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
AKR7L	246181	broad.mit.edu	37	1	19597012	19597012	+	Missense_Mutation	SNP	G	C	C	rs76741883	byFrequency	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19597012G>C	uc010ocx.1	-	4	440	c.440C>G	c.(439-441)GCC>GGC	p.A147G	AKR7L_uc010ocy.1_Missense_Mutation_p.A147G	NM_201252	NP_957704			aflatoxin B1 aldehyde reductase 3 isoform 1												0						CACTTCCCAGGCGGCATAGTT	0.622													5	108	---	---	---	---	PASS
HSPG2	3339	broad.mit.edu	37	1	22207181	22207181	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22207181C>A	uc001bfj.2	-	15	2006	c.1966G>T	c.(1966-1968)GCT>TCT	p.A656S	HSPG2_uc009vqd.2_Missense_Mutation_p.A657S	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	656	Laminin IV type A 1.				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)	TGGTTCAGAGCACCAGGTTGG	0.662													12	7	---	---	---	---	PASS
AGL	178	broad.mit.edu	37	1	100327247	100327247	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100327247T>C	uc001dsi.1	+	3	671	c.271T>C	c.(271-273)TTT>CTT	p.F91L	AGL_uc001dsj.1_Missense_Mutation_p.F91L|AGL_uc001dsk.1_Missense_Mutation_p.F91L|AGL_uc001dsl.1_Missense_Mutation_p.F91L|AGL_uc001dsm.1_Missense_Mutation_p.F75L|AGL_uc001dsn.1_Missense_Mutation_p.F74L	NM_000642	NP_000633	P35573	GDE_HUMAN	amylo-1,6-glucosidase,	91	4-alpha-glucanotransferase.				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		ATCTGGTTCATTTCAGTATTA	0.313													37	108	---	---	---	---	PASS
NHLH2	4808	broad.mit.edu	37	1	116380707	116380707	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116380707G>T	uc009wgz.2	-	2	792	c.287C>A	c.(286-288)GCC>GAC	p.A96D	NHLH2_uc001efy.2_Missense_Mutation_p.A96D	NM_001111061	NP_001104531	Q02577	HEN2_HUMAN	nescient helix loop helix 2	96	Helix-loop-helix motif.				cell differentiation|central nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0	Lung SC(450;0.184)	all_cancers(81;1.75e-06)|all_epithelial(167;1.16e-06)|all_lung(203;9.55e-06)|Lung NSC(69;5.83e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		CTCGGCGAAGGCCAAGTTGAA	0.672													3	14	---	---	---	---	PASS
TDRKH	11022	broad.mit.edu	37	1	151751596	151751596	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151751596C>G	uc009wnb.1	-	5	726	c.544G>C	c.(544-546)GAA>CAA	p.E182Q	TDRKH_uc001eyy.2_5'UTR|TDRKH_uc001ezb.3_Missense_Mutation_p.E178Q|TDRKH_uc001ezc.3_Missense_Mutation_p.E137Q|TDRKH_uc001eza.3_Missense_Mutation_p.E182Q|TDRKH_uc001ezd.3_Missense_Mutation_p.E182Q|TDRKH_uc010pdn.1_5'UTR	NM_006862	NP_006853	Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing isoform a	182	KH 2.						RNA binding			ovary(1)|pancreas(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCTGCCACTTCCTTCTGTGTT	0.398													98	293	---	---	---	---	PASS
BCAN	63827	broad.mit.edu	37	1	156616762	156616762	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156616762G>T	uc001fpp.2	+	3	597	c.261G>T	c.(259-261)GAG>GAT	p.E87D	BCAN_uc001fpo.2_Missense_Mutation_p.E87D	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	87	Ig-like V-type.				cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGGCCGGGAGGCAGAGGTGC	0.706													4	60	---	---	---	---	PASS
CADM3	57863	broad.mit.edu	37	1	159163314	159163314	+	Silent	SNP	C	A	A	rs3026987	byFrequency	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159163314C>A	uc001ftl.2	+	4	626	c.484C>A	c.(484-486)CGG>AGG	p.R162R	CADM3_uc009wsx.1_Silent_p.R196R|CADM3_uc009wsy.1_Silent_p.R162R|CADM3_uc001ftk.2_Silent_p.R196R	NM_001127173	NP_001120645	Q8N126	CADM3_HUMAN	cell adhesion molecule 3 isoform 2	162	Ig-like C2-type 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly|heterophilic cell-cell adhesion|homophilic cell adhesion	cell-cell junction|integral to membrane	protein homodimerization activity			ovary(2)	2	all_hematologic(112;0.0429)					GCCTGCAGCCCGGCTCACCTG	0.512													15	90	---	---	---	---	PASS
FAM163A	148753	broad.mit.edu	37	1	179782917	179782917	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179782917T>C	uc009wxj.2	+	6	556	c.97T>C	c.(97-99)TAC>CAC	p.Y33H	FAM163A_uc001gnj.2_Missense_Mutation_p.Y33H|FAM163A_uc009wxk.2_Missense_Mutation_p.Y33H	NM_173509	NP_775780	Q96GL9	F163A_HUMAN	hypothetical protein LOC148753	33						integral to membrane				ovary(1)	1						CGCACAGTATTACTGCTGCAA	0.627													8	59	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214782168	214782168	+	Intron	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214782168G>A	uc001hkm.2	+						uc001hkn.1_Silent_p.L6L	NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F						cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGCTCACTCAGCGACAGCCCG	0.572													3	16	---	---	---	---	PASS
GMCL1	64395	broad.mit.edu	37	2	70057010	70057010	+	5'UTR	SNP	G	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70057010G>T	uc002sfu.2	+	1						NM_178439	NP_848526	Q96IK5	GMCL1_HUMAN	germ cell-less						cell differentiation|multicellular organismal development|spermatogenesis	nuclear matrix				ovary(3)	3						CTGAAGTCTCGGGGAGCCGTG	0.726													4	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89399776	89399776	+	Intron	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89399776G>A	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		TCCTTACCTGGGAAACAGAGC	0.498													65	77	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89495655	89495655	+	RNA	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89495655C>T	uc010ytr.1	-	25		c.3206G>A			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		GTCCCTGACCCGCTGCCACTG	0.507													16	30	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125204422	125204422	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125204422C>T	uc002tno.2	+	6	1190	c.826C>T	c.(826-828)CGG>TGG	p.R276W	CNTNAP5_uc010flu.2_Missense_Mutation_p.R276W	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	276	Laminin G-like 1.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		CCTCATTGAGCGGGTGGGCAA	0.597													51	79	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141473656	141473656	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141473656G>T	uc002tvj.1	-	37	6881	c.5909C>A	c.(5908-5910)ACA>AAA	p.T1970K		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1970	Extracellular (Potential).|LDL-receptor class B 20.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACCATGATCTGTCCAATATAT	0.318										TSP Lung(27;0.18)			22	344	---	---	---	---	PASS
GAD1	2571	broad.mit.edu	37	2	171705302	171705302	+	Intron	SNP	A	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171705302A>T	uc002ugi.2	+						GAD1_uc010fqc.2_5'Flank	NM_000817	NP_000808	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 isoform GAD67						glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion|protein-pyridoxal-5-phosphate linkage	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|plasma membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(1)	1					L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	AACATGCATCATGGTACCCAC	0.418													36	60	---	---	---	---	PASS
ANO10	55129	broad.mit.edu	37	3	43618737	43618737	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43618737G>T	uc003cmv.2	-	6	780	c.609C>A	c.(607-609)TAC>TAA	p.Y203*	ANO10_uc011azs.1_Nonsense_Mutation_p.Y203*|ANO10_uc003cmw.2_Nonsense_Mutation_p.Y137*|ANO10_uc010hil.2_Intron|ANO10_uc011azt.1_Nonsense_Mutation_p.Y92*	NM_018075	NP_060545	Q9NW15	ANO10_HUMAN	transmembrane protein 16K	203	Cytoplasmic (Potential).				cell death	chloride channel complex	chloride channel activity			ovary(2)	2						TTTCCCCAAAGTAGCCACGAA	0.338													4	19	---	---	---	---	PASS
DOCK3	1795	broad.mit.edu	37	3	50879110	50879110	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50879110G>A	uc011bds.1	+	3	149	c.126G>A	c.(124-126)TGG>TGA	p.W42*		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	42	SH3.					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		TTTTAGGTTGGTACAGAGGAG	0.294													7	10	---	---	---	---	PASS
TMSL3	7117	broad.mit.edu	37	4	91760120	91760120	+	Silent	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91760120C>T	uc003hsy.2	-	1	150	c.69G>A	c.(67-69)ACG>ACA	p.T23T	FAM190A_uc003hsv.3_Intron|FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsx.2_Intron	NM_183049	NP_898870			thymosin-like 3												0		all_cancers(2;6.48e-24)|all_epithelial(2;3.86e-25)|Colorectal(2;8.52e-12)|all_lung(2;3.73e-07)|Lung NSC(2;7.99e-07)|Renal(2;0.0243)|Hepatocellular(203;0.0411)		Epithelial(2;5.28e-11)|OV - Ovarian serous cystadenocarcinoma(123;8.9e-10)|all cancers(2;3.21e-09)|STAD - Stomach adenocarcinoma(1;0.0201)		TTTTCTCTTGCGTCTCTGTCT	0.507													119	160	---	---	---	---	PASS
TNIP3	79931	broad.mit.edu	37	4	122053645	122053645	+	3'UTR	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122053645C>T	uc010ing.2	-	11					TNIP3_uc010inh.2_3'UTR|TNIP3_uc011cgj.1_3'UTR	NM_024873	NP_079149	Q96KP6	TNIP3_HUMAN	TNFAIP3 interacting protein 3											ovary(1)	1						GTATTCATACCAAAGGAAAAC	0.423													9	13	---	---	---	---	PASS
