568_1573	Central fibrous rod domain.|Potential.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AGCTGCAGCTGCAGAAGCAGAAGGTGGAAGAGGAGC	0.551													34	47	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34079166	34079167	+	Intron	DEL	CA	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34079166_34079167delCA	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc010jvk.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	ACCAACCGTGcacacacacaca	0.411													7	4	---	---	---	---	
KIAA0240	23506	broad.mit.edu	37	6	42789978	42789978	+	Intron	DEL	T	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42789978delT	uc003osn.1	+						KIAA0240_uc003osm.1_Intron|KIAA0240_uc011duw.1_Intron|KIAA0240_uc003oso.1_Intron|KIAA0240_uc003osp.1_Intron	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506											ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)			TCAGTAAttcttttttttttt	0.124													4	3	---	---	---	---	
SCIN	85477	broad.mit.edu	37	7	12669023	12669024	+	Intron	INS	-	CA	CA	rs147409814	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12669023_12669024insCA	uc003ssn.3	+						SCIN_uc010ktt.2_Intron|SCIN_uc003sso.3_Intron	NM_001112706	NP_001106177	Q9Y6U3	ADSV_HUMAN	scinderin isoform 1						actin filament capping|actin filament severing|actin nucleation|calcium ion-dependent exocytosis|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of megakaryocyte differentiation|positive regulation of secretion|regulation of chondrocyte differentiation	cell cortex|cytoskeleton	1-phosphatidylinositol binding|actin filament binding|calcium ion binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		CAGTTGCCATCCACAGGCAGCA	0.361													3	3	---	---	---	---	
DNAH11	8701	broad.mit.edu	37	7	21804843	21804844	+	Intron	INS	-	TG	TG	rs145919459	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21804843_21804844insTG	uc003svc.2	+							NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						AGCAGTGTTTCTGTGTCCAGTG	0.381									Kartagener_syndrome				3	9	---	---	---	---	
RAPGEF5	9771	broad.mit.edu	37	7	22194363	22194364	+	Intron	INS	-	T	T	rs150777301	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22194363_22194364insT	uc003svg.2	-						RAPGEF5_uc011jyl.1_Intron	NM_012294	NP_036426	Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1						ACAGAGTTAGATTTTTTATATA	0.386													7	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	55659699	55659699	+	IGR	DEL	C	-	-	rs140374894		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55659699delC								VOPP1 (19499 upstream) : LOC442308 (53613 downstream)																							CTCAGCTGCACCCCCCCTCTT	0.587													2	5	---	---	---	---	
COPG2	26958	broad.mit.edu	37	7	130329956	130329956	+	Intron	DEL	G	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130329956delG	uc003vqh.1	-							NM_012133	NP_036265	Q9UBF2	COPG2_HUMAN	coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)					aaaaaaaaaagaaaaGAAATG	0.179													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142448200	142448207	+	Intron	DEL	GGTGGAAA	-	-	rs112413030	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142448200_142448207delGGTGGAAA	uc011krr.1	+						uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|uc011ksl.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		GTTAACACTGGGTGGAAAGGTGGAAAGA	0.457													6	5	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151898379	151898380	+	Intron	DEL	AC	-	-	rs3839689		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151898379_151898380delAC	uc003wla.2	-						MLL3_uc003wkz.2_Intron	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		acagacacagacacacacacac	0.327			N		medulloblastoma								3	3	---	---	---	---	
