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
WASH7P	653635	broad.mit.edu	37	1	14933	14933	+	Intron	SNP	G	A	A	rs138566748	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14933G>A	uc009vis.2	-						WASH7P_uc009vit.2_Intron|WASH7P_uc001aae.3_Intron|WASH7P_uc009viu.2_Intron|WASH7P_uc001aab.3_Intron|WASH7P_uc001aah.3_Intron|WASH7P_uc009vir.2_Intron|WASH7P_uc009viq.2_Intron|WASH7P_uc001aac.3_Intron|WASH7P_uc009viv.2_RNA|WASH7P_uc009viw.2_RNA					Homo sapiens cDNA FLJ31670 fis, clone NT2RI2004984.												0						GAATTACAAGGTGCTGGCCCA	0.592													4	16	---	---	---	---	PASS
SPEN	23013	broad.mit.edu	37	1	16257094	16257094	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16257094C>T	uc001axk.1	+	11	4563	c.4359C>T	c.(4357-4359)TCC>TCT	p.S1453S	SPEN_uc010obp.1_Silent_p.S1412S	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1453					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GAGCTAAATCCCTCTCTTCAT	0.363													66	163	---	---	---	---	PASS
SPATA21	374955	broad.mit.edu	37	1	16748492	16748492	+	Intron	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16748492C>A	uc001ayn.2	-						SPATA21_uc001ayl.1_RNA|SPATA21_uc010occ.1_Intron	NM_198546	NP_940948	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21								calcium ion binding			ovary(2)|breast(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		ACATTGGGGGCATTGCTTCCT	0.597													5	198	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16918727	16918727	+	5'UTR	SNP	G	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918727G>C	uc009vos.1	-	6					NBPF1_uc010oce.1_5'UTR	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CGAGGTGCCTGAACTCAGAGC	0.463													4	21	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16955128	16955128	+	5'Flank	SNP	A	G	G	rs1762949	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16955128A>G	uc010ocf.1	-						CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA|CROCCL1_uc001azg.1_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						CAGGCTGTGGACCAGGTTGCT	0.682													2	9	---	---	---	---	PASS
ARHGEF10L	55160	broad.mit.edu	37	1	17958926	17958926	+	Silent	SNP	C	T	T	rs116425261	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17958926C>T	uc001ban.2	+	16	1854	c.1695C>T	c.(1693-1695)CTC>CTT	p.L565L	ARHGEF10L_uc009vpe.1_Silent_p.L526L|ARHGEF10L_uc001bao.2_Silent_p.L526L|ARHGEF10L_uc001bap.2_Silent_p.L526L|ARHGEF10L_uc010ocr.1_Silent_p.L323L|ARHGEF10L_uc001baq.2_Silent_p.L331L|ARHGEF10L_uc010ocs.1_Silent_p.L343L|ARHGEF10L_uc001bar.2_Silent_p.L273L|ARHGEF10L_uc009vpf.2_RNA	NM_018125	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF)	565					regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		TCTTCCTGCTCAACGACATGC	0.602													7	288	---	---	---	---	PASS
NBPF3	84224	broad.mit.edu	37	1	21799965	21799965	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21799965C>A	uc001ber.2	+	7	1177	c.827C>A	c.(826-828)TCC>TAC	p.S276Y	NBPF3_uc001bes.2_Missense_Mutation_p.S220Y|NBPF3_uc009vqb.2_Missense_Mutation_p.S276Y|NBPF3_uc010odm.1_Missense_Mutation_p.S206Y	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	276	NBPF 1.					cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CCTTGTGAGTCCAACCAGCCT	0.493													7	436	---	---	---	---	PASS
ZMYM4	9202	broad.mit.edu	37	1	35855556	35855556	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35855556A>G	uc001byt.2	+	15	2524	c.2444A>G	c.(2443-2445)AAA>AGA	p.K815R	ZMYM4_uc009vuu.2_Missense_Mutation_p.K783R|ZMYM4_uc001byu.2_Missense_Mutation_p.K491R|ZMYM4_uc009vuv.2_Missense_Mutation_p.K554R	NM_005095	NP_005086	Q5VZL5	ZMYM4_HUMAN	zinc finger protein 262	815	MYM-type 9.				multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TAGATGGCCAAATGTGATGCT	0.368													24	87	---	---	---	---	PASS
NFIA	4774	broad.mit.edu	37	1	61869854	61869854	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61869854A>C	uc001czw.2	+	8	1638	c.1154A>C	c.(1153-1155)CAC>CCC	p.H385P	NFIA_uc001czy.2_Missense_Mutation_p.H377P|NFIA_uc010oos.1_Missense_Mutation_p.H430P|NFIA_uc001czv.2_Missense_Mutation_p.H385P|NFIA_uc001czx.2_Missense_Mutation_p.H33P|NFIA_uc009wae.2_5'Flank	NM_001134673	NP_001128145	Q12857	NFIA_HUMAN	nuclear factor I/A isoform 1	385					DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2						TACTTCTCACACCCAGCCATC	0.527													16	218	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75072359	75072359	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75072359A>T	uc001dgg.2	-	10	1634	c.1415T>A	c.(1414-1416)GTG>GAG	p.V472E	uc001dgh.2_Intron|C1orf173_uc001dgi.3_Missense_Mutation_p.V266E	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	472	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						CATTTCCTCCACAGCAGTTAC	0.363													9	495	---	---	---	---	PASS
CDC7	8317	broad.mit.edu	37	1	91989955	91989955	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91989955C>A	uc001doe.2	+	12	1853	c.1688C>A	c.(1687-1689)GCT>GAT	p.A563D	CDC7_uc001dof.2_Missense_Mutation_p.A563D|CDC7_uc010osw.1_Missense_Mutation_p.A535D|CDC7_uc009wdc.2_Missense_Mutation_p.A563D|CDC7_uc009wdd.2_Missense_Mutation_p.A206D	NM_003503	NP_003494	O00311	CDC7_HUMAN	cell division cycle 7	563	Protein kinase.				cell cycle checkpoint|cell division|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|positive regulation of cell proliferation|regulation of S phase	cytoplasm|nucleoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|large_intestine(1)|ovary(1)|central_nervous_system(1)	5		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		GCAGAAGAAGCTTTGTTGCAT	0.328													14	263	---	---	---	---	PASS
BRDT	676	broad.mit.edu	37	1	92442729	92442729	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92442729C>G	uc001dok.3	+	6	1097	c.748C>G	c.(748-750)CCA>GCA	p.P250A	BRDT_uc001dol.3_Missense_Mutation_p.P250A|BRDT_uc010osz.1_Missense_Mutation_p.P254A|BRDT_uc009wdf.2_Missense_Mutation_p.P177A|BRDT_uc010ota.1_Missense_Mutation_p.P204A|BRDT_uc010otb.1_Missense_Mutation_p.P204A|BRDT_uc001dom.3_Missense_Mutation_p.P250A	NM_207189	NP_997072	Q58F21	BRDT_HUMAN	testis-specific bromodomain protein	250					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		AGAAAATATGCCAAAGAATGT	0.348													4	140	---	---	---	---	PASS
LRIG2	9860	broad.mit.edu	37	1	113655223	113655223	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113655223A>G	uc001edf.1	+	14	2119	c.1921A>G	c.(1921-1923)ACT>GCT	p.T641A	LRIG2_uc009wgn.1_Missense_Mutation_p.T538A	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	641	Ig-like C2-type 2.|Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		AGATGGTGGTACTGACTTTCC	0.493													5	201	---	---	---	---	PASS