PLK4	10733	broad.mit.edu	37	4	128814966	128814966	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128814966G>A	uc003ifo.2	+	13	2737	c.2492G>A	c.(2491-2493)AGA>AAA	p.R831K	PLK4_uc011cgs.1_Missense_Mutation_p.R799K|PLK4_uc011cgt.1_Missense_Mutation_p.R790K	NM_014264	NP_055079	O00444	PLK4_HUMAN	polo-like kinase 4	831					G2/M transition of mitotic cell cycle|positive regulation of centriole replication|trophoblast giant cell differentiation	centriole|cleavage furrow|cytosol|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0						ACGAGAGAGAGAGCATCTTTC	0.299													9	306	---	---	---	---	PASS
F11	2160	broad.mit.edu	37	4	187197050	187197050	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187197050G>T	uc003iza.1	+	6	928	c.595G>T	c.(595-597)GCT>TCT	p.A199S		NM_000128	NP_000119	P03951	FA11_HUMAN	coagulation factor XI precursor	199					blood coagulation, intrinsic pathway|plasminogen activation|positive regulation of fibrinolysis	extracellular space|plasma membrane	heparin binding|serine-type endopeptidase activity				0		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	TTCTAATCTGGGTAATTATCG	0.408													18	40	---	---	---	---	PASS
SKIV2L2	23517	broad.mit.edu	37	5	54603876	54603876	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54603876T>A	uc003jpy.3	+	1	301	c.35T>A	c.(34-36)GTG>GAG	p.V12E	SKIV2L2_uc011cqi.1_5'UTR|DHX29_uc003jpx.2_5'Flank|DHX29_uc010ivw.2_5'Flank	NM_015360	NP_056175	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2	12					maturation of 5.8S rRNA	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)|skin(1)	2		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				CTGTTCAGCGTGTTCGAGGGC	0.582													23	110	---	---	---	---	PASS
NR2F1	7025	broad.mit.edu	37	5	92923847	92923847	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92923847G>A	uc003kkj.2	+	2	2375	c.688G>A	c.(688-690)GCC>ACC	p.A230T		NM_005654	NP_005645	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	230					negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding			urinary_tract(1)|ovary(1)|lung(1)	3		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		GCTCTTCAGCGCCGTCGAGTG	0.637													14	105	---	---	---	---	PASS
DAAM2	23500	broad.mit.edu	37	6	39835571	39835571	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39835571G>T	uc003oow.2	+	6	870	c.714G>T	c.(712-714)CAG>CAT	p.Q238H	DAAM2_uc010jxc.2_Missense_Mutation_p.Q238H|DAAM2_uc003oox.2_Missense_Mutation_p.Q238H	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of	238	GBD/FH3.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					AGGTGCTGCAGGCCATGCTGC	0.632													3	22	---	---	---	---	PASS
FAM135A	57579	broad.mit.edu	37	6	71232237	71232237	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71232237T>G	uc003pfj.2	+	11	1184	c.1051T>G	c.(1051-1053)TTC>GTC	p.F351V	FAM135A_uc003pfi.2_Missense_Mutation_p.F351V|FAM135A_uc003pfh.2_Missense_Mutation_p.F334V|FAM135A_uc003pfk.2_Missense_Mutation_p.F377V|FAM135A_uc003pfl.2_Missense_Mutation_p.F214V|FAM135A_uc003pfn.2_5'Flank|FAM135A_uc003pfo.1_5'Flank	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c	351										central_nervous_system(1)	1						TTCTGAGGCATTCTTTTGTTT	0.333													72	192	---	---	---	---	PASS
DFNA5	1687	broad.mit.edu	37	7	24756951	24756951	+	Missense_Mutation	SNP	C	T	T	rs12540919	byFrequency	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24756951C>T	uc010kus.1	-	5	707	c.619G>A	c.(619-621)GTG>ATG	p.V207M	DFNA5_uc003swz.2_Missense_Mutation_p.V43M|DFNA5_uc003sxa.1_Missense_Mutation_p.V207M|DFNA5_uc010kut.1_Missense_Mutation_p.V43M|DFNA5_uc003sxb.2_Missense_Mutation_p.V207M	NM_001127453	NP_001120925	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5 protein isoform	207					sensory perception of sound					ovary(1)	1						TCCAGCACCACGTTGGAGTCC	0.577													28	45	---	---	---	---	PASS
TECPR1	25851	broad.mit.edu	37	7	97851719	97851719	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97851719C>T	uc003upg.2	-	22	3248	c.3043G>A	c.(3043-3045)GTG>ATG	p.V1015M		NM_015395	NP_056210	Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	1015	TECPR 7.					integral to membrane	protein binding			pancreas(1)	1						GAGGGGTACACGGATCCCCGG	0.672													6	10	---	---	---	---	PASS
TMEM130	222865	broad.mit.edu	37	7	98460809	98460809	+	Silent	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98460809G>A	uc003upo.2	-	2	489	c.300C>T	c.(298-300)CCC>CCT	p.P100P	TMEM130_uc011kiq.1_Silent_p.P81P|TMEM130_uc011kir.1_Silent_p.P100P|TMEM130_uc003upn.2_Intron	NM_001134450	NP_001127922	Q8N3G9	TM130_HUMAN	transmembrane protein 130 isoform a	100	Extracellular (Potential).					Golgi membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GGAATTCCCCGGGCACGTGGC	0.637													11	117	---	---	---	---	PASS
ZNF800	168850	broad.mit.edu	37	7	127013912	127013912	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127013912C>T	uc003vlx.1	-	5	1741	c.1478G>A	c.(1477-1479)CGT>CAT	p.R493H	ZNF800_uc003vlw.1_Missense_Mutation_p.R396H|ZNF800_uc003vly.1_Missense_Mutation_p.R493H|ZNF800_uc010lla.2_Missense_Mutation_p.R493H	NM_176814	NP_789784	Q2TB10	ZN800_HUMAN	zinc finger protein 800	493	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						AGTAAACTGACGTTTACAAAG	0.383													34	189	---	---	---	---	PASS
PTPRN2	5799	broad.mit.edu	37	7	157903565	157903565	+	Silent	SNP	G	A	A	rs149853423	byFrequency	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157903565G>A	uc003wno.2	-	10	1720	c.1599C>T	c.(1597-1599)GTC>GTT	p.V533V	PTPRN2_uc003wnp.2_Silent_p.V516V|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Silent_p.V495V|PTPRN2_uc011kwa.1_Silent_p.V556V	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	533	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GGAGGCGGGCGACGTCCTCCA	0.652													3	0	---	---	---	---	PASS
TNKS	8658	broad.mit.edu	37	8	9413594	9413594	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9413594A>G	uc003wss.2	+	1	150	c.145A>G	c.(145-147)ACG>GCG	p.T49A	TNKS_uc011kwv.1_Missense_Mutation_p.T49A|uc003wsr.1_RNA	NM_003747	NP_003738	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related	49					mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)		AGCCTCTCCCACGGCCAGCGG	0.776													4	5	---	---	---	---	PASS
RP1L1	94137	broad.mit.edu	37	8	10464307	10464307	+	3'UTR	SNP	G	A	A	rs12542104	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10464307G>A	uc003wtc.2	-	4						NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1						intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)		ATGTACTATGGACATCTCCAG	0.463													5	10	---	---	---	---	PASS
MTMR9	66036	broad.mit.edu	37	8	11174484	11174484	+	Intron	SNP	G	C	C	rs11784572	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11174484G>C	uc003wtm.2	+						MTMR9_uc010lrx.2_Intron|MTMR9_uc011kxa.1_Intron|uc003wtn.1_RNA	NM_015458	NP_056273	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9							cytoplasm	phosphatase activity|protein binding				0			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		CCTAGGAGACGACGATTTGGA	0.363													15	38	---	---	---	---	PASS
FDFT1	2222	broad.mit.edu	37	8	11667248	11667248	+	Silent	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11667248G>A	uc003wui.2	+	3	422	c.270G>A	c.(268-270)GTG>GTA	p.V90V	FDFT1_uc003wuh.2_Silent_p.V26V|FDFT1_uc010lsa.1_Silent_p.V5V|FDFT1_uc011kxe.1_Silent_p.V26V|FDFT1_uc011kxf.1_Silent_p.V90V|FDFT1_uc011kxg.1_Intron|FDFT1_uc003wuj.2_Silent_p.V83V|FDFT1_uc010lsb.2_Silent_p.V26V|FDFT1_uc011kxh.1_Silent_p.V26V|FDFT1_uc011kxi.1_RNA|FDFT1_uc011kxj.1_Silent_p.V26V|FDFT1_uc003wuk.2_Silent_p.V149V|FDFT1_uc011kxk.1_Silent_p.V5V	NM_004462	NP_004453	P37268	FDFT_HUMAN	squalene synthase	90					cholesterol biosynthetic process|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	farnesyl-diphosphate farnesyltransferase activity|oxidoreductase activity|protein binding|squalene synthase activity				0	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		CCATCAGTGTGGAAAAGAAGG	0.463													6	95	---	---	---	---	PASS
PIWIL2	55124	broad.mit.edu	37	8	22163488	22163488	+	Missense_Mutation	SNP	G	A	A	rs138817329		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22163488G>A	uc003xbn.2	+	13	1652	c.1504G>A	c.(1504-1506)GGA>AGA	p.G502R	PIWIL2_uc011kzf.1_Missense_Mutation_p.G502R|PIWIL2_uc010ltv.2_Missense_Mutation_p.G502R	NM_018068	NP_060538	Q8TC59	PIWL2_HUMAN	piwi-like 2	502					DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		TTTTATGACCGGAATCCCAGA	0.468													33	93	---	---	---	---	PASS
EBF2	64641	broad.mit.edu	37	8	25890478	25890478	+	Intron	SNP	G	C	C	rs1872497	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25890478G>C	uc003xes.1	-						PPP2R2A_uc003xek.2_Intron|EBF2_uc003xet.1_3'UTR	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		TGTTGGATGAGCTTAGTGACT	0.433													7	19	---	---	---	---	PASS