FBXO25	26260	broad.mit.edu	37	8	363407	363407	+	Intron	DEL	T	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:363407delT	uc003wox.2	+						FBXO25_uc003woy.2_Intron|FBXO25_uc003woz.2_Intron	NM_183421	NP_904357	Q8TCJ0	FBX25_HUMAN	F-box only protein 25 isoform 1							nucleus|SCF ubiquitin ligase complex	actin binding|ubiquitin-protein ligase activity			lung(1)	1		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		TGCTTTCGTCTTTTTTTTTTT	0.100													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	2896876	2896876	+	Intron	DEL	C	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2896876delC	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		cgccttccttccttcctcctt	0.035													1	11	---	---	---	---	
PBK	55872	broad.mit.edu	37	8	27678359	27678359	+	Intron	DEL	A	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27678359delA	uc003xgi.2	-						PBK_uc011lap.1_Intron	NM_018492	NP_060962	Q96KB5	TOPK_HUMAN	PDZ binding kinase						mitosis		ATP binding|protein binding|protein serine/threonine kinase activity				0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		ttttttttttaaaacggagtc	0.134													4	2	---	---	---	---	
UBR5	51366	broad.mit.edu	37	8	103317191	103317191	+	Intron	DEL	A	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103317191delA	uc003ykr.1	-						UBR5_uc003yks.1_Intron	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			CTGAGAAAGTAAAAAAAAAAA	0.269													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137968133	137968134	+	IGR	INS	-	TC	TC			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137968133_137968134insTC								None (None upstream) : None (None downstream)																							cctccctccctttcttccctcc	0.000													4	3	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139668090	139668090	+	Intron	DEL	C	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139668090delC	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GATCTCCAATCCCGCCATCAC	0.413										HNSCC(7;0.00092)			92	89	---	---	---	---	
ZDHHC21	340481	broad.mit.edu	37	9	14632052	14632053	+	Intron	INS	-	AC	AC			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14632052_14632053insAC	uc003zli.2	-						ZDHHC21_uc003zlg.1_Intron	NM_178566	NP_848661	Q8IVQ6	ZDH21_HUMAN	zinc finger, DHHC-type containing 21						nitric oxide metabolic process|regulation of nitric-oxide synthase activity	Golgi membrane|integral to membrane	palmitoyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(50;4.31e-06)		aactagttaaaacacacacaaa	0.064													4	2	---	---	---	---	
PLXDC2	84898	broad.mit.edu	37	10	20450991	20451008	+	Intron	DEL	GAGAGAGAGAGAAGGAAG	-	-	rs71959057		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20450991_20451008delGAGAGAGAGAGAAGGAAG	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron|PLXDC2_uc009xkc.1_Intron	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4						gagagagagagagagagagagaaggaaggaaggaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42388292	42388292	+	IGR	DEL	G	-	-	rs72505277		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42388292delG								None (None upstream) : LOC441666 (439023 downstream)																							aacatcgaatggaatcgaatg	0.000													1	11	---	---	---	---	
HPS1	3257	broad.mit.edu	37	10	100195341	100195341	+	Intron	DEL	C	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100195341delC	uc010qpf.1	-						HPS1_uc001kpi.1_Intron|HPS1_uc001kpj.1_Intron|HPS1_uc001kpk.1_Intron|HPS1_uc009xwb.2_Intron|HPS1_uc010qph.1_Intron|HPS1_uc001kpl.2_Intron	NM_000195	NP_000186	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1 protein isoform a						lysosome organization|response to stimulus|visual perception	cytoplasmic membrane-bounded vesicle|integral to plasma membrane|lysosome|membrane fraction|soluble fraction	protein dimerization activity			skin(1)	1		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		CCTGTGGACTCCCCATCAAGC	0.532									Hermansky-Pudlak_syndrome				51	85	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	96853580	96853583	+	IGR	DEL	TTCC	-	-	rs80320476	byFrequency	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96853580_96853583delTTCC								JRKL (726853 upstream) : None (None downstream)																							tctctctcctttccttccttcctt	0.103													5	10	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2547550	2547552	+	Intron	DEL	TCA	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2547550_2547552delTCA	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	gtgatggtggtcatggtagtcat	0.138													4	2	---	---	---	---	