OR10Z1	128368	broad.mit.edu	37	1	158576525	158576525	+	Silent	SNP	C	T	T	rs146841755		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158576525C>T	uc010pio.1	+	1	297	c.297C>T	c.(295-297)GCC>GCT	p.A99A		NM_001004478	NP_001004478	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z,	99	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)|skin(1)	2	all_hematologic(112;0.0378)					GCTGTGCTGCCCAGATGTTCT	0.542													107	396	---	---	---	---	PASS
TOR1AIP2	163590	broad.mit.edu	37	1	179833985	179833985	+	Intron	SNP	G	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179833985G>T	uc001gnk.2	-						TOR1AIP2_uc001gnl.2_Intron|TOR1AIP2_uc001gnn.2_Missense_Mutation_p.N109K|TOR1AIP2_uc001gnm.2_Missense_Mutation_p.N109K	NM_145034	NP_659471	Q8NFQ8	TOIP2_HUMAN	torsin A interacting protein 2							endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1						GTAATGCAGGGTTAAAACCAG	0.383													9	276	---	---	---	---	PASS
SMG7	9887	broad.mit.edu	37	1	183513545	183513545	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183513545G>C	uc001gqg.2	+	15	2022	c.1900G>C	c.(1900-1902)GTA>CTA	p.V634L	SMG7_uc010pob.1_Missense_Mutation_p.V617L|SMG7_uc001gqf.2_Missense_Mutation_p.V588L|SMG7_uc001gqh.2_Missense_Mutation_p.V588L|SMG7_uc001gqi.2_Missense_Mutation_p.V546L|SMG7_uc010poc.1_Missense_Mutation_p.V592L	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1	634					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						AAAAACACCTGTAACTCAAAC	0.423													4	182	---	---	---	---	PASS
IRF6	3664	broad.mit.edu	37	1	209963071	209963071	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209963071A>C	uc001hhq.1	-	8	1383	c.1120T>G	c.(1120-1122)TGC>GGC	p.C374G	IRF6_uc010psm.1_Missense_Mutation_p.C279G|IRF6_uc009xct.1_Missense_Mutation_p.C374G	NM_006147	NP_006138	O14896	IRF6_HUMAN	interferon regulatory factor 6	374			C -> W (in VWS).		cell cycle arrest|interferon-gamma-mediated signaling pathway|mammary gland epithelial cell differentiation|negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		TCCCCAAAGCATAAGTAGATC	0.443										HNSCC(57;0.16)			3	156	---	---	---	---	PASS
LBR	3930	broad.mit.edu	37	1	225607439	225607439	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225607439T>C	uc001hoy.2	-	4	571	c.428A>G	c.(427-429)GAC>GGC	p.D143G	LBR_uc001hoz.2_Missense_Mutation_p.D143G|LBR_uc001hpa.1_Missense_Mutation_p.D143G	NM_002296	NP_002287	Q14739	LBR_HUMAN	lamin B receptor	143	Nucleoplasmic (Potential).				cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		ATGAGGTGCGTCATTTCTCTC	0.348													4	297	---	---	---	---	PASS
REG3G	130120	broad.mit.edu	37	2	79255008	79255008	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79255008C>G	uc002snw.2	+	5	494	c.409C>G	c.(409-411)CCC>GCC	p.P137A	REG3G_uc002snx.2_Missense_Mutation_p.P137A|REG3G_uc010ffu.2_Missense_Mutation_p.P91A	NM_198448	NP_940850	Q6UW15	REG3G_HUMAN	regenerating islet-derived 3 gamma precursor	137	C-type lectin.				acute-phase response	extracellular region	sugar binding				0						GGAGAAAAATCCCTCCACCAT	0.517													70	183	---	---	---	---	PASS
ZC3H6	376940	broad.mit.edu	37	2	113089935	113089935	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113089935A>G	uc002thq.1	+	12	3834	c.3440A>G	c.(3439-3441)GAT>GGT	p.D1147G		NM_198581	NP_940983	P61129	ZC3H6_HUMAN	zinc finger CCCH-type domain containing 6	1147							nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4						CAGTACAGTGATCCAAGGCAG	0.517													6	149	---	---	---	---	PASS
GYPC	2995	broad.mit.edu	37	2	127453705	127453705	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127453705A>T	uc002tnq.2	+	4	530	c.374A>T	c.(373-375)GAG>GTG	p.E125V	GYPC_uc002tnr.2_Missense_Mutation_p.E106V|GYPC_uc010flv.2_RNA	NM_002101	NP_002092	P04921	GLPC_HUMAN	glycophorin C isoform 1	125	Cytoplasmic.					cortical cytoskeleton|integral to plasma membrane	protein binding			central_nervous_system(1)	1	Colorectal(110;0.0533)			BRCA - Breast invasive adenocarcinoma(221;0.075)		AGCAGAAAGGAGTACTTTATT	0.547													14	76	---	---	---	---	PASS
HOXD3	3232	broad.mit.edu	37	2	177034058	177034058	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177034058C>T	uc002ukt.1	+	2	392	c.216C>T	c.(214-216)AGC>AGT	p.S72S		NM_006898	NP_008829	P31249	HXD3_HUMAN	homeobox D3	72					anterior/posterior pattern formation|cartilage development|cell-matrix adhesion|embryonic skeletal system morphogenesis|Notch signaling pathway|positive regulation of gene expression|positive regulation of neuron differentiation|thyroid gland development		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		CCATCCAGAGCTCTGCCCCTC	0.652													36	101	---	---	---	---	PASS
C2orf67	151050	broad.mit.edu	37	2	210993851	210993851	+	Silent	SNP	A	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210993851A>C	uc002vds.2	-	3	1342	c.1134T>G	c.(1132-1134)GTT>GTG	p.V378V	C2orf67_uc002vdt.2_Silent_p.V378V|C2orf67_uc002vdw.2_Silent_p.V378V|C2orf67_uc002vdv.2_Silent_p.V378V|C2orf67_uc002vdx.1_Silent_p.V378V	NM_152519	NP_689732	A0AUZ9	CB067_HUMAN	hypothetical protein LOC151050	378										ovary(3)	3		Renal(323;0.202)		Epithelial(149;0.00435)|Lung(261;0.0529)|LUSC - Lung squamous cell carcinoma(261;0.0551)|all cancers(144;0.0696)		ATCGGCTGCCAACTCGTGCTC	0.428													11	113	---	---	---	---	PASS
TNS1	7145	broad.mit.edu	37	2	218750505	218750505	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218750505T>C	uc002vgt.2	-	13	1101	c.703A>G	c.(703-705)ACC>GCC	p.T235A	TNS1_uc002vgr.2_Missense_Mutation_p.T235A|TNS1_uc002vgs.2_Missense_Mutation_p.T235A|TNS1_uc010zjv.1_Missense_Mutation_p.T235A|TNS1_uc010fvj.1_Missense_Mutation_p.T303A|TNS1_uc010fvk.1_Missense_Mutation_p.T360A|TNS1_uc002vgu.3_Missense_Mutation_p.T266A|TNS1_uc010fvi.1_5'UTR	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin	235	C2 tensin-type.					cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GGCTCGATGGTGATGCAGACG	0.532													6	145	---	---	---	---	PASS
PLCD4	84812	broad.mit.edu	37	2	219498481	219498481	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219498481G>T	uc002vij.1	+	11	1798	c.1603G>T	c.(1603-1605)GCT>TCT	p.A535S	PLCD4_uc010zkk.1_Missense_Mutation_p.A85S	NM_032726	NP_116115	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	535	PI-PLC Y-box.				intracellular signal transduction|lipid catabolic process	endoplasmic reticulum|membrane|nucleus	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(3)	3		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CATCAAGGAGGCTGGTCAGGA	0.507													5	60	---	---	---	---	PASS