MCM4	4173	broad.mit.edu	37	8	48878815	48878815	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48878815G>A	uc003xqk.1	+	9	996	c.901G>A	c.(901-903)GAG>AAG	p.E301K	MCM4_uc003xql.1_Missense_Mutation_p.E301K|MCM4_uc011ldi.1_Missense_Mutation_p.E288K	NM_182746	NP_877423	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	301					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|DNA binding|helicase activity|protein binding			ovary(2)|skin(2)	4		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				CGAGATGCAGGAGGCCTTCTT	0.617													93	76	---	---	---	---	PASS
SOX17	64321	broad.mit.edu	37	8	55372608	55372608	+	3'UTR	SNP	C	G	G			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55372608C>G	uc003xsb.3	+	2						NM_022454	NP_071899	Q9H6I2	SOX17_HUMAN	SRY-box 17						angiogenesis|cardiac cell fate determination|endocardial cell differentiation|endocardium formation|endoderm formation|heart formation|heart looping|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell growth|outflow tract morphogenesis|positive regulation of transcription, DNA-dependent|protein destabilization|protein stabilization|regulation of embryonic development|renal system development|vasculogenesis|Wnt receptor signaling pathway	transcription factor complex	beta-catenin binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			lung(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.176)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;1.9e-07)|Epithelial(17;1.7e-05)|all cancers(17;0.000159)			TACACACTTCCTGGAGGAGCT	0.468													43	33	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113277665	113277665	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113277665C>T	uc003ynu.2	-	60	9822	c.9663G>A	c.(9661-9663)TGG>TGA	p.W3221*	CSMD3_uc003yns.2_Nonsense_Mutation_p.W2423*|CSMD3_uc003ynt.2_Nonsense_Mutation_p.W3181*|CSMD3_uc011lhx.1_Nonsense_Mutation_p.W3052*	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3221	Extracellular (Potential).|Sushi 24.					integral to membrane|plasma membrane		p.T3214_W3221del(1)		ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TTACTCCACTCCATGTGCCAT	0.328										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			104	288	---	---	---	---	PASS
TLE1	7088	broad.mit.edu	37	9	84202844	84202844	+	Intron	SNP	T	C	C			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84202844T>C	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_3'UTR	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2						tgtgtgtgtgtgtgtgtgtgt	0.368													2	2	---	---	---	---	PASS
TLE1	7088	broad.mit.edu	37	9	84202845	84202845	+	Intron	SNP	G	C	C			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84202845G>C	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_3'UTR	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2						gtgtgtgtgtgtgtgtgtgtg	0.368													2	3	---	---	---	---	PASS
TTLL11	158135	broad.mit.edu	37	9	124751554	124751554	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124751554C>A	uc004blt.1	-	4	1647	c.1459G>T	c.(1459-1461)GTC>TTC	p.V487F	TTLL11_uc011lyl.1_Missense_Mutation_p.V487F|TTLL11_uc004blr.2_RNA|TTLL11_uc011lym.1_Missense_Mutation_p.V164F|TTLL11_uc004blu.1_3'UTR	NM_194252	NP_919228	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	487	TTL.				protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0						AGCGCGATGACCGTCTTAATC	0.532													25	239	---	---	---	---	PASS
LCN8	138307	broad.mit.edu	37	9	139651558	139651558	+	Silent	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139651558C>T	uc004cjb.1	-	2	436	c.87G>A	c.(85-87)CCG>CCA	p.P29P	LCN8_uc004cja.2_5'Flank|LCN8_uc004cjc.1_Silent_p.P29P	NM_178469	NP_848564	Q6JVE9	LCN8_HUMAN	lipocalin 8	52					transport	extracellular region	binding			pancreas(1)	1	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)		CCACCCGCTTCGGGGCCGTCA	0.587													4	49	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37508619	37508619	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37508619C>A	uc001iza.1	+	34	3910	c.3811C>A	c.(3811-3813)CAA>AAA	p.Q1271K		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1327	Potential.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						ATTTCAACTACAAAGCAAAAA	0.338													7	78	---	---	---	---	PASS
OR52A1	23538	broad.mit.edu	37	11	5172693	5172693	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5172693G>A	uc010qyy.1	-	1	907	c.907C>T	c.(907-909)CGC>TGC	p.R303C		NM_012375	NP_036507	Q9UKL2	O52A1_HUMAN	olfactory receptor, family 52, subfamily A,	303	Cytoplasmic (Potential).				sensory perception of smell	integral to plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2		Medulloblastoma(188;0.00106)|Breast(177;0.0155)|all_neural(188;0.0189)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACATGAATGCGAATCTGTGTG	0.358													32	341	---	---	---	---	PASS
MICAL2	9645	broad.mit.edu	37	11	12280080	12280080	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12280080G>A	uc001mjz.2	+	25	3496	c.3208G>A	c.(3208-3210)GCA>ACA	p.A1070T	MICAL2_uc010rch.1_Missense_Mutation_p.A880T|MICAL2_uc001mka.2_Missense_Mutation_p.A1070T|MICAL2_uc010rci.1_Missense_Mutation_p.A1049T|MICAL2_uc001mkb.2_Missense_Mutation_p.A844T|MICAL2_uc001mkc.2_Missense_Mutation_p.A823T|MICAL2_uc001mkd.2_Missense_Mutation_p.A652T|MICAL2_uc010rcj.1_Missense_Mutation_p.A282T|MICAL2_uc001mkf.2_RNA	NM_014632	NP_055447	O94851	MICA2_HUMAN	microtubule associated monoxygenase, calponin	1070	Potential.					cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding			upper_aerodigestive_tract(2)	2				Epithelial(150;0.00552)		GAAGAGACGGGCAGAGTTGAA	0.428													50	81	---	---	---	---	PASS
KCNA4	3739	broad.mit.edu	37	11	30034072	30034072	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30034072C>T	uc001msk.2	-	2	1306	c.154G>A	c.(154-156)GAA>AAA	p.E52K		NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	52						voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CCGCTACCTTCGACAGCAGCT	0.677													10	21	---	---	---	---	PASS
CHRM4	1132	broad.mit.edu	37	11	46407006	46407006	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46407006G>T	uc001nct.1	-	1	1102	c.1102C>A	c.(1102-1104)CGC>AGC	p.R368S		NM_000741	NP_000732	P08173	ACM4_HUMAN	cholinergic receptor, muscarinic 4	368	Cytoplasmic (By similarity).				cell proliferation	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity				0				GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)|Tropicamide(DB00809)	GCCGCAGGGCGCATGCCAGCC	0.627													7	75	---	---	---	---	PASS
OR4C16	219428	broad.mit.edu	37	11	55339695	55339695	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55339695G>A	uc010rih.1	+	1	92	c.92G>A	c.(91-93)CGT>CAT	p.R31H		NM_001004701	NP_001004701	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C,	31	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)				ATTTTTTTGCGTCTCTACTTG	0.368													79	204	---	---	---	---	PASS
SLC15A3	51296	broad.mit.edu	37	11	60714292	60714292	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60714292A>C	uc001nqn.2	-	2	794	c.560T>G	c.(559-561)GTG>GGG	p.V187G	SLC15A3_uc001nqo.2_Missense_Mutation_p.V187G	NM_016582	NP_057666	Q8IY34	S15A3_HUMAN	solute carrier family 15, member 3	187					oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0						GAGATCCATCACCTGCCATTC	0.592													21	78	---	---	---	---	PASS
NPAS4	266743	broad.mit.edu	37	11	66188671	66188671	+	Silent	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66188671C>A	uc001ohx.1	+	1	197	c.21C>A	c.(19-21)GGC>GGA	p.G7G	NPAS4_uc010rpc.1_5'UTR	NM_178864	NP_849195	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	7	Potential.|Basic motif.				transcription, DNA-dependent		DNA binding|signal transducer activity				0						CCACCAAGGGCGCCTCCAAGG	0.711													5	14	---	---	---	---	PASS
KIAA1826	84437	broad.mit.edu	37	11	105880177	105880177	+	3'UTR	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105880177G>A	uc001piy.2	-	3					KIAA1826_uc001piz.2_3'UTR	NM_032424	NP_115800	Q8NCY6	K1826_HUMAN	hypothetical protein LOC84437							nucleus				breast(1)	1		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.56e-05)|Epithelial(105;0.00432)|all cancers(92;0.0309)		AGAAACCACAGCTAATCCAGC	0.368													17	7	---	---	---	---	PASS
MLEC	9761	broad.mit.edu	37	12	121132062	121132062	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121132062C>A	uc001tyy.1	+	2	555	c.404C>A	c.(403-405)TCC>TAC	p.S135Y		NM_014730	NP_055545	Q14165	MLEC_HUMAN	malectin precursor	135	Lumenal (Potential).				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	carbohydrate binding			ovary(1)	1						TTTGCACAGTCCCAGCAAAAG	0.522													37	87	---	---	---	---	PASS
WDR66	144406	broad.mit.edu	37	12	122396884	122396884	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122396884G>C	uc009zxk.2	+	13	2159	c.2017G>C	c.(2017-2019)GTT>CTT	p.V673L		NM_144668	NP_653269	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	673	WD 7.						calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		AGAGGGGACAGTTTACATTCT	0.368													83	140	---	---	---	---	PASS