SOAT2	8435	broad.mit.edu	37	12	53514402	53514403	+	Intron	INS	-	A	A	rs35658019		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53514402_53514403insA	uc001sbv.2	+						SOAT2_uc009zms.2_Intron	NM_003578	NP_003569	O75908	SOAT2_HUMAN	acyl-CoA:cholesterol acyltransferase 2						cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|macrophage derived foam cell differentiation|very-low-density lipoprotein particle assembly	brush border|endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			ovary(1)	1						cagcctgtctcaaaaaaaaaaa	0.193													6	4	---	---	---	---	
PA2G4	5036	broad.mit.edu	37	12	56505493	56505494	+	Intron	INS	-	AT	AT	rs143474707	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56505493_56505494insAT	uc001sjm.2	+						PA2G4_uc009zol.2_Intron|PA2G4_uc009zom.2_Intron	NM_006191	NP_006182	Q9UQ80	PA2G4_HUMAN	ErbB3-binding protein 1						cell cycle arrest|cell proliferation|negative regulation of transcription, DNA-dependent|regulation of translation|rRNA processing	cytoplasm|nucleolus|ribonucleoprotein complex	DNA binding|RNA binding|sequence-specific DNA binding transcription factor activity|ubiquitin protein ligase binding				0			OV - Ovarian serous cystadenocarcinoma(18;0.0739)			tggattttaaaatatatataTA	0.035													4	2	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	81655692	81655693	+	Intron	INS	-	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81655692_81655693insT	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010suf.1_Intron|PPFIA2_uc009zsh.2_Intron	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6						ATTTTTTTGTCTTTTTTTTTTT	0.406													4	2	---	---	---	---	
ATP2B1	490	broad.mit.edu	37	12	90010464	90010464	+	Intron	DEL	A	-	-	rs113951213		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90010464delA	uc001tbh.2	-						ATP2B1_uc001tbg.2_Intron|ATP2B1_uc001tbf.2_Intron	NM_001682	NP_001673	P20020	AT2B1_HUMAN	plasma membrane calcium ATPase 1 isoform 1b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						GTTCACACAGAAAAAAAAAAA	0.343													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119145754	119145756	+	IGR	DEL	TGG	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119145754_119145756delTGG								SUDS3 (289915 upstream) : SRRM4 (273640 downstream)																							gtgatggtgatggtggtggtggt	0.000													3	4	---	---	---	---	
ULK1	8408	broad.mit.edu	37	12	132403267	132403275	+	Intron	DEL	GGGTGTGTG	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132403267_132403275delGGGTGTGTG	uc001uje.2	+							NM_003565	NP_003556	O75385	ULK1_HUMAN	Unc-51-like kinase 1						autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		TCTGGCTGGAGGGTgtgtggggtgtgtgg	0.316													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19957362	19957362	+	IGR	DEL	G	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19957362delG								LOC100101938 (38249 upstream) : TPTE2 (39659 downstream)																							TGGGAGGACTGGTTGTGCTGC	0.632													13	15	---	---	---	---	
NALCN	259232	broad.mit.edu	37	13	102028868	102028872	+	Intron	DEL	AAAAT	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102028868_102028872delAAAAT	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Intron|NALCN_uc001vpa.2_Intron	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ctccatctcaaaaataaaataaaat	0.141													1	8	---	---	---	---	