ANKMY1	51281	broad.mit.edu	37	2	241418964	241418964	+	3'UTR	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241418964G>A	uc002vyz.1	-	17					ANKMY1_uc002vza.1_3'UTR|ANKMY1_uc010fzd.1_3'UTR|ANKMY1_uc002vzb.1_3'UTR|ANKMY1_uc002vzc.1_3'UTR|ANKMY1_uc002vzd.1_3'UTR	NM_016552	NP_057636	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1								zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		AGGTGGCTCAGGCAGGTAAGA	0.542													63	222	---	---	---	---	PASS
WDR6	11180	broad.mit.edu	37	3	49051423	49051423	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49051423C>A	uc003cvj.2	+	2	2684	c.2546C>A	c.(2545-2547)ACT>AAT	p.T849N	WDR6_uc011bbx.1_3'UTR|WDR6_uc011bby.1_Missense_Mutation_p.T297N|WDR6_uc010hkn.2_Missense_Mutation_p.T793N|WDR6_uc011bbz.1_Missense_Mutation_p.T768N	NM_018031	NP_060501	Q9NNW5	WDR6_HUMAN	WD repeat domain 6 protein	819					cell cycle arrest|negative regulation of cell proliferation	cytoplasm				central_nervous_system(1)	1				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		ATCATGGTTACTCCGGACCCC	0.647											OREG0015565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	107	---	---	---	---	PASS
EIF2B5	8893	broad.mit.edu	37	3	183857963	183857963	+	Intron	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183857963A>G	uc003fmp.2	+						EIF2B5_uc003fmq.2_5'UTR	NM_003907	NP_003898	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B,						astrocyte development|myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|positive regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus|RNA metabolic process	cytosol|eukaryotic translation initiation factor 2B complex|nucleus	guanyl-nucleotide exchange factor activity|transferase activity|translation initiation factor activity|translation initiation factor binding			ovary(5)	5	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			AAGTCTTCCAATGCCTCTTTA	0.423													14	68	---	---	---	---	PASS
UTP3	57050	broad.mit.edu	37	4	71555682	71555682	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71555682C>T	uc003hfo.2	+	1	1487	c.1288C>T	c.(1288-1290)CGC>TGC	p.R430C		NM_020368	NP_065101	Q9NQZ2	SAS10_HUMAN	UTP3, small subunit processome component	430					brain development|chromatin modification|gene silencing	nucleolus					0			Lung(101;0.235)			GAAGATTGATCGCAATCCCAG	0.408													5	215	---	---	---	---	PASS
LRAT	9227	broad.mit.edu	37	4	155670309	155670309	+	3'UTR	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155670309G>A	uc003iom.1	+	2					LRAT_uc003ion.1_3'UTR	NM_004744	NP_004735	O95237	LRAT_HUMAN	lecithin retinol acyltransferase						response to stimulus|retinoid metabolic process|steroid metabolic process|visual perception	endoplasmic reticulum membrane|integral to membrane|multivesicular body|perinuclear region of cytoplasm|rough endoplasmic reticulum	phosphatidylcholine-retinol O-acyltransferase activity			central_nervous_system(1)	1	all_hematologic(180;0.215)	Renal(120;0.0458)			Vitamin A(DB00162)	CCATGTCAGTGTGTGTATTCT	0.363													7	425	---	---	---	---	PASS
KLHL2	11275	broad.mit.edu	37	4	166218818	166218818	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166218818A>C	uc003irb.2	+	7	971	c.712A>C	c.(712-714)ATG>CTG	p.M238L	KLHL2_uc011cjm.1_Missense_Mutation_p.M242L|KLHL2_uc003irc.2_Missense_Mutation_p.M150L|KLHL2_uc010ira.2_5'UTR	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1	238					intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		GCAAGAGTTTATGGCCCGACT	0.393													4	174	---	---	---	---	PASS
SDHA	6389	broad.mit.edu	37	5	228288	228288	+	Intron	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:228288C>T	uc003jao.3	+						SDHA_uc003jan.2_Intron|SDHA_uc011clv.1_Intron|SDHA_uc011clw.1_Intron|SDHA_uc003jap.3_Intron|SDHA_uc003jaq.3_5'UTR|SDHA_uc003jar.3_5'Flank	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,						nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	CTTTTTTTTTCCTTTCTTTTA	0.418									Familial_Paragangliomas				5	135	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21755850	21755850	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21755850G>A	uc010iuc.2	-	11	2193	c.1735C>T	c.(1735-1737)CAG>TAG	p.Q579*	CDH12_uc011cno.1_Nonsense_Mutation_p.Q539*|CDH12_uc003jgk.2_Nonsense_Mutation_p.Q579*|uc003jgj.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	579	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						GTGCTGCTCTGGACAGGGTAG	0.468										HNSCC(59;0.17)			4	207	---	---	---	---	PASS
CDH6	1004	broad.mit.edu	37	5	31317551	31317551	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31317551G>A	uc003jhe.1	+	10	1908	c.1582G>A	c.(1582-1584)GCC>ACC	p.A528T	CDH6_uc003jhd.1_Missense_Mutation_p.A528T	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein	528	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7						GTTTTCCTTGGCCCCTGAAGC	0.413													51	163	---	---	---	---	PASS
MTMR12	54545	broad.mit.edu	37	5	32274132	32274132	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32274132A>C	uc003jhq.2	-	3	409	c.239T>G	c.(238-240)TTC>TGC	p.F80C	MTMR12_uc010iuk.2_Missense_Mutation_p.F80C|MTMR12_uc010iul.2_Missense_Mutation_p.F80C	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	80						cytoplasm	phosphatase activity			ovary(1)	1						GGCAATCTTGAAGTCTGTGCA	0.483													12	310	---	---	---	---	PASS
SKIV2L2	23517	broad.mit.edu	37	5	54635836	54635836	+	Splice_Site	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54635836A>G	uc003jpy.3	+	6	782	c.516_splice	c.e6-2	p.E172_splice	SKIV2L2_uc011cqi.1_Splice_Site_p.E71_splice	NM_015360	NP_056175	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2						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)				TCACATTTGTAGGTATGCCAT	0.303													25	120	---	---	---	---	PASS
KCNN2	3781	broad.mit.edu	37	5	113740445	113740445	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113740445C>G	uc003kqo.2	+	3	1350	c.893C>G	c.(892-894)ACA>AGA	p.T298R		NM_021614	NP_067627	Q9H2S1	KCNN2_HUMAN	small conductance calcium-activated potassium	298						integral to membrane	calmodulin binding|small conductance calcium-activated potassium channel activity			ovary(2)	2		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)		AACTTCAATACACGTTTTGTT	0.383													7	376	---	---	---	---	PASS