TUBA3C	7278	broad.mit.edu	37	13	19751196	19751196	+	Silent	SNP	G	A	A	rs139349483		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19751196G>A	uc009zzj.2	-	4	976	c.927C>T	c.(925-927)CAC>CAT	p.H309H		NM_006001	NP_005992	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	309					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(3)|skin(2)	5		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		TGTACTTGCCGTGGCGAGGGT	0.587													8	235	---	---	---	---	PASS
SLC25A15	10166	broad.mit.edu	37	13	41383817	41383817	+	3'UTR	SNP	G	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41383817G>T	uc001uxn.2	+	7					SUGT1L1_uc001uxp.1_Intron|SLC25A15_uc010tfb.1_3'UTR|SUGT1L1_uc001uxo.1_5'Flank|MIR621_hsa-mir-621|MI0003635_5'Flank	NM_014252	NP_055067	Q9Y619	ORNT1_HUMAN	mitochondrial ornithine transporter 1						cellular amino acid metabolic process|mitochondrial ornithine transport|urea cycle	integral to membrane|mitochondrial inner membrane	L-ornithine transmembrane transporter activity				0		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.48e-08)|Epithelial(112;7.51e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000191)|GBM - Glioblastoma multiforme(144;0.00231)|BRCA - Breast invasive adenocarcinoma(63;0.0704)	L-Ornithine(DB00129)	GTCTTGGTGGGCCTGAGCCAA	0.453													9	90	---	---	---	---	PASS
NYNRIN	57523	broad.mit.edu	37	14	24878180	24878180	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24878180C>A	uc001wpf.3	+	4	1498	c.1180C>A	c.(1180-1182)CAG>AAG	p.Q394K		NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN	hypothetical protein LOC57523	394					DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3						CCCCTTCTGGCAGAGACCTCT	0.567													11	34	---	---	---	---	PASS
NRXN3	9369	broad.mit.edu	37	14	80271470	80271470	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80271470C>A	uc001xun.2	+	16	3312	c.2821C>A	c.(2821-2823)CTT>ATT	p.L941I	NRXN3_uc001xum.1_RNA|NRXN3_uc001xup.2_RNA|NRXN3_uc001xuq.2_Missense_Mutation_p.L309I|NRXN3_uc010asw.2_Missense_Mutation_p.L339I|NRXN3_uc001xur.3_Missense_Mutation_p.L309I	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	1314	Extracellular (Potential).				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		ATCAGATGATCTTGTTTCATC	0.383													9	228	---	---	---	---	PASS
KIAA0125	9834	broad.mit.edu	37	14	106382687	106382687	+	Intron	SNP	C	T	T	rs2857339	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106382687C>T	uc001ysq.2	+						ADAM6_uc010tyt.1_RNA|KIAA0125_uc001ysr.2_Intron|KIAA0125_uc001yss.2_Intron|KIAA0125_uc001yst.2_5'Flank					SubName: Full=HCG2029388, isoform CRA_d; SubName: Full=FAM30A protein;												0						TCACTGTGGGCATAGCAGCTG	0.592													53	65	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106494236	106494236	+	RNA	SNP	T	C	C			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106494236T>C	uc010tyt.1	-	1760		c.34762A>G								Parts of antibodies, mostly variable regions.												0						GTGAGCCTGCTCTTCAGAGAT	0.532													81	102	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106573482	106573482	+	RNA	SNP	T	C	C			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106573482T>C	uc010tyt.1	-	1362		c.29043A>G								Parts of antibodies, mostly variable regions.												0						TCAGGGACCCTCCAGGCTTGA	0.562													6	159	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107159986	107159986	+	RNA	SNP	G	A	A	rs7161273	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107159986G>A	uc010tyt.1	-	42		c.2943C>T								Parts of antibodies, mostly variable regions.												0						TGCATAGTTGGTGTTACCATT	0.517													49	98	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107178941	107178941	+	RNA	SNP	T	A	A	rs10133751	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107178941T>A	uc010tyt.1	-	32		c.2297A>T								Parts of antibodies, mostly variable regions.												0						TGTGCTGTAGTATTTATCATC	0.522													57	145	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107179106	107179106	+	RNA	SNP	C	T	T	rs10144703	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107179106C>T	uc010tyt.1	-	32		c.2132G>A								Parts of antibodies, mostly variable regions.												0						ACCAGACTCCCTCAAGGTGAC	0.507													20	70	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	33835896	33835896	+	Silent	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33835896C>T	uc001zhi.2	+	8	790	c.720C>T	c.(718-720)GAC>GAT	p.D240D	RYR3_uc010bar.2_Silent_p.D240D	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	240	MIR 3.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CATCTACAGACCAGAATGATT	0.398													46	262	---	---	---	---	PASS
TGM7	116179	broad.mit.edu	37	15	43577105	43577105	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43577105C>T	uc001zrf.1	-	7	916	c.911G>A	c.(910-912)CGT>CAT	p.R304H		NM_052955	NP_443187	Q96PF1	TGM7_HUMAN	transglutaminase 7	304					peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)	2		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	GTGCGCGGAACGGAAATTGGA	0.423													41	205	---	---	---	---	PASS
STRC	161497	broad.mit.edu	37	15	43896963	43896963	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43896963G>A	uc001zsf.2	-	20	4090	c.4012C>T	c.(4012-4014)CGA>TGA	p.R1338*	STRC_uc010bdl.2_Nonsense_Mutation_p.R565*|STRC_uc001zse.2_Translation_Start_Site	NM_153700	NP_714544	Q7RTU9	STRC_HUMAN	stereocilin precursor	1338					sensory perception of sound	cell surface					0		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		GGGATCTGTCGTGTGCTCTCT	0.552													44	50	---	---	---	---	PASS
CEP152	22995	broad.mit.edu	37	15	49036526	49036526	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49036526C>T	uc001zwy.2	-	23	3612	c.3578G>A	c.(3577-3579)GGG>GAG	p.G1193E	CEP152_uc001zwz.2_Missense_Mutation_p.G1249E|CEP152_uc001zxa.1_Missense_Mutation_p.G1156E	NM_014985	NP_055800	O94986	CE152_HUMAN	centrosomal protein 152kDa	1193					centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding			lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TTCAATGGCCCCTGCTGACAA	0.328													47	58	---	---	---	---	PASS
VPS13C	54832	broad.mit.edu	37	15	62266506	62266506	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62266506G>A	uc002agz.2	-	25	2593	c.2519C>T	c.(2518-2520)GCC>GTC	p.A840V	VPS13C_uc002aha.2_Missense_Mutation_p.A797V|VPS13C_uc002ahb.1_Missense_Mutation_p.A840V|VPS13C_uc002ahc.1_Missense_Mutation_p.A797V	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	840					protein localization					ovary(2)	2						TGGAGACTGGGCTGATGATTT	0.373													82	140	---	---	---	---	PASS
ACAN	176	broad.mit.edu	37	15	89386657	89386657	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89386657G>A	uc010upo.1	+	6	1203	c.829G>A	c.(829-831)GGT>AGT	p.G277S	ACAN_uc002bmx.2_Missense_Mutation_p.G277S|ACAN_uc010upp.1_Missense_Mutation_p.G277S|ACAN_uc002bna.2_RNA	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor	277					cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CCGGCGGCTGGGTGCCCGGCT	0.647													6	13	---	---	---	---	PASS
MSLN	10232	broad.mit.edu	37	16	818698	818698	+	Missense_Mutation	SNP	G	A	A	rs74953641		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:818698G>A	uc002cjw.1	+	17	1909	c.1858G>A	c.(1858-1860)GTC>ATC	p.V620I	MSLN_uc002cjt.1_Missense_Mutation_p.V612I|MSLN_uc002cju.1_Missense_Mutation_p.V612I|MSLN_uc010brd.1_Missense_Mutation_p.V611I|MSLN_uc002cjv.1_Missense_Mutation_p.V602I|MSLN_uc002cjx.1_Missense_Mutation_p.V612I|MSLN_uc002cjy.1_Missense_Mutation_p.R304H|MIR662_hsa-mir-662|MI0003670_5'Flank	NM_013404	NP_037536	Q13421	MSLN_HUMAN	mesothelin isoform 2 preproprotein	620					cell adhesion	anchored to membrane|extracellular region|Golgi apparatus|plasma membrane				pancreas(1)	1		Hepatocellular(780;0.00335)				TGTTCTCACCGTCCTGGCACT	0.701													5	96	---	---	---	---	PASS
TCEB2	6923	broad.mit.edu	37	16	2827129	2827129	+	Splice_Site	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2827129C>T	uc002crn.2	-	2	61	c.4_splice	c.e2-1	p.D2_splice	TCEB2_uc002crm.2_Splice_Site_p.D2_splice	NM_007108	NP_009039	Q15370	ELOB_HUMAN	elongin B isoform a						positive regulation of viral transcription|protein complex assembly|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|nucleoplasm	protein binding				0						GGAACACGTCCTGGGGGCGGC	0.448													7	10	---	---	---	---	PASS
ZNF213	7760	broad.mit.edu	37	16	3190970	3190970	+	Silent	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3190970G>A	uc010uws.1	+	6	1449	c.1002G>A	c.(1000-1002)CGG>CGA	p.R334R	ZNF213_uc002cud.2_RNA|ZNF213_uc010btf.2_3'UTR|ZNF213_uc010bth.2_Silent_p.R334R|ZNF213_uc010uwt.1_3'UTR	NM_004220	NP_004211	O14771	ZN213_HUMAN	zinc finger protein 213	334	C2H2-type 1.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						ACCTGGCGCGGCACCAGCGCA	0.697													3	20	---	---	---	---	PASS
TMC7	79905	broad.mit.edu	37	16	19056429	19056429	+	Intron	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19056429C>T	uc002dfq.2	+						TMC7_uc010vao.1_3'UTR|TMC7_uc002dfp.2_Intron|TMC7_uc010vap.1_Intron	NM_024847	NP_079123	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7 isoform a							integral to membrane				skin(2)|ovary(1)	3						GCATTTGCTTCGCTTTCTTGT	0.552													45	66	---	---	---	---	PASS