HEATR5A	25938	broad.mit.edu	37	14	31819967	31819970	+	Intron	DEL	TTTG	-	-	rs72055697		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31819967_31819970delTTTG	uc001wrf.3	-						HEATR5A_uc010ami.2_Intron|HEATR5A_uc001wrg.1_Intron|HEATR5A_uc010tpk.1_Intron	NM_015473	NP_056288	Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A								binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		TAGGTAAGTTtttgtttgtttgtt	0.176													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82284325	82284326	+	IGR	INS	-	T	T			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82284325_82284326insT								SEL1L (284120 upstream) : None (None downstream)																							tccttccttccttcttccttcc	0.208													3	3	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40921694	40921706	+	Intron	DEL	TTTTTTTTTTTTT	-	-	rs71104709		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40921694_40921706delTTTTTTTTTTTTT	uc010bbs.1	+						CASC5_uc010bbt.1_Intron	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		ttgccttttcttttttttttttttttttttttt	0.103													3	3	---	---	---	---	
TP53BP1	7158	broad.mit.edu	37	15	43787694	43787695	+	Intron	DEL	CA	-	-	rs71659753		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43787694_43787695delCA	uc001zrs.2	-						TP53BP1_uc001zrq.3_5'Flank|TP53BP1_uc001zrr.3_5'Flank|TP53BP1_uc010udq.1_5'Flank	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3						double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		gagactccgtcacacacacaca	0.000								Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	44028129	44028129	+	IGR	DEL	T	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44028129delT								CKMT1A (36710 upstream) : CATSPER2P1 (19 downstream)																							agcccggcaattttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	48198789	48198790	+	IGR	DEL	AC	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48198789_48198790delAC								SEMA6D (132370 upstream) : SLC24A5 (214379 downstream)																							tttcttgcttacacacacacac	0.010													4	2	---	---	---	---	
SLC28A1	9154	broad.mit.edu	37	15	85443229	85443232	+	Intron	DEL	AGGC	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85443229_85443232delAGGC	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)			gaaAAGAAAAaggcaggcaggcag	0.025													6	8	---	---	---	---	
RRN3	54700	broad.mit.edu	37	16	15177335	15177335	+	Intron	DEL	T	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15177335delT	uc002dde.2	-						PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzp.1_Intron|RRN3_uc010uzq.1_Intron|RRN3_uc002ddf.1_Intron	NM_018427	NP_060897	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor						regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1						TACAAACAACTTTTCCATGAT	0.269													39	23	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28600201	28600202	+	Intron	INS	-	T	T	rs139158764	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28600201_28600202insT	uc010vct.1	-						CCDC101_uc002dqf.2_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		CAGATTTCTAGTTTCACCATGA	0.163													6	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33371342	33371342	+	IGR	DEL	G	-	-	rs28624695		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33371342delG								SLC6A10P (474879 upstream) : MIR1826 (594166 downstream)																							acttgaacccggggggcagag	0.020													5	3	---	---	---	---	
CDH8	1006	broad.mit.edu	37	16	61689381	61689381	+	Frame_Shift_Del	DEL	C	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61689381delC	uc002eog.1	-	11	2151	c.1899delG	c.(1897-1899)TTGfs	p.L633fs		NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	633	Helical; (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		TACCTAACAGCAAAATGATGC	0.428													26	53	---	---	---	---	