SNCAIP	9627	broad.mit.edu	37	5	121786251	121786251	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121786251G>T	uc003ksw.1	+	10	1915	c.1709G>T	c.(1708-1710)AGA>ATA	p.R570I	SNCAIP_uc011cwl.1_Missense_Mutation_p.R128I|SNCAIP_uc003ksx.1_Missense_Mutation_p.R617I|SNCAIP_uc003ksy.1_Missense_Mutation_p.R204I|SNCAIP_uc003ksz.1_Missense_Mutation_p.R204I|SNCAIP_uc010jcu.2_Missense_Mutation_p.R166I|SNCAIP_uc011cwm.1_Missense_Mutation_p.R204I|SNCAIP_uc003kta.1_Missense_Mutation_p.R202I|SNCAIP_uc010jcv.1_RNA|SNCAIP_uc010jcw.1_Missense_Mutation_p.R264I|SNCAIP_uc010jcx.1_Missense_Mutation_p.R510I|uc003ktb.1_RNA|SNCAIP_uc003ktc.1_Missense_Mutation_p.R86I	NM_005460	NP_005451	Q9Y6H5	SNCAP_HUMAN	synuclein alpha interacting protein	570					cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		CCTGCCTCCAGAAAGTCCCAG	0.458													11	348	---	---	---	---	PASS
MATR3	9782	broad.mit.edu	37	5	138643657	138643657	+	Silent	SNP	A	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138643657A>C	uc003ldu.2	+	5	980	c.553A>C	c.(553-555)AGA>CGA	p.R185R	MATR3_uc003lds.2_Silent_p.R185R|MATR3_uc010jfb.2_Silent_p.R185R|MATR3_uc003ldt.2_Intron|MATR3_uc003ldw.2_Silent_p.R185R|MATR3_uc003ldx.2_Silent_p.R185R|MATR3_uc010jfc.2_Silent_p.R185R|MATR3_uc003ldy.2_Intron|MATR3_uc011czb.1_Intron|MATR3_uc003ldz.2_Silent_p.R185R|MATR3_uc003lea.2_Silent_p.R185R	NM_199189	NP_954659	P43243	MATR3_HUMAN	matrin 3	185						nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAGGCACTTTAGAAGAGATAG	0.443													5	143	---	---	---	---	PASS
PCDHB2	56133	broad.mit.edu	37	5	140476346	140476346	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140476346G>A	uc003lil.2	+	1	2110	c.1972G>A	c.(1972-1974)GCC>ACC	p.A658T	PCDHB2_uc003lim.1_Missense_Mutation_p.A319T	NM_018936	NP_061759	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2 precursor	658	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(3)|upper_aerodigestive_tract(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTCGGCCACCGCCACGCTGCA	0.711													23	58	---	---	---	---	PASS
SH3TC2	79628	broad.mit.edu	37	5	148407223	148407223	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148407223G>A	uc003lpu.2	-	11	2224	c.2072C>T	c.(2071-2073)GCC>GTC	p.A691V	SH3TC2_uc003lpp.1_RNA|SH3TC2_uc010jgw.2_Missense_Mutation_p.A335V|SH3TC2_uc003lps.2_RNA|SH3TC2_uc003lpt.2_Missense_Mutation_p.A238V|SH3TC2_uc010jgx.2_Missense_Mutation_p.A684V|SH3TC2_uc003lpv.1_Missense_Mutation_p.A238V|SH3TC2_uc011dbz.1_Missense_Mutation_p.A576V	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	691							binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGACAGAGGCCACTGCAAG	0.527													49	176	---	---	---	---	PASS
SH3TC2	79628	broad.mit.edu	37	5	148408101	148408101	+	Silent	SNP	A	G	G	rs1432793	byFrequency	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148408101A>G	uc003lpu.2	-	11	1346	c.1194T>C	c.(1192-1194)GGT>GGC	p.G398G	SH3TC2_uc003lpp.1_RNA|SH3TC2_uc010jgw.2_Silent_p.G42G|SH3TC2_uc003lps.2_RNA|SH3TC2_uc003lpt.2_5'UTR|SH3TC2_uc010jgx.2_Silent_p.G391G|SH3TC2_uc003lpv.1_5'UTR|SH3TC2_uc011dbz.1_Silent_p.G283G	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	398							binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTCCTTGAAACCTTCAGGCT	0.607													5	87	---	---	---	---	PASS
ATP10B	23120	broad.mit.edu	37	5	160042863	160042863	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160042863T>G	uc003lym.1	-	17	3482	c.2635A>C	c.(2635-2637)AAT>CAT	p.N879H	ATP10B_uc010jit.1_Missense_Mutation_p.N196H|ATP10B_uc003lyn.2_Missense_Mutation_p.N437H	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	879	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTGAGTTGATTCTCCAGATGC	0.493													114	173	---	---	---	---	PASS
HIST1H2BH	8345	broad.mit.edu	37	6	26252136	26252136	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26252136G>T	uc003nhh.2	+	1	258	c.258G>T	c.(256-258)AAG>AAT	p.K86N	HIST1H3F_uc003nhg.1_5'Flank	NM_003524	NP_003515	Q93079	H2B1H_HUMAN	histone cluster 1, H2bh	86					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(3)	3						ATTACAACAAGCGTTCGACCA	0.607													15	167	---	---	---	---	PASS
BTN3A1	11119	broad.mit.edu	37	6	26407900	26407900	+	Silent	SNP	A	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26407900A>T	uc003nhv.2	+	4	803	c.435A>T	c.(433-435)GCA>GCT	p.A145A	BTN3A1_uc011dkj.1_Silent_p.A145A|BTN3A1_uc011dkk.1_Intron|BTN3A1_uc010jqj.2_Silent_p.A145A	NM_007048	NP_008979	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1 isoform a	145	Ig-like V-type 2.|Extracellular (Potential).				lipid metabolic process	integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2						CTTCCACAGCACTGGGTTCTG	0.353													4	111	---	---	---	---	PASS
PPP2R5D	5528	broad.mit.edu	37	6	42975223	42975223	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42975223C>T	uc003oth.2	+	6	791	c.705C>T	c.(703-705)ATC>ATT	p.I235I	MEA1_uc010jyc.1_Intron|PPP2R5D_uc003otg.2_Silent_p.I203I|PPP2R5D_uc010jyd.2_Silent_p.I129I|PPP2R5D_uc011dva.1_Silent_p.I84I|PPP2R5D_uc003oti.2_Silent_p.I84I|PPP2R5D_uc003otj.2_Silent_p.I84I	NM_006245	NP_006236	Q14738	2A5D_HUMAN	delta isoform of regulatory subunit B56, protein	235					nervous system development|signal transduction	cytoplasm|nucleus|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			breast(1)|central_nervous_system(1)	2			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			AGAAGTACATCGACCAGAAGT	0.512													16	224	---	---	---	---	PASS
ROS1	6098	broad.mit.edu	37	6	117663708	117663708	+	Splice_Site	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117663708C>A	uc003pxp.1	-	28	4724	c.4525_splice	c.e28-1	p.E1509_splice	ROS1_uc011ebi.1_Splice_Site|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor						transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CCTGAAATTCCTGTAATTGAT	0.254			T	GOPC|ROS1	glioblastoma|NSCLC								14	46	---	---	---	---	PASS
SEMA3D	223117	broad.mit.edu	37	7	84694822	84694822	+	Silent	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84694822A>G	uc003uic.2	-	6	676	c.636T>C	c.(634-636)GAT>GAC	p.D212D	SEMA3D_uc010led.2_Silent_p.D212D|SEMA3D_uc010lee.1_Silent_p.D212D	NM_152754	NP_689967	O95025	SEM3D_HUMAN	semaphorin 3D precursor	212	Sema.				cell differentiation|nervous system development	extracellular region|membrane	receptor activity			ovary(3)|large_intestine(2)	5						TGAATGCAGTATCTTTGCCAA	0.423													6	95	---	---	---	---	PASS