ABCC12	94160	broad.mit.edu	37	16	48121966	48121966	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48121966C>T	uc002efc.1	-	25	3852	c.3506G>A	c.(3505-3507)CGT>CAT	p.R1169H	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	1169	ABC transporter 2.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)				CTCCACCAGACGAAACAAAGC	0.433													27	32	---	---	---	---	PASS
HSF4	3299	broad.mit.edu	37	16	67199716	67199716	+	Silent	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67199716C>A	uc002erl.1	+	5	1292	c.327C>A	c.(325-327)GGC>GGA	p.G109G	HSF4_uc002erm.1_Silent_p.G109G|HSF4_uc002ern.1_RNA|HSF4_uc010cec.1_RNA	NM_001040667	NP_001035757	Q9ULV5	HSF4_HUMAN	heat shock transcription factor 4 isoform b	109	By similarity.				response to stress	nucleus	sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		TCGTGCGCGGCCGCGAGCAGC	0.692													5	16	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90162513	90162513	+	3'UTR	SNP	T	C	C			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90162513T>C	uc002fqp.2	+	3					uc002fqq.2_3'UTR					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		GCAACATGAATGACCTGGTGT	0.537													5	136	---	---	---	---	PASS
TLK2	11011	broad.mit.edu	37	17	60654069	60654069	+	Splice_Site	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60654069G>A	uc010ddp.2	+	14	1456	c.1188_splice	c.e14-1	p.R396_splice	TLK2_uc002izx.3_Splice_Site_p.T222_splice|TLK2_uc002izz.3_Splice_Site_p.T374_splice|TLK2_uc002jaa.3_Splice_Site_p.T342_splice|TLK2_uc010wpd.1_Splice_Site_p.T342_splice	NM_006852	NP_006843	Q86UE8	TLK2_HUMAN	tousled-like kinase 2 isoform A						cell cycle|chromatin modification|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|kidney(1)	2						CTGTTTTTCAGGTTAACGTTA	0.313													9	271	---	---	---	---	PASS
EVPL	2125	broad.mit.edu	37	17	74017554	74017554	+	Missense_Mutation	SNP	G	T	T	rs74955334	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74017554G>T	uc002jqi.2	-	9	1234	c.1006C>A	c.(1006-1008)CGC>AGC	p.R336S	EVPL_uc010wss.1_Missense_Mutation_p.R336S|EVPL_uc010wst.1_5'UTR	NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	336	Globular 1.				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			pancreas(2)|central_nervous_system(1)|skin(1)	4						CTCACCCGGCGGTAGTCCTCC	0.517													3	12	---	---	---	---	PASS
NDC80	10403	broad.mit.edu	37	18	2610828	2610828	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2610828G>A	uc002kli.2	+	16	1941	c.1759G>A	c.(1759-1761)GAG>AAG	p.E587K		NM_006101	NP_006092	O14777	NDC80_HUMAN	kinetochore associated 2	587	Potential.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.|Interaction with NEK2 and ZWINT.				attachment of spindle microtubules to kinetochore|cell division|establishment of mitotic spindle orientation|mitotic prometaphase|mitotic sister chromatid segregation|mitotic spindle organization|phosphatidylinositol-mediated signaling	condensed nuclear chromosome outer kinetochore|cytosol|Ndc80 complex	protein binding			ovary(1)	1						ACGTCTGTTAGAGATGGTTGC	0.373													14	255	---	---	---	---	PASS
KIAA0802	23255	broad.mit.edu	37	18	8825067	8825067	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8825067C>A	uc002knr.2	+	15	3701	c.3559C>A	c.(3559-3561)CAG>AAG	p.Q1187K	KIAA0802_uc002knq.2_Missense_Mutation_p.Q1146K|KIAA0802_uc002kns.2_Missense_Mutation_p.Q527K	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	1497											0						CCTCACCGAGCAGTCGGGGTT	0.642													17	62	---	---	---	---	PASS
LMAN1	3998	broad.mit.edu	37	18	57006162	57006162	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57006162C>T	uc002lhz.2	-	9	1011	c.979G>A	c.(979-981)GGA>AGA	p.G327R		NM_005570	NP_005561	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1 precursor	327	Lumenal (Potential).				blood coagulation|ER to Golgi vesicle-mediated transport|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	mannose binding|metal ion binding|unfolded protein binding			skin(1)	1		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	TCTCGATCTCCTACACTCTCA	0.368													41	178	---	---	---	---	PASS
LOC284441	284441	broad.mit.edu	37	19	20370043	20370043	+	Missense_Mutation	SNP	C	T	T	rs116773809	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20370043C>T	uc002nov.2	+	1	1587	c.836C>T	c.(835-837)GCG>GTG	p.A279V		NR_003128				SubName: Full=cDNA FLJ51655, highly similar to Actin-like protein 2;												0						AAGGATGATGCGGAAAAACTT	0.423													9	95	---	---	---	---	PASS
ZNF99	7652	broad.mit.edu	37	19	22939861	22939861	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22939861G>T	uc010xrh.1	-	6	2470	c.2470C>A	c.(2470-2472)CAT>AAT	p.H824N		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TCCCTAGTATGAATTAGCTTA	0.378													94	132	---	---	---	---	PASS
C20orf165	128497	broad.mit.edu	37	20	44515342	44515342	+	Silent	SNP	G	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44515342G>A	uc002xqf.2	-	2	507	c.498C>T	c.(496-498)ACC>ACT	p.T166T		NM_080608	NP_542175	Q9BR10	CT165_HUMAN	chromosome 20 open reading frame 165	166	Helical; (Potential).					integral to membrane					0		Myeloproliferative disorder(115;0.0122)				GGACGGGCACGGTGGGGATGC	0.642													56	89	---	---	---	---	PASS
CYP24A1	1591	broad.mit.edu	37	20	52790178	52790178	+	5'UTR	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52790178C>A	uc002xwv.2	-	1					CYP24A1_uc002xwu.1_5'Flank|CYP24A1_uc002xww.2_5'UTR	NM_000782	NP_000773	Q07973	CP24A_HUMAN	cytochrome P450 family 24 subfamily A						hormone biosynthetic process|osteoblast differentiation|vitamin D catabolic process|vitamin D receptor signaling pathway|xenobiotic metabolic process	mitochondrial inner membrane	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity|electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	GAGGTTGGTACGAGGTGCTAG	0.647													2	4	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11047582	11047582	+	3'UTR	SNP	C	T	T	rs3908556		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11047582C>T	uc002yit.1	-	5						NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ATCTTGCTATCTTCTCCCGAT	0.358													74	783	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22758835	22758835	+	RNA	SNP	C	T	T	rs62225019	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22758835C>T	uc011aim.1	+	52		c.5920C>T								Parts of antibodies, mostly variable regions.												0						CTGGAAGCAGCTCCGACATGG	0.572													61	17	---	---	---	---	PASS
PRAME	23532	broad.mit.edu	37	22	22899234	22899234	+	Missense_Mutation	SNP	A	G	G	rs2266988	byFrequency	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22899234A>G	uc002zwf.2	-	2	175	c.19T>C	c.(19-21)TGG>CGG	p.W7R	LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_5'Flank|PRAME_uc010gtr.2_Missense_Mutation_p.W7R|PRAME_uc002zwg.2_Missense_Mutation_p.W7R|PRAME_uc002zwh.2_Missense_Mutation_p.W7R|PRAME_uc002zwi.2_Missense_Mutation_p.W7R|PRAME_uc002zwj.2_Missense_Mutation_p.W7R|PRAME_uc002zwk.2_Missense_Mutation_p.W7R|LOC648691_uc011ais.1_5'Flank	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	7					apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|regulation of growth|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding	p.W7R(1)		central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CTTCTTACCCACAAACGCCTT	0.562													136	28	---	---	---	---	PASS
PRAME	23532	broad.mit.edu	37	22	22899363	22899363	+	Intron	SNP	G	A	A	rs8139318	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22899363G>A	uc002zwf.2	-						LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_5'Flank|PRAME_uc010gtr.2_Intron|PRAME_uc002zwg.2_Intron|PRAME_uc002zwh.2_Intron|PRAME_uc002zwi.2_Intron|PRAME_uc002zwj.2_Intron|PRAME_uc002zwk.2_5'UTR|LOC648691_uc011ais.1_5'Flank	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma						apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|regulation of growth|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CCAAAAAGAAGAATACATGTA	0.468													19	4	---	---	---	---	PASS
PRAME	23532	broad.mit.edu	37	22	22899364	22899364	+	Intron	SNP	A	G	G	rs60201072	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22899364A>G	uc002zwf.2	-						LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_5'Flank|PRAME_uc010gtr.2_Intron|PRAME_uc002zwg.2_Intron|PRAME_uc002zwh.2_Intron|PRAME_uc002zwi.2_Intron|PRAME_uc002zwj.2_Intron|PRAME_uc002zwk.2_5'UTR|LOC648691_uc011ais.1_5'Flank	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma						apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|regulation of growth|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CAAAAAGAAGAATACATGTAT	0.463													18	3	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22922750	22922750	+	RNA	SNP	A	T	T	rs12158077	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22922750A>T	uc011aim.1	+	91		c.7278A>T								Parts of antibodies, mostly variable regions.												0						TTATTACTGCAGCTCATATGC	0.557													95	12	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22977640	22977640	+	Intron	SNP	G	C	C	rs113599461		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22977640G>C	uc011aim.1	+						POM121L1P_uc011ait.1_RNA|uc002zwm.2_5'Flank					Parts of antibodies, mostly variable regions.												0						CCTCTGCTTCGGTCCTCTACA	0.612													3	0	---	---	---	---	PASS