ZFHX3	463	broad.mit.edu	37	16	72991632	72991636	+	Frame_Shift_Del	DEL	GCCAG	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72991632_72991636delGCCAG	uc002fck.2	-	2	3082_3086	c.2409_2413delCTGGC	c.(2407-2415)ACCTGGCGGfs	p.T803fs	ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	803_805	C2H2-type 5; atypical.				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				ACCTCGCACCGCCAGGTGGGTTTGG	0.439													53	54	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25289230	25289233	+	IGR	DEL	TCTA	-	-	rs138697975		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25289230_25289233delTCTA								None (None upstream) : WSB1 (331873 downstream)																							GTTTGTTACCTCTATCTATTGACT	0.343													5	4	---	---	---	---	
NGFR	4804	broad.mit.edu	37	17	47580229	47580230	+	Intron	INS	-	CTTC	CTTC	rs71743494		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47580229_47580230insCTTC	uc002ioz.3	+							NM_002507	NP_002498	P08138	TNR16_HUMAN	nerve growth factor receptor precursor						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|negative regulation of axonogenesis|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis	cell surface|cytosol|endosome|extracellular region|integral to plasma membrane|nucleoplasm				ovary(1)|lung(1)	2	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					ttccttccttcctttctctctc	0.153													5	3	---	---	---	---	
TAC4	255061	broad.mit.edu	37	17	47925054	47925055	+	Intron	INS	-	AC	AC	rs150685532	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47925054_47925055insAC	uc002ipo.1	-						TAC4_uc002ipp.1_Intron|TAC4_uc002ipq.1_Intron|TAC4_uc002ipr.1_Intron|TAC4_uc002ips.1_Intron|TAC4_uc002ipt.2_Intron|TAC4_uc002ipu.2_Intron	NM_170685	NP_733786	Q86UU9	TKN4_HUMAN	tachykinin 4 isoform alpha						regulation of blood pressure	extracellular region				breast(1)	1						cacacacacagacacacacaca	0.183													7	4	---	---	---	---	
TSEN54	283989	broad.mit.edu	37	17	73513183	73513191	+	Intron	DEL	GCCCTCCCT	-	-	rs113075319		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73513183_73513191delGCCCTCCCT	uc002jof.1	+						CASKIN2_uc002joc.2_5'Flank|CASKIN2_uc002jod.2_5'Flank|TSEN54_uc002joe.1_Intron	NM_207346	NP_997229	Q7Z6J9	SEN54_HUMAN	tRNA splicing endonuclease 54 homolog						mRNA processing|tRNA splicing, via endonucleolytic cleavage and ligation	nucleolus				ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			ACCGGGGACCgccctccctgccctccctg	0.574													2	4	---	---	---	---	
SRP68	6730	broad.mit.edu	37	17	74056231	74056232	+	Intron	DEL	AG	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74056231_74056232delAG	uc002jqk.1	-						SRP68_uc010wsu.1_Intron|SRP68_uc002jql.1_Intron	NM_014230	NP_055045	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa						response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			ovary(1)	1						aaaaaaaaaaagaaaaaGTTTT	0.114													4	2	---	---	---	---	
DNAH17	8632	broad.mit.edu	37	17	76548595	76548596	+	Intron	DEL	TT	-	-	rs35637364		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76548595_76548596delTT	uc002jvv.1	-											RecName: Full=Dynein heavy chain 17, axonemal; AltName: Full=Axonemal beta dynein heavy chain 17; AltName: Full=Ciliary dynein heavy chain 17; AltName: Full=Ciliary dynein heavy chain-like protein 1; AltName: Full=Axonemal dynein heavy chain-like protein 1; AltName: Full=Dynein light chain 2, axonemal;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			ACAGATGGGCTTTTTTTTTTTT	0.495													9	6	---	---	---	---	
FOXK2	3607	broad.mit.edu	37	17	80544327	80544327	+	Intron	DEL	G	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80544327delG	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)			aaggtgggccggggggggaaa	0.000													4	2	---	---	---	---	
SPIRE1	56907	broad.mit.edu	37	18	12451072	12451072	+	Intron	DEL	A	-	-	rs76865998		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12451072delA	uc002kre.2	-						SPIRE1_uc002krc.2_Intron|SPIRE1_uc010wzw.1_Intron|SPIRE1_uc010wzx.1_Intron|SPIRE1_uc010wzy.1_Intron	NM_001128626	NP_001122098	Q08AE8	SPIR1_HUMAN	spire homolog 1 isoform a							cytoskeleton|perinuclear region of cytoplasm	actin binding				0						TGTCCATTTGAAAAAAAAAAA	0.184													4	2	---	---	---	---	