PON2	5445	broad.mit.edu	37	7	95053856	95053856	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95053856A>G	uc003unv.2	-	2	237	c.116T>C	c.(115-117)CTT>CCT	p.L39P	PON2_uc003unu.2_Missense_Mutation_p.L39P|PON2_uc010lfk.2_RNA|PON2_uc003unw.2_5'UTR	NM_000305	NP_000296	Q15165	PON2_HUMAN	paraoxonase 2 isoform 1	39					aromatic compound catabolic process	extracellular region|plasma membrane	arylesterase activity|identical protein binding|metal ion binding				0	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			GCAGTGTGGAAGGTCTACAGA	0.299													16	183	---	---	---	---	PASS
PAXIP1	22976	broad.mit.edu	37	7	154754078	154754078	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154754078G>A	uc003wlp.2	-	10	2123	c.2080C>T	c.(2080-2082)CAC>TAC	p.H694Y	PAXIP1_uc003wlq.1_Missense_Mutation_p.H660Y|PAXIP1_uc011kvs.1_Missense_Mutation_p.H658Y	NM_007349	NP_031375	Q6ZW49	PAXI1_HUMAN	PAX interacting protein 1	694	Interaction with TP53BP1.|BRCT 3.				DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent	histone methyltransferase complex|nuclear matrix				lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		ACTGGGAAGTGAAGGGCTCGG	0.468													5	163	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	12427974	12427974	+	Intron	SNP	T	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12427974T>C	uc003wvy.3	-						uc003wvz.1_RNA|uc003wwa.2_RNA					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		CTCCATGCCTTTCAAACCCAG	0.438													4	22	---	---	---	---	PASS
CCDC25	55246	broad.mit.edu	37	8	27605731	27605731	+	Silent	SNP	G	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27605731G>C	uc003xgc.2	-	7	527	c.414C>G	c.(412-414)GTC>GTG	p.V138V	CCDC25_uc003xgd.2_Silent_p.V70V|CCDC25_uc011lan.1_RNA|CCDC25_uc011lao.1_RNA|CCDC25_uc003xge.2_RNA|CCDC25_uc003xgf.1_RNA	NM_018246	NP_060716	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25	138	Potential.										0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)		GGAACCGCTCGACTTTGGTCT	0.393													39	175	---	---	---	---	PASS
MPDZ	8777	broad.mit.edu	37	9	13224386	13224386	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13224386T>G	uc010mia.1	-	3	437	c.380A>C	c.(379-381)AAA>ACA	p.K127T	MPDZ_uc010mhy.2_Missense_Mutation_p.K127T|MPDZ_uc010mhz.2_Missense_Mutation_p.K127T|MPDZ_uc011lmn.1_Missense_Mutation_p.K127T|MPDZ_uc003zlb.3_Missense_Mutation_p.K127T	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein	127					interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)		GGCCATATTTTTGATAAGCTG	0.338													53	207	---	---	---	---	PASS
TAF1L	138474	broad.mit.edu	37	9	32632973	32632973	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32632973C>T	uc003zrg.1	-	1	2695	c.2605G>A	c.(2605-2607)GCT>ACT	p.A869T	uc003zrh.1_5'Flank	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	869					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TTGAAGTCAGCGCAGAGCTTT	0.463													11	307	---	---	---	---	PASS
AQP7	364	broad.mit.edu	37	9	33385641	33385641	+	Intron	SNP	C	A	A	rs116511952	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33385641C>A	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_Missense_Mutation_p.C158F|AQP7_uc010mjt.2_Missense_Mutation_p.C158F|AQP7_uc011lnx.1_Missense_Mutation_p.C250F|AQP7_uc011lny.1_Missense_Mutation_p.C249F|AQP7_uc003zss.3_Missense_Mutation_p.C158F|AQP7_uc011lnz.1_Missense_Mutation_p.C158F|AQP7_uc011loa.1_Silent_p.L118L	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		TGGGCAGGGGCAGTACCTGAA	0.602													8	164	---	---	---	---	PASS
MSMP	692094	broad.mit.edu	37	9	35753744	35753744	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35753744T>G	uc003zyb.1	-	2	298	c.152A>C	c.(151-153)AAA>ACA	p.K51T		NM_001044264	NP_001037729	Q1L6U9	MSMP_HUMAN	PC3-secreted microprotein precursor	51						extracellular region					0						GGTAAAATATTTCCCCTCATA	0.537													9	60	---	---	---	---	PASS
COL15A1	1306	broad.mit.edu	37	9	101748355	101748355	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101748355C>T	uc004azb.1	+	3	815	c.609C>T	c.(607-609)TTC>TTT	p.F203F	COL15A1_uc004aza.2_Silent_p.F203F	NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor	203	TSP N-terminal.				angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)				CTGGAATCTTCATGGGCAATG	0.557													4	138	---	---	---	---	PASS
GOLGA2	2801	broad.mit.edu	37	9	131023799	131023799	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131023799T>A	uc011maw.1	-	15	1198	c.1185A>T	c.(1183-1185)AAA>AAT	p.K395N	GOLGA2_uc010mxw.2_Intron|GOLGA2_uc004buh.2_5'Flank|GOLGA2_uc004bul.1_Missense_Mutation_p.K296N|uc004bun.2_5'Flank	NM_004486	NP_004477	Q08379	GOGA2_HUMAN	Golgi autoantigen, golgin subfamily a, 2	395	Potential.					Golgi cisterna membrane	protein binding			ovary(1)	1						TCTCCGCATATTTATCTCTCT	0.507													9	217	---	---	---	---	PASS
ARID5B	84159	broad.mit.edu	37	10	63851205	63851205	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63851205C>G	uc001jlt.1	+	10	2009	c.1983C>G	c.(1981-1983)GAC>GAG	p.D661E		NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	661					liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)					AAGACAAAGACCTGACTGGGC	0.537													3	59	---	---	---	---	PASS
CBARA1	10367	broad.mit.edu	37	10	74135571	74135571	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74135571C>G	uc001jtb.1	-	12	1379	c.1246G>C	c.(1246-1248)GAT>CAT	p.D416H	CBARA1_uc010qjw.1_Missense_Mutation_p.D216H|CBARA1_uc010qjx.1_Missense_Mutation_p.D216H|CBARA1_uc009xqo.1_RNA	NM_006077	NP_006068	Q9BPX6	MICU1_HUMAN	calcium binding atopy-related autoantigen 1	414	EF-hand 2.				calcium ion import|defense response|elevation of mitochondrial calcium ion concentration	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			ovary(1)	1						AACACCACATCACACACGTGG	0.537													6	22	---	---	---	---	PASS
PTEN	5728	broad.mit.edu	37	10	89692871	89692871	+	Missense_Mutation	SNP	G	T	T	rs139767111		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89692871G>T	uc001kfb.2	+	6	1386	c.355G>T	c.(355-357)GTT>TTT	p.V119F		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	119	Phosphatase tensin-type.		V -> L (in multiple cancers).		activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R55fs*1(4)|p.V119fs*15(3)|p.?(2)|p.Y27fs*1(2)|p.Y27_N212>Y(2)|p.V119F(1)|p.V119D(1)|p.F56fs*2(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TGACAATCATGTTGCAGCAAT	0.403		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			58	83	---	---	---	---	PASS