GGTLC2	91227	broad.mit.edu	37	22	22988911	22988911	+	Silent	SNP	G	A	A	rs9612135	byFrequency	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22988911G>A	uc010gtt.2	+	1	130	c.96G>A	c.(94-96)CCG>CCA	p.P32P	LOC96610_uc011aim.1_Intron|POM121L1P_uc011ait.1_5'Flank|GGTLC2_uc010gts.2_Silent_p.P32P	NM_199127	NP_954578	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase-like 4 isoform 1	32					glutathione biosynthetic process		gamma-glutamyltransferase activity			ovary(1)	1	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)		TCTACACGCCGGTTGATGGGG	0.617													10	16	---	---	---	---	PASS
GGTLC2	91227	broad.mit.edu	37	22	22989256	22989256	+	Missense_Mutation	SNP	A	G	G	rs2904923	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22989256A>G	uc010gtt.2	+	2	243	c.209A>G	c.(208-210)GAG>GGG	p.E70G	LOC96610_uc011aim.1_Intron|POM121L1P_uc011ait.1_5'Flank|GGTLC2_uc010gts.2_Missense_Mutation_p.E70G	NM_199127	NP_954578	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase-like 4 isoform 1	70					glutathione biosynthetic process		gamma-glutamyltransferase activity			ovary(1)	1	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)		CCGGTCAGCGAGATCCTGTTC	0.587													111	28	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	23040767	23040767	+	RNA	SNP	G	T	T	rs5751516	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23040767G>T	uc011aim.1	+	137		c.8674G>T								Parts of antibodies, mostly variable regions.												0						ATTTATGAGGGCAGTAAGCGG	0.552													221	52	---	---	---	---	PASS
SMARCB1	6598	broad.mit.edu	37	22	24145587	24145587	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24145587C>A	uc002zyb.2	+	5	813	c.606C>A	c.(604-606)GAC>GAA	p.D202E	SMARCB1_uc002zya.2_Intron|SMARCB1_uc002zyc.2_Missense_Mutation_p.D193E|SMARCB1_uc002zyd.2_Missense_Mutation_p.D211E	NM_003073	NP_003064	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin	202	HIV-1 integrase-binding.|1.|2 X approximate tandem repeats.|MYC-binding.				cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex	p53 binding	p.?(5)|p.A203fs*13(1)		soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1)	407		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				AGCTGCGAGACGCCTTCACCT	0.602			D|N|F|S		malignant rhabdoid 	malignant rhabdoid			Rhabdoid_Predisposition_syndrome|Schwannomatosis				3	56	---	---	---	---	PASS
GABRE	2564	broad.mit.edu	37	X	151138738	151138738	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151138738C>T	uc004ffi.2	-	2	247	c.193G>A	c.(193-195)GTT>ATT	p.V65I	GABRE_uc011myd.1_RNA|GABRE_uc011mye.1_RNA	NM_004961	NP_004952	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor,	65	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)					AGTTTGCCAACTCTGCTCCCA	0.532													10	220	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	4204666	4204667	+	IGR	DEL	CA	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4204666_4204667delCA								LOC100133612 (370789 upstream) : LOC284661 (267444 downstream)																							ccaccaccatcacaccattatc	0.025													3	4	---	---	---	---	
KIF17	57576	broad.mit.edu	37	1	21039807	21039808	+	Intron	INS	-	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21039807_21039808insA	uc001bdr.3	-						KIF17_uc001bds.3_Intron	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN	kinesin family member 17 isoform a						microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)|skin(1)	4		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		tttttttaattaaaaaaaaaaa	0.257													6	3	---	---	---	---	
DRAM2	128338	broad.mit.edu	37	1	111663004	111663025	+	Intron	DEL	AAAAAAAAAAAAAAAAAAAAAA	-	-	rs71751427		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111663004_111663025delAAAAAAAAAAAAAAAAAAAAAA	uc001ead.3	-						DRAM2_uc001eae.3_Intron|DRAM2_uc009wfy.2_Intron|DRAM2_uc001eaf.3_Intron	NM_178454	NP_848549	Q6UX65	DRAM2_HUMAN	transmembrane protein 77						apoptosis|induction of apoptosis	Golgi apparatus|integral to membrane|lysosomal membrane					0						TCTCTCCTACaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa	0.275													5	4	---	---	---	---	
FCRL3	115352	broad.mit.edu	37	1	157665544	157665544	+	Intron	DEL	A	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157665544delA	uc001frb.2	-						FCRL3_uc001fqx.3_Intron|FCRL3_uc001fqy.3_Intron|FCRL3_uc001fqz.3_Intron|FCRL3_uc009wsn.2_Intron|FCRL3_uc009wso.2_Intron|FCRL3_uc001fra.2_Intron|FCRL3_uc001frc.1_Intron	NM_052939	NP_443171	Q96P31	FCRL3_HUMAN	Fc receptor-like 3 precursor							integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(1)	4	all_hematologic(112;0.0378)					TAACAATCAGAAGCATTTCCC	0.423													4	2	---	---	---	---	
RCSD1	92241	broad.mit.edu	37	1	167663323	167663324	+	Intron	INS	-	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167663323_167663324insT	uc001gem.2	+						RCSD1_uc010pli.1_Intron	NM_052862	NP_443094	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1											ovary(2)|central_nervous_system(2)|skin(1)	5	all_hematologic(923;0.215)					AATTGTTCATCTTTTCTTGACA	0.495													90	7	---	---	---	---	
C2orf7	84279	broad.mit.edu	37	2	73460294	73460298	+	5'UTR	DEL	GGGCC	-	-	rs3832032		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73460294_73460298delGGGCC	uc002siy.2	-	1					CCT7_uc002siz.2_5'Flank|CCT7_uc002sja.2_5'Flank|CCT7_uc010yrf.1_5'Flank|CCT7_uc010feu.2_5'Flank|CCT7_uc010yrg.1_5'Flank|CCT7_uc010yrh.1_5'Flank|CCT7_uc010yri.1_5'Flank	NM_032319	NP_115695	Q9BSG0	PADC1_HUMAN	chromosome 2 open reading frame 7 precursor							extracellular region					0						ACCATCTCCAgggccgggcccggcc	0.639													4	3	---	---	---	---	
SNRNP200	23020	broad.mit.edu	37	2	96950487	96950488	+	Intron	INS	-	T	T	rs150751016		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96950487_96950488insT	uc002svu.2	-						SNRNP200_uc002svt.2_5'Flank|SNRNP200_uc010yuj.1_Intron|SNRNP200_uc002svv.1_5'UTR	NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10						GCAGCtttttcttttttttttt	0.243													4	3	---	---	---	---	
IMP4	92856	broad.mit.edu	37	2	131100711	131100711	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131100711delA	uc002tra.1	+	2	73	c.56delA	c.(55-57)GAGfs	p.E19fs	CCDC115_uc002tqw.1_5'Flank|CCDC115_uc010zaf.1_5'Flank|CCDC115_uc002tqx.2_5'Flank|CCDC115_uc002tqy.1_5'Flank|CCDC115_uc002tqz.1_5'Flank	NM_033416	NP_219484	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein,	19	Arg-rich.				rRNA processing|translation	nucleolus|ribonucleoprotein complex	aminoacyl-tRNA ligase activity|ATP binding|protein binding			central_nervous_system(2)	2	Colorectal(110;0.1)					AAGGCCCGGGAGGAGGCGCAG	0.726													4	2	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179498718	179498718	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179498718delT	uc010zfg.1	-	180	35028	c.34804delA	c.(34804-34806)ATGfs	p.M11602fs	TTN_uc010zfh.1_Frame_Shift_Del_p.M5297fs|TTN_uc010zfi.1_Frame_Shift_Del_p.M5230fs|TTN_uc010zfj.1_Frame_Shift_Del_p.M5105fs	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	12529							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)			ACTACATGCATTTTTTCATGA	0.363													403	249	---	---	---	---	
MYH15	22989	broad.mit.edu	37	3	108129282	108129283	+	Intron	INS	-	C	C			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108129282_108129283insC	uc003dxa.1	-							NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						CATCTAAAGTAAAAAAAAAATA	0.337													6	5	---	---	---	---	
GAP43	2596	broad.mit.edu	37	3	115342811	115342811	+	Intron	DEL	T	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115342811delT	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		CTAGAAATAATTTTTTTTTTT	0.423													5	5	---	---	---	---	
C3orf1	51300	broad.mit.edu	37	3	119217940	119217941	+	Intron	DEL	TT	-	-	rs34000460		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119217940_119217941delTT	uc003ecn.2	+						C3orf1_uc003eco.2_Intron|C3orf1_uc003ecp.2_Intron	NM_016589	NP_057673	Q9NPL8	TIDC1_HUMAN	hypothetical protein LOC51300							integral to membrane|mitochondrial inner membrane	protein transporter activity				0				GBM - Glioblastoma multiforme(114;0.186)		tttttctttctttttttttttt	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	183332602	183332603	+	IGR	INS	-	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183332602_183332603insA								KLHL6 (59103 upstream) : KLHL24 (20808 downstream)																							gtctccgtctcaaaaaaaaaaa	0.163													4	3	---	---	---	---	