KCNN1	3780	broad.mit.edu	37	19	18076829	18076844	+	Intron	DEL	CCTGCCTTCCTTCCTT	-	-	rs72017725		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18076829_18076844delCCTGCCTTCCTTCCTT	uc002nht.2	+						KCNN1_uc010xqa.1_Intron	NM_002248	NP_002239	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance						synaptic transmission	voltage-gated potassium channel complex	calmodulin binding|small conductance calcium-activated potassium channel activity				0						tgcctgcctgcctgccttccttccttccttccttcc	0.329													4	2	---	---	---	---	
TULP2	7288	broad.mit.edu	37	19	49384468	49384468	+	Intron	DEL	C	-	-	rs68173909		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49384468delC	uc002pkz.2	-							NM_003323	NP_003314	O00295	TULP2_HUMAN	tubby like protein 2						visual perception	cytoplasm|extracellular region				ovary(1)|kidney(1)|skin(1)	3		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		ttttttttttctttttttttt	0.199													20	9	---	---	---	---	
CGB	1082	broad.mit.edu	37	19	49543006	49543006	+	Intron	DEL	A	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49543006delA	uc010yad.1	-						CGB1_uc002plx.2_5'Flank	NM_033183	NP_149439	P01233	CGHB_HUMAN	chorionic gonadotropin, beta polypeptide 8						apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)	actccatctcaaaaaaaaaaa	0.204													4	2	---	---	---	---	
ZNF587	84914	broad.mit.edu	37	19	58367778	58367778	+	Intron	DEL	T	-	-	rs113480202		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58367778delT	uc002qql.2	+						ZNF587_uc002qqb.2_Intron|ZNF587_uc010yhh.1_Intron|ZNF587_uc002qqi.1_Intron|ZNF587_uc002qqj.1_Intron|ZNF814_uc002qqk.2_Intron|ZNF587_uc010yhk.1_Intron	NM_032828	NP_116217	Q96SQ5	ZN587_HUMAN	zinc finger protein 587						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		TCCTCTCCTGttttttttttt	0.244													5	3	---	---	---	---	
DNMT3B	1789	broad.mit.edu	37	20	31387738	31387741	+	Intron	DEL	TAGT	-	-	rs145092112		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31387738_31387741delTAGT	uc002wyc.2	+						DNMT3B_uc010zty.1_Intron|DNMT3B_uc002wyd.2_Intron|DNMT3B_uc002wye.2_Intron|DNMT3B_uc010gee.2_Intron|DNMT3B_uc010gef.2_Intron|DNMT3B_uc010ztz.1_Intron|DNMT3B_uc010zua.1_Intron|DNMT3B_uc002wyf.2_Intron|DNMT3B_uc002wyg.2_Intron|DNMT3B_uc010geg.2_5'Flank|DNMT3B_uc010geh.2_5'Flank	NM_006892	NP_008823	Q9UBC3	DNM3B_HUMAN	DNA cytosine-5 methyltransferase 3 beta isoform						negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5						GGAGATAAACTAGTTAACAACTAC	0.363													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	32711134	32711134	+	IGR	DEL	A	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32711134delA								EIF2S2 (11049 upstream) : ASIP (137037 downstream)																							ATTAAGCCTGAAAAAAAAAAA	0.313													6	3	---	---	---	---	
C20orf111	51526	broad.mit.edu	37	20	42831626	42831626	+	Frame_Shift_Del	DEL	A	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42831626delA	uc002xlk.2	-	3	303	c.166delT	c.(166-168)TGTfs	p.C56fs		NM_016470	NP_057554	Q9NX31	CT111_HUMAN	oxidative stress responsive 1	56											0		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			TTAGATGCACATGTGGTTTTA	0.408													60	37	---	---	---	---	
SLC9A8	23315	broad.mit.edu	37	20	48500779	48500779	+	Intron	DEL	G	-	-	rs11478900		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48500779delG	uc002xuv.1	+						SLC9A8_uc010zym.1_Intron|SLC9A8_uc010gic.2_3'UTR|SLC9A8_uc010gid.2_Intron	NM_015266	NP_056081	Q9Y2E8	SL9A8_HUMAN	sodium/hydrogen exchanger 8							Golgi membrane|integral to membrane	sodium:hydrogen antiporter activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			acacacacacgacacacacac	0.154													3	3	---	---	---	---	