CCDC147	159686	broad.mit.edu	37	10	106125599	106125599	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106125599A>C	uc001kyh.2	+	5	759	c.625A>C	c.(625-627)AAC>CAC	p.N209H		NM_001008723	NP_001008723	Q5T655	CC147_HUMAN	coiled-coil domain containing 147	209	Potential.									ovary(2)|central_nervous_system(2)|skin(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		GCAACGTCAGAACGAAGCTTC	0.512													4	86	---	---	---	---	PASS
EIF3M	10480	broad.mit.edu	37	11	32605404	32605404	+	5'UTR	SNP	T	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32605404T>C	uc001mtu.2	+	1					EIF3M_uc010ref.1_5'UTR	NM_006360	NP_006351	Q7L2H7	EIF3M_HUMAN	eukaryotic translation initiation factor 3,							eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)|breast(1)|skin(1)	3	Breast(20;0.109)					GTCTTGCGAGTGGAGTGTCCG	0.672													9	24	---	---	---	---	PASS
QSER1	79832	broad.mit.edu	37	11	32996944	32996944	+	Intron	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32996944C>T	uc001mty.2	+						QSER1_uc001mtz.1_Intron|QSER1_uc001mua.2_Silent_p.L1213L	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1											ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					TAAGGAGACTCTAGCCATAGT	0.284													8	42	---	---	---	---	PASS
OR5T1	390155	broad.mit.edu	37	11	56043918	56043918	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56043918C>T	uc001nio.1	+	1	804	c.804C>T	c.(802-804)CTC>CTT	p.L268L		NM_001004745	NP_001004745	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T,	268	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)	3	Esophageal squamous(21;0.00448)					GGACAATCCTCTTCATGTATG	0.428													165	329	---	---	---	---	PASS
OR5B12	390191	broad.mit.edu	37	11	58207266	58207266	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58207266C>T	uc010rkh.1	-	1	359	c.359G>A	c.(358-360)CGC>CAC	p.R120H		NM_001004733	NP_001004733	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B,	120	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TGCTGCATAGCGGTCATAGGC	0.433													48	112	---	---	---	---	PASS
VWCE	220001	broad.mit.edu	37	11	61034970	61034970	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61034970C>T	uc001nra.2	-	16	2208	c.1929G>A	c.(1927-1929)CCG>CCA	p.P643P	VWCE_uc001nrb.2_RNA	NM_152718	NP_689931	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	643	VWFC 5.					extracellular region	calcium ion binding			ovary(1)	1						CCAGCACAGACGGGAAGGTCT	0.597													40	83	---	---	---	---	PASS
FERMT3	83706	broad.mit.edu	37	11	63978262	63978262	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63978262G>T	uc001nyl.2	+	3	489	c.340G>T	c.(340-342)GCC>TCC	p.A114S	FERMT3_uc001nym.2_Missense_Mutation_p.A114S	NM_178443	NP_848537	Q86UX7	URP2_HUMAN	fermitin family homolog 3 long form	114					integrin activation|leukocyte cell-cell adhesion|platelet aggregation|regulation of cell-cell adhesion mediated by integrin	cell junction|cell projection|podosome	integrin binding			ovary(1)	1						GCGCCTCCGTGCCAGCTTCTC	0.667													6	192	---	---	---	---	PASS
TIGD3	220359	broad.mit.edu	37	11	65123663	65123663	+	Silent	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65123663A>G	uc001odo.3	+	2	547	c.384A>G	c.(382-384)AAA>AAG	p.K128K		NM_145719	NP_663771	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	128	H-T-H motif (By similarity).|HTH CENPB-type.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0						TCCGCTGGAAACGCCGAAACA	0.657													7	62	---	---	---	---	PASS
DPP3	10072	broad.mit.edu	37	11	66259193	66259193	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66259193C>T	uc001oig.1	+	9	1016	c.954C>T	c.(952-954)TAC>TAT	p.Y318Y	DPP3_uc001oif.1_Silent_p.Y318Y|DPP3_uc010rpe.1_Silent_p.Y307Y	NM_005700	NP_005691	Q9NY33	DPP3_HUMAN	dipeptidyl peptidase III	318					proteolysis	cytoplasm	aminopeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity			ovary(1)|skin(1)	2						TCGAGAGCTACCGCGACCCCT	0.612													6	390	---	---	---	---	PASS
KRTAP5-11	440051	broad.mit.edu	37	11	71293806	71293806	+	Silent	SNP	A	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71293806A>T	uc001oqu.2	-	1	116	c.78T>A	c.(76-78)TCT>TCA	p.S26S		NM_001005405	NP_001005405	Q6L8G4	KR511_HUMAN	keratin associated protein 5-11	26						keratin filament					0						CCCCACAGCCAGAGCCACAGC	0.637													8	32	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	103090670	103090670	+	Silent	SNP	T	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103090670T>G	uc001pho.2	+	56	9003	c.8859T>G	c.(8857-8859)CTT>CTG	p.L2953L	DYNC2H1_uc001phn.1_Silent_p.L2953L|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2953	Potential.|Stalk (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AAACAGAACTTGAAAGACTGA	0.259													3	8	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108205768	108205768	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108205768G>A	uc001pkb.1	+	55	8468	c.8083G>A	c.(8083-8085)GGT>AGT	p.G2695S	ATM_uc009yxr.1_Missense_Mutation_p.G2695S|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Missense_Mutation_p.G1347S	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2695			G -> A (in T-prolymphocytic leukemia and B-cell chronic lymphocytic leukemia).		cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding	p.G2695A(2)		haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		CTTAGCAGGAGGTGTAAATTT	0.398			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			28	185	---	---	---	---	PASS
KIF5A	3798	broad.mit.edu	37	12	57962799	57962799	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57962799C>T	uc001sor.1	+	9	976	c.768C>T	c.(766-768)AAC>AAT	p.N256N	KIF5A_uc010srr.1_Silent_p.N167N	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A	256	Kinesin-motor.|Microtubule-binding.		N -> S (in SPG10; slightly decreases microtubule affinity; reduces gliding velocity; reduces microtubule-dependent ATP turnover).|Missing (in SPG10).		blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3						AGAATATCAACAAGTCACTGT	0.557													16	97	---	---	---	---	PASS
HELB	92797	broad.mit.edu	37	12	66696411	66696411	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66696411C>A	uc001sti.2	+	1	56	c.28C>A	c.(28-30)CAA>AAA	p.Q10K	HELB_uc010ssz.1_RNA|HELB_uc009zqt.1_RNA	NM_033647	NP_387467	Q8NG08	HELB_HUMAN	helicase (DNA) B	10					DNA replication, synthesis of RNA primer		ATP binding|ATP-dependent 5'-3' DNA helicase activity|single-stranded DNA-dependent ATP-dependent DNA helicase activity			central_nervous_system(1)|pancreas(1)	2			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		GTACCTGCGCCAACTTCAGGG	0.557													6	116	---	---	---	---	PASS