THAP9	79725	broad.mit.edu	37	4	83838140	83838141	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83838140_83838141insT	uc003hnt.2	+	5	894_895	c.775_776insT	c.(775-777)ATTfs	p.I259fs	THAP9_uc003hns.1_Frame_Shift_Ins_p.I115fs|THAP9_uc003hnu.1_RNA|THAP9_uc003hnv.2_5'UTR	NM_024672	NP_078948	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	259							DNA binding|metal ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	5		Hepatocellular(203;0.114)				CAACAGCAACATTTTTTCTTTT	0.361													437	30	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	143066776	143066777	+	Intron	INS	-	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143066776_143066777insA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_Intron|INPP4B_uc011cho.1_Intron|INPP4B_uc011chp.1_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					GGTAAGATAAGAAAAAAAAAAG	0.347													2	8	---	---	---	---	
EDNRA	1909	broad.mit.edu	37	4	148453477	148453478	+	Intron	INS	-	A	A	rs71594222		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148453477_148453478insA	uc003iky.2	+						EDNRA_uc011cid.1_Intron|EDNRA_uc010ipe.1_Intron|EDNRA_uc010ipf.1_Intron|EDNRA_uc010ipg.1_Intron	NM_001957	NP_001948	P25101	EDNRA_HUMAN	endothelin receptor type A isoform a precursor						activation of adenylate cyclase activity|artery smooth muscle contraction|cell proliferation|glucose transport|respiratory gaseous exchange	integral to plasma membrane	endothelin-A receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|breast(1)	2	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Bosentan(DB00559)	gattttgcctcaaaaaaaaaaa	0.144													8	5	---	---	---	---	
TLL1	7092	broad.mit.edu	37	4	166986834	166986834	+	Splice_Site	DEL	G	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166986834delG	uc003irh.1	+	16	2655	c.2008_splice	c.e16-1	p.V670_splice	TLL1_uc011cjn.1_Splice_Site_p.V693_splice|TLL1_uc011cjo.1_Splice_Site_p.V494_splice	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		TTTTTTTCTAGGTTTGCAAAT	0.363													224	7	---	---	---	---	
FBXO4	26272	broad.mit.edu	37	5	41927295	41927296	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41927295_41927296delTT	uc003jmq.2	+	2	426_427	c.370_371delTT	c.(370-372)TTAfs	p.L124fs	FBXO4_uc003jmp.2_Frame_Shift_Del_p.L124fs|FBXO4_uc003jmr.2_Frame_Shift_Del_p.L124fs	NM_012176	NP_036308	Q9UKT5	FBX4_HUMAN	F-box only protein 4 isoform 1	124					positive regulation of protein ubiquitination|protein polyubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|telomere maintenance|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	protein binding|protein homodimerization activity|ubiquitin-protein ligase activity			liver(1)	1		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				TCTAGAAATCTTAAAAAAGCCT	0.351													360	18	---	---	---	---	
AQPEP	206338	broad.mit.edu	37	5	115351601	115351601	+	Intron	DEL	T	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115351601delT	uc003kro.2	+						AQPEP_uc003krp.2_Intron|AQPEP_uc003krq.2_Intron|AQPEP_uc003krr.2_Intron|AQPEP_uc003krs.2_Intron	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin						proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0						AAAGTTATCATTTTTCCTTTG	0.378													4	7	---	---	---	---	
SRFBP1	153443	broad.mit.edu	37	5	121356088	121356088	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121356088delA	uc003kst.1	+	6	730	c.658delA	c.(658-660)AAGfs	p.K220fs		NM_152546	NP_689759	Q8NEF9	SRFB1_HUMAN	serum response factor binding protein 1	220					regulation of transcription, DNA-dependent|transcription, DNA-dependent	perinuclear region of cytoplasm					0		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		TGAGTCCCAGAAGACACCTGC	0.403													96	58	---	---	---	---	
LYRM7	90624	broad.mit.edu	37	5	130522818	130522819	+	Intron	INS	-	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130522818_130522819insA	uc003kvg.1	+							NM_181705	NP_859056	Q5U5X0	LYRM7_HUMAN	Lyrm7 homolog												0		all_cancers(142;0.0377)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TAAAATTAAAGAAAAATGGTTT	0.302													12	9	---	---	---	---	
TIMD4	91937	broad.mit.edu	37	5	156381895	156381896	+	Intron	INS	-	T	T	rs71922795		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156381895_156381896insT	uc003lwh.2	-						TIMD4_uc010jii.2_Intron	NM_138379	NP_612388	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain							integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			cttttctttccttttttttttt	0.168													6	3	---	---	---	---	
SLC35B3	51000	broad.mit.edu	37	6	8417377	8417377	+	Intron	DEL	A	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8417377delA	uc010joe.2	-						SLC35B3_uc003mya.2_Intron|SLC35B3_uc003myc.2_Intron|SLC35B3_uc003myb.2_Intron|SLC35B3_uc011did.1_Intron|SLC35B3_uc003myd.2_Intron	NM_001142541	NP_001136013	Q9H1N7	S35B3_HUMAN	solute carrier family 35, member B3						transmembrane transport	Golgi membrane|integral to membrane					0	Ovarian(93;0.0569)					TGATTTAATGAAAAAAAAATG	0.259													4	2	---	---	---	---	
LOC100132354	100132354	broad.mit.edu	37	6	43872656	43872659	+	Intron	DEL	TTCC	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43872656_43872659delTTCC	uc011dvm.1	+							NR_024478				Homo sapiens cDNA FLJ38229 fis, clone FCBBF2004256.												0						Attccttcctttccttccttcctt	0.240													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57929464	57929464	+	IGR	DEL	G	-	-	rs76511107		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57929464delG								ZNF716 (396199 upstream) : None (None downstream)																							AGGACCTTTCGAAATAAAATG	0.423													4	2	---	---	---	---	
STAG3L1	54441	broad.mit.edu	37	7	74991540	74991540	+	Intron	DEL	T	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74991540delT	uc003ucu.1	+						STAG3L1_uc010lcz.1_Intron|STAG3L1_uc003ucv.1_Intron|STAG3L1_uc011kfw.1_Intron|STAG3L1_uc011kfx.1_Intron	NM_018991	NP_061864	P0CL83	ST3L1_HUMAN	stromal antigen 3-like 1 isoform 1							nucleus	binding				0						GAGCATGttcttttttttttt	0.174													5	3	---	---	---	---	
CCDC146	57639	broad.mit.edu	37	7	76796901	76796901	+	Intron	DEL	A	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76796901delA	uc003uga.2	+						CCDC146_uc003ufz.1_Intron	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				GTTTATTTTTATTATTTTCCA	0.264													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	102021199	102021199	+	Intron	DEL	A	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102021199delA	uc003uzd.1	+						uc003uze.1_Intron|PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_Intron	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																		TTTTTCCCTTAAAAAAAAAAA	0.358													4	2	---	---	---	---	
IRF5	3663	broad.mit.edu	37	7	128582510	128582510	+	Intron	DEL	T	-	-	rs5887397		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128582510delT	uc003vog.2	+						IRF5_uc010llr.1_Intron|IRF5_uc011kot.1_Intron|IRF5_uc011kou.1_Intron|IRF5_uc010lls.1_Intron|IRF5_uc003voh.2_Intron|IRF5_uc010llt.2_Intron|IRF5_uc003voi.2_Intron|IRF5_uc010llu.1_Intron|IRF5_uc003vok.2_Intron|IRF5_uc003voj.3_Intron|IRF5_uc010llv.1_Intron|IRF5_uc010llw.1_Intron	NM_002200	NP_002191	Q13568	IRF5_HUMAN	interferon regulatory factor 5 isoform a						interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0						ACCtttttccttttttttttt	0.303													4	2	---	---	---	---	
FBXO25	26260	broad.mit.edu	37	8	363407	363407	+	Intron	DEL	T	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									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	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	67328399	67328406	+	IGR	DEL	GAAGGAAG	-	-	rs150500788	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67328399_67328406delGAAGGAAG								CRH (237701 upstream) : RRS1 (12857 downstream)																							aggaaggaaagaaggaaggaaggaagga	0.000													5	5	---	---	---	---	
OTUD6B	51633	broad.mit.edu	37	8	92083177	92083177	+	Intron	DEL	T	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92083177delT	uc003yeu.3	+						uc003yet.2_5'Flank|OTUD6B_uc011lgh.1_Intron	NM_016023	NP_057107	Q8N6M0	OTU6B_HUMAN	OTU domain containing 6B											ovary(2)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(11;0.0187)			GTTAATGAAGTTTTTTTTTTT	0.358													6	4	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139668054	139668055	+	Intron	INS	-	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139668054_139668055insA	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)			AATAGTTGTTCAAAAAAAACCC	0.361										HNSCC(7;0.00092)			429	14	---	---	---	---	