CBR3	874	broad.mit.edu	37	21	37510401	37510402	+	Intron	INS	-	TTTAGTTTAG	TTTAGTTTAG			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37510401_37510402insTTTAGTTTAG	uc002yve.2	+						uc002yvc.1_Intron|uc002yvd.1_Intron	NM_001236	NP_001227	O75828	CBR3_HUMAN	carbonyl reductase 3							cytosol|nucleus	carbonyl reductase (NADPH) activity|NADPH binding				0						CACTCCAACATtttagtttagt	0.287													5	3	---	---	---	---	
CLDN14	23562	broad.mit.edu	37	21	37886916	37886919	+	Intron	DEL	AGAA	-	-	rs141197637	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37886916_37886919delAGAA	uc002yvn.1	-						CLDN14_uc002yvo.1_Intron	NM_001146078	NP_001139550	O95500	CLD14_HUMAN	claudin 14						calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0						TTATCGTGAGAGAAAgtgtgtgtg	0.216													4	2	---	---	---	---	
TTC3	7267	broad.mit.edu	37	21	38536643	38536643	+	Intron	DEL	T	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38536643delT	uc002yvz.2	+						TTC3_uc011aee.1_Intron|TTC3_uc002ywa.2_Intron|TTC3_uc002ywb.2_Intron|TTC3_uc010gnf.2_Intron|TTC3_uc002ywc.2_Intron|TTC3_uc002ywd.1_Intron	NM_001001894	NP_001001894	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)				TAATTTAGGAttttttttttt	0.144													4	4	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26272012	26272013	+	Intron	DEL	TA	-	-	rs56708676		TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26272012_26272013delTA	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						tgtgtgtgtgtatgtgtTTTAA	0.376													4	2	---	---	---	---	
RFPL2	10739	broad.mit.edu	37	22	32595898	32595899	+	Intron	INS	-	C	C	rs150809092	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32595898_32595899insC	uc003amg.3	-						RFPL2_uc003amf.3_Intron|RFPL2_uc003amh.3_Intron	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2								zinc ion binding			skin(1)	1						CCGCTCGCCCACTCACAGGCCA	0.634													8	8	---	---	---	---	
USP9X	8239	broad.mit.edu	37	X	41047083	41047084	+	Intron	DEL	TT	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41047083_41047084delTT	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						CGCCCCCACCtttttttttttt	0.203													4	3	---	---	---	---	
SSX3	10214	broad.mit.edu	37	X	48213720	48213721	+	Intron	INS	-	A	A			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48213720_48213721insA	uc004djd.1	-						SSX3_uc004dje.2_Intron|SSX3_uc010nic.2_Intron	NM_021014	NP_066294	Q99909	SSX3_HUMAN	synovial sarcoma, X breakpoint 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0						ctgactcaaacaaaaaaaaaaa	0.248													4	2	---	---	---	---	
HUWE1	10075	broad.mit.edu	37	X	53652829	53652852	+	Intron	DEL	GCCGGGGCCGGGGCCGGGGCCGGT	-	-	rs78801842	by1000genomes	TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53652829_53652852delGCCGGGGCCGGGGCCGGGGCCGGT	uc004dsp.2	-							NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1						base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						cggggccggggccggggccggggccggggccggtgccgggactg	0.219													4	44	---	---	---	---	
BEX1	55859	broad.mit.edu	37	X	102318390	102318393	+	Intron	DEL	GCCC	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102318390_102318393delGCCC	uc004ejt.1	-							NM_018476	NP_060946	Q9HBH7	BEX1_HUMAN	brain expressed, X-linked 1						cell differentiation|nervous system development	cytoplasm|nucleus				ovary(1)	1						CCCCATTCGAGCCCGCCCCCCCCC	0.564													5	3	---	---	---	---	
PLAC1	10761	broad.mit.edu	37	X	133785195	133785195	+	Intron	DEL	A	-	-			TCGA-34-5240-01	TCGA-34-5240-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133785195delA	uc004exo.1	-						PLAC1_uc004exp.1_Intron	NM_021796	NP_068568	Q9HBJ0	PLAC1_HUMAN	placenta-specific 1 precursor						placenta development	extracellular region				pancreas(1)	1	Acute lymphoblastic leukemia(192;0.000127)					TACAAAAAATAAGCAAAAGCA	0.413													12	23	---	---	---	---	