TUBA3C	7278	broad.mit.edu	37	13	19755937	19755937	+	Splice_Site	SNP	G	A	A	rs146915657	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19755937G>A	uc009zzj.2	-	1	1	c.-48_splice	c.e1-1			NM_006001	NP_005992	Q13748	TBA3C_HUMAN	tubulin, alpha 3c						'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)		GACCTCAACCGCCGCTGCAGC	0.682													12	13	---	---	---	---	PASS
GZMH	2999	broad.mit.edu	37	14	25076555	25076555	+	Missense_Mutation	SNP	T	G	G	rs144759599		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25076555T>G	uc001wpr.1	-	4	442	c.397A>C	c.(397-399)AAG>CAG	p.K133Q	GZMH_uc010aly.1_Intron|GZMH_uc010alz.1_Intron	NM_033423	NP_219491	P20718	GRAH_HUMAN	granzyme H precursor	133	Peptidase S1.				apoptosis|cytolysis|proteolysis	cytoplasm	serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(265;0.0267)		ACCTGGGCCTTGCTGCTAGGT	0.572													7	116	---	---	---	---	PASS
G2E3	55632	broad.mit.edu	37	14	31066642	31066642	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31066642C>T	uc001wqk.2	+	7	699	c.545C>T	c.(544-546)GCG>GTG	p.A182V	G2E3_uc010tpe.1_Missense_Mutation_p.A136V|G2E3_uc010tpf.1_Missense_Mutation_p.A136V	NM_017769	NP_060239	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin ligase	182	PHD-type 2; degenerate.				apoptosis|multicellular organismal development|protein modification process	Golgi apparatus|nucleolus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						GCAATAAATGCGGGAGTGTTT	0.313													9	380	---	---	---	---	PASS
RALGAPA1	253959	broad.mit.edu	37	14	36096769	36096769	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36096769C>A	uc001wti.2	-	33	5257	c.4866G>T	c.(4864-4866)TTG>TTT	p.L1622F	RALGAPA1_uc010amp.2_RNA|RALGAPA1_uc001wtj.2_Missense_Mutation_p.L1622F|RALGAPA1_uc010tpv.1_Missense_Mutation_p.L1635F|RALGAPA1_uc010tpw.1_Missense_Mutation_p.L1669F	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1	1622	Minimal domain that binds to TCF3/E12 (By similarity).				activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						TAGGTTCTGACAAGCCACTTA	0.413													9	86	---	---	---	---	PASS
OTX2	5015	broad.mit.edu	37	14	57268617	57268617	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57268617C>G	uc001xcp.2	-	3	877	c.706G>C	c.(706-708)GCT>CCT	p.A236P	OTX2_uc010aou.2_Missense_Mutation_p.A236P|OTX2_uc001xcq.2_Missense_Mutation_p.A244P	NM_172337	NP_758840	P32243	OTX2_HUMAN	orthodenticle homeobox 2 isoform b	236					axon guidance|forebrain development|midbrain development|positive regulation of embryonic development|positive regulation of gastrulation|primitive streak formation|protein complex assembly|regulation of fibroblast growth factor receptor signaling pathway|regulation of smoothened signaling pathway	growth cone|nucleus|protein complex	eukaryotic initiation factor 4E binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding			ovary(1)	1	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					GAAAGAGAAGCTGGGGACTGA	0.502													66	128	---	---	---	---	PASS
KIAA1409	57578	broad.mit.edu	37	14	94060090	94060090	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94060090C>A	uc001ybv.1	+	20	2649	c.2566C>A	c.(2566-2568)CAT>AAT	p.H856N	KIAA1409_uc001ybs.1_Missense_Mutation_p.H856N	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	1033						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		TCTTCTCCTCCATGCCCTGTC	0.493													5	279	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	33990173	33990173	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33990173C>T	uc001zhi.2	+	40	6295	c.6225C>T	c.(6223-6225)AAC>AAT	p.N2075N	RYR3_uc010bar.2_Silent_p.N2075N	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2075	4 X approximate repeats.|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)		TGATGGTGAACGTGTTGGGTA	0.493													47	212	---	---	---	---	PASS
TLN2	83660	broad.mit.edu	37	15	62978869	62978869	+	Silent	SNP	G	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62978869G>T	uc002alb.3	+	9	987	c.987G>T	c.(985-987)GTG>GTT	p.V329V		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	329	FERM.|Interaction with PIP5K1C (By similarity).				cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						ACAAGCTGGTGCCTCGCCTGC	0.537													12	31	---	---	---	---	PASS
ADAMTS7	11173	broad.mit.edu	37	15	79051880	79051880	+	Silent	SNP	C	T	T	rs1045121	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79051880C>T	uc002bej.3	-	24	5155	c.4944G>A	c.(4942-4944)ACG>ACA	p.T1648T		NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1648	PLAC.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						GTAGGCGCAGCGTCTCGCAGA	0.697													5	7	---	---	---	---	PASS
ADAMTS7	11173	broad.mit.edu	37	15	79051886	79051886	+	Silent	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79051886G>A	uc002bej.3	-	24	5149	c.4938C>T	c.(4936-4938)TGC>TGT	p.C1646C		NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1646	PLAC.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						GCAGCGTCTCGCAGAACCCGA	0.701													5	7	---	---	---	---	PASS
LRRK1	79705	broad.mit.edu	37	15	101593153	101593153	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101593153A>G	uc002bwr.2	+	25	4035	c.3716A>G	c.(3715-3717)GAG>GGG	p.E1239G	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA|LRRK1_uc002bws.2_5'Flank	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	1239					small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AGCAAGCTGGAGCACAGCGAG	0.692													3	60	---	---	---	---	PASS
WASH3P	374666	broad.mit.edu	37	15	102516473	102516473	+	3'UTR	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102516473G>A	uc002cdi.2	+	11					WASH3P_uc002cdl.2_3'UTR|WASH3P_uc002cdk.2_RNA|WASH3P_uc002cdp.2_3'UTR|WASH3P_uc010bpo.2_RNA|WASH3P_uc002cdq.2_RNA|WASH3P_uc002cdr.2_RNA	NR_003659				RecName: Full=WAS protein family homolog 2; AltName: Full=Protein FAM39B; AltName: Full=CXYorf1-like protein on chromosome 2;												0						ATCCTAGGGGGCTCCATGACA	0.642													4	31	---	---	---	---	PASS
OR2C1	4993	broad.mit.edu	37	16	3406160	3406160	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3406160G>A	uc002cuw.1	+	1	272	c.220G>A	c.(220-222)GCT>ACT	p.A74T		NM_012368	NP_036500	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C,	74	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						CCTTGCTTTCGCTACTAGTTC	0.522													40	297	---	---	---	---	PASS