DMRT3	58524	broad.mit.edu	37	9	987413	987426	+	Intron	DEL	TGTGTGTGTGTGTG	-	-	rs6150885		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:987413_987426delTGTGTGTGTGTGTG	uc003zgw.1	+							NM_021240	NP_067063	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor						cell differentiation|multicellular organismal development|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(2)|central_nervous_system(1)	3		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		aatatcccactgtgtgtgtgtgtgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49088590	49088590	+	IGR	DEL	C	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49088590delC								OR4A47 (577318 upstream) : FOLH1 (79598 downstream)																							TTTTTTTTTTCTCTCTCTCTC	0.274													182	7	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	81671207	81671208	+	Intron	INS	-	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81671207_81671208insA	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.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						ttttttttattaaaaaaaaaaa	0.337													5	3	---	---	---	---	
FAM177A1	283635	broad.mit.edu	37	14	35546674	35546674	+	Intron	DEL	C	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35546674delC	uc001wsp.2	+						FAM177A1_uc001wsq.2_Intron	NM_001079519	NP_001072987	Q8N128	F177A_HUMAN	hypothetical protein LOC283635 isoform 2												0						TTTTCAAGttctttttttttt	0.129													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106714826	106714826	+	Intron	DEL	A	-	-	rs111944422		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106714826delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						CTCCATGGTGAGTCCTCTGTG	0.478													58	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	35376193	35376194	+	IGR	INS	-	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35376193_35376194insA								ZNF770 (95739 upstream) : LOC723972 (153333 downstream)																							GATCCAATAGGAAAAAAAAAAA	0.267													9	5	---	---	---	---	
C15orf41	84529	broad.mit.edu	37	15	36983573	36983573	+	Intron	DEL	T	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36983573delT	uc001zje.3	+						C15orf41_uc001zjd.2_Intron|C15orf41_uc010bbb.1_Intron|C15orf41_uc001zjf.2_Intron|C15orf41_uc010uci.1_Intron	NM_001130010	NP_001123482	Q9Y2V0	CO041_HUMAN	hypothetical protein LOC84529 isoform 1								protein binding			pancreas(1)	1		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		TATTTTCTGATTTTTTTTTTT	0.303													4	2	---	---	---	---	
GOLGA6L10	647042	broad.mit.edu	37	15	83014189	83014189	+	Intron	DEL	A	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83014189delA	uc010unt.1	-						uc002bhl.2_Intron|uc002bhm.2_Intron|GOLGA6L10_uc010uny.1_Intron|GOLGA6L10_uc002bia.1_5'Flank			A6NI86	GG6LA_HUMAN	Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0						CTGGATTCTCAAAAAAAAAAA	0.517													5	3	---	---	---	---	
TMC5	79838	broad.mit.edu	37	16	19502280	19502281	+	Intron	INS	-	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19502280_19502281insT	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron|TMC5_uc002dgd.1_Intron|TMC5_uc002dge.3_Intron|TMC5_uc002dgf.3_Intron|TMC5_uc002dgg.3_Intron	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1						ctttccccttcccctcccttcc	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54822016	54822043	+	IGR	DEL	TTCCTTCCTTCCTTCCTTCCTTCCTCCC	-	-	rs60730909		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54822016_54822043delTTCCTTCCTTCCTTCCTTCCTTCCTCCC								IRX3 (501638 upstream) : IRX5 (143068 downstream)																							tttccttcctttccttccttccttccttccttcctcccttccttcctt	0.057													5	5	---	---	---	---	
IGF2BP1	10642	broad.mit.edu	37	17	47121400	47121400	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47121400delG	uc002iom.2	+	11	1606	c.1272delG	c.(1270-1272)AAGfs	p.K424fs	IGF2BP1_uc010dbj.2_Frame_Shift_Del_p.K285fs	NM_006546	NP_006537	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding	424	KH 3.|Necessary for interaction with ELAVL4 and binding to TAU mRNA (By similarity).				CRD-mediated mRNA stabilization|negative regulation of translation|regulation of mRNA stability involved in response to stress	CRD-mediated mRNA stability complex|cytosol|dendritic spine|lamellipodium|nucleus|plasma membrane|stress granule	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			kidney(1)	1						TCGGCAAGAAGGGGCAGCACA	0.597													153	55	---	---	---	---	
KIAA1632	57724	broad.mit.edu	37	18	43456027	43456028	+	Intron	INS	-	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43456027_43456028insA	uc002lbm.2	-						KIAA1632_uc010xcq.1_Intron|KIAA1632_uc010xcr.1_Intron|KIAA1632_uc010xcs.1_Intron|KIAA1632_uc002lbn.2_Intron	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724						autophagy						0						atctccaaaagaaaaaaaaaaa	0.119													4	2	---	---	---	---	
C3	718	broad.mit.edu	37	19	6697215	6697215	+	Intron	DEL	T	-	-	rs11569474		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6697215delT	uc002mfm.2	-							NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor						complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)		GCTTCTGAAATTCTGGGACTT	0.473													1	5	---	---	---	---	
RDH13	112724	broad.mit.edu	37	19	55574413	55574414	+	5'UTR	INS	-	CAGGCGT	CAGGCGT	rs140709118	by1000genomes	TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55574413_55574414insCAGGCGT	uc002qio.3	-	1					RDH13_uc002qip.2_Intron|RDH13_uc010yfq.1_RNA	NM_001145971	NP_001139443	Q8NBN7	RDH13_HUMAN	retinol dehydrogenase 13 isoform 1								binding|oxidoreductase activity			large_intestine(1)|ovary(1)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)	CGGGCCGGGGACAGGCGTCAGG	0.718													3	3	---	---	---	---	
ATRN	8455	broad.mit.edu	37	20	3557613	3557614	+	In_Frame_Ins	INS	-	CCC	CCC			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3557613_3557614insCCC	uc002wim.2	+	14	2412_2413	c.2322_2323insCCC	c.(2320-2325)insCCC	p.775_776insP	ATRN_uc002wil.2_In_Frame_Ins_p.775_776insP	NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1	775_776	Extracellular (Potential).|PSI 2.				inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2						GCCAGTGGGAGCCCCGGAATCA	0.550													226	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	45502691	45502691	+	IGR	DEL	A	-	-	rs74735132		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45502691delA								SLC2A10 (137708 upstream) : EYA2 (20572 downstream)																							actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
TMPRSS2	7113	broad.mit.edu	37	21	42851292	42851293	+	Intron	INS	-	T	T			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42851292_42851293insT	uc002yzj.2	-						TMPRSS2_uc010gor.2_Intron|TMPRSS2_uc010gos.1_Intron	NM_005656	NP_005647	O15393	TMPS2_HUMAN	transmembrane protease, serine 2 isoform 2						proteolysis	cytoplasm|extracellular region|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity		TMPRSS2/ERG(2499)|TMPRSS2/ETV1(24)	prostate(2523)|central_nervous_system(1)	2524		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				ACCGCTCATACGACATTCAGAA	0.312			T	ERG|ETV1|ETV4|ETV5	prostate 								6	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	21022401	21022401	+	IGR	DEL	G	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21022401delG								MED15 (80483 upstream) : POM121L4P (21442 downstream)																							GGTGAGCGGCGAGTGCAGCAC	0.652													9	4	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	23248852	23248852	+	RNA	DEL	A	-	-	rs71797740		TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23248852delA	uc011aim.1	+	374		c.16364delA			uc002zws.2_RNA					Parts of antibodies, mostly variable regions.												0						CTCACCCCCCACCACGGGAGA	0.572													10	12	---	---	---	---	
CYTSA	23384	broad.mit.edu	37	22	24665264	24665264	+	5'Flank	DEL	A	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24665264delA	uc002zzw.2	+						CYTSA_uc002zzv.3_5'Flank|CYTSA_uc011ajq.1_5'Flank	NM_015330	NP_056145	Q69YQ0	CYTSA_HUMAN	cytospin A						cell cycle|cell division						0						TTTTTTTTTTAAGTCTTTTTG	0.234													4	2	---	---	---	---	
ARHGAP6	395	broad.mit.edu	37	X	11242375	11242377	+	Intron	DEL	AAG	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11242375_11242377delAAG	uc004cup.1	-						ARHGAP6_uc004cuo.1_Intron|ARHGAP6_uc004cur.1_Intron|ARHGAP6_uc004cum.1_Intron|ARHGAP6_uc004cun.1_Intron|ARHGAP6_uc010neb.1_Intron|ARHGAP6_uc011mif.1_Intron	NM_013427	NP_038286	O43182	RHG06_HUMAN	Rho GTPase activating protein 6 isoform 1						actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2						ATGAAGAAGAAAGAAGAAGGAGC	0.419													2	8	---	---	---	---	
TBC1D8B	54885	broad.mit.edu	37	X	106062176	106062176	+	Intron	DEL	T	-	-			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106062176delT	uc004emo.2	+						MORC4_uc004emp.3_Intron|TBC1D8B_uc004emm.2_Intron|TBC1D8B_uc004emn.2_Intron	NM_017752	NP_060222	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4						GGTTATTAAGTTTTTTTTTTT	0.338													3	3	---	---	---	---	
GPC4	2239	broad.mit.edu	37	X	132458656	132458657	+	Intron	INS	-	A	A			TCGA-CH-5753-01	TCGA-CH-5753-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132458656_132458657insA	uc004exc.1	-						GPC4_uc011mvg.1_Intron	NM_001448	NP_001439	O75487	GPC4_HUMAN	glypican 4 precursor						anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	Acute lymphoblastic leukemia(192;0.000127)					TTGAAAACTGGAAAAAAAACAC	0.297													22	21	---	---	---	---	