BTBD12	84464	broad.mit.edu	37	16	3640681	3640681	+	Silent	SNP	G	A	A	rs148111699		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3640681G>A	uc002cvp.2	-	12	3585	c.2958C>T	c.(2956-2958)CTC>CTT	p.L986L		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	986	Interaction with PLK1 and TERF2-TERF2IP.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0						TTGATGAGAAGAGCTGTTCGT	0.557								Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				7	180	---	---	---	---	PASS
GSPT1	2935	broad.mit.edu	37	16	12009738	12009738	+	5'UTR	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12009738G>A	uc002dbt.2	-	1					GSPT1_uc002dbu.2_5'UTR|GSPT1_uc010bux.2_Intron	NM_002094	NP_002085	P15170	ERF3A_HUMAN	G1 to S phase transition 1 isoform 1						G1/S transition of mitotic cell cycle|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|protein methylation	intracellular	GTP binding|GTPase activity|protein binding|translation release factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						AGCAGCTCCAGTCCCGACTCC	0.697													7	19	---	---	---	---	PASS
PDILT	204474	broad.mit.edu	37	16	20370791	20370791	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20370791C>T	uc002dhc.1	-	12	1828	c.1605G>A	c.(1603-1605)TCG>TCA	p.S535S		NM_174924	NP_777584	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis	535					cell differentiation|cell redox homeostasis|multicellular organismal development|spermatogenesis	endoplasmic reticulum	isomerase activity			large_intestine(1)	1						CCAGCTCAGGCGACTGCTGTT	0.502													12	468	---	---	---	---	PASS
CES1	1066	broad.mit.edu	37	16	55862883	55862883	+	Missense_Mutation	SNP	C	A	A	rs3826190	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55862883C>A	uc002eim.2	-	2	161	c.53G>T	c.(52-54)GGG>GTG	p.G18V	CES1_uc002eil.2_Missense_Mutation_p.G19V|CES1_uc002ein.2_Missense_Mutation_p.G18V	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor	18			G -> GA.		response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	GGACGGATGCCCTGCTGGACA	0.403													7	17	---	---	---	---	PASS
GNAO1	2775	broad.mit.edu	37	16	56362633	56362633	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56362633T>C	uc002eit.3	+	4	1291	c.394T>C	c.(394-396)TGG>CGG	p.W132R	GNAO1_uc002eiu.3_Missense_Mutation_p.W132R	NM_138736	NP_620073	P09471	GNAO_HUMAN	guanine nucleotide binding protein, alpha	132					dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			lung(1)|breast(1)	2		all_neural(199;0.159)				GATGCGGCTCTGGGGCGACTC	0.587													16	91	---	---	---	---	PASS
DPEP1	1800	broad.mit.edu	37	16	89703762	89703762	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89703762G>A	uc010cin.2	+	7	945	c.742G>A	c.(742-744)GTG>ATG	p.V248M	DPEP1_uc002fnr.3_Missense_Mutation_p.V248M|DPEP1_uc002fns.3_Missense_Mutation_p.V248M	NM_001128141	NP_001121613	P16444	DPEP1_HUMAN	dipeptidase 1 precursor	248					proteolysis	anchored to membrane|apical plasma membrane|microvillus membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity|protein binding			large_intestine(1)	1		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)	CCGGCGCAACGTGCCTGACGA	0.682													3	42	---	---	---	---	PASS
FAM64A	54478	broad.mit.edu	37	17	6353457	6353457	+	Intron	SNP	T	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6353457T>G	uc002gcw.1	+						FAM64A_uc002gct.1_3'UTR|FAM64A_uc002gcu.1_Intron|FAM64A_uc002gcv.1_Intron|FAM64A_uc002gcx.1_Intron|FAM64A_uc002gcy.1_Intron|FAM64A_uc002gcz.1_Intron|FAM64A_uc002gda.1_Intron|FAM64A_uc002gdb.1_Intron	NM_019013	NP_061886	Q9BSJ6	FA64A_HUMAN	family with sequence similarity 64, member A							nucleolus	protein binding				0				COAD - Colon adenocarcinoma(228;0.141)		ATGAGCAAGTTAAAGAAAAAG	0.507													4	80	---	---	---	---	PASS
RHOT1	55288	broad.mit.edu	37	17	30477885	30477885	+	Intron	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30477885C>T	uc002hgz.2	+						RHOT1_uc002hgw.2_Intron|RHOT1_uc002hgy.2_Intron|RHOT1_uc002hha.2_Intron|RHOT1_uc010csv.2_Intron|RHOT1_uc002hgx.2_Intron|RHOT1_uc010wby.1_Intron|RHOT1_uc002hhb.2_Intron|RHOT1_uc002hgv.2_Intron|ARGFXP2_uc002hhc.2_RNA	NM_018307	NP_060777	Q8IXI2	MIRO1_HUMAN	ras homolog gene family, member T1 isoform 3						apoptosis|cellular homeostasis|mitochondrion transport along microtubule|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to mitochondrial outer membrane|plasma membrane	calcium ion binding|GTP binding|GTPase activity|protein binding			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				TCTGAAACCACGGGAGAAAAA	0.478													16	122	---	---	---	---	PASS
FBXO47	494188	broad.mit.edu	37	17	37093416	37093416	+	3'UTR	SNP	C	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37093416C>G	uc002hrc.2	-	11						NM_001008777	NP_001008777	Q5MNV8	FBX47_HUMAN	F-box protein 47												0						AAAGGCAAGGCTTTCTGAGGA	0.388													47	84	---	---	---	---	PASS
SKAP1	8631	broad.mit.edu	37	17	46262165	46262165	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46262165G>A	uc002ini.1	-	7	599	c.487C>T	c.(487-489)CGG>TGG	p.R163W	SKAP1_uc002inj.1_Missense_Mutation_p.R163W|SKAP1_uc010dbd.1_Missense_Mutation_p.R69W|SKAP1_uc010dbe.1_Missense_Mutation_p.R163W	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform	163	PH.				positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						GGGGCCATCCGTACACCGTAG	0.542													29	165	---	---	---	---	PASS
KIF2B	84643	broad.mit.edu	37	17	51900688	51900688	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51900688G>T	uc002iua.2	+	1	450	c.294G>T	c.(292-294)TTG>TTT	p.L98F	uc010wna.1_RNA	NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	98					blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)|skin(3)	8						TATCCCCCTTGGCTCTGGCGC	0.587													6	260	---	---	---	---	PASS
TRIM25	7706	broad.mit.edu	37	17	54969322	54969322	+	Silent	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54969322G>A	uc002iut.2	-	9	1692	c.1632C>T	c.(1630-1632)CGC>CGT	p.R544R	TRIM25_uc010dcj.2_Silent_p.R336R	NM_005082	NP_005073	Q14258	TRI25_HUMAN	tripartite motif-containing 25	544	B30.2/SPRY.				innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|response to virus	cell junction|cytosol|nucleus	sequence-specific DNA binding transcription factor activity|ubiquitin-protein ligase activity|zinc ion binding			lung(1)|breast(1)|skin(1)	3	Breast(9;6.15e-08)					AGGCGCTGTTGCGGCCGAGCC	0.602													37	94	---	---	---	---	PASS
HN1	51155	broad.mit.edu	37	17	73142764	73142764	+	Missense_Mutation	SNP	G	A	A	rs62620707	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73142764G>A	uc002jna.1	-	4	596	c.313C>T	c.(313-315)CAT>TAT	p.H105Y	HN1_uc002jmz.1_Missense_Mutation_p.H59Y|HN1_uc002jnb.1_Intron|HN1_uc010dgc.1_RNA|HN1_uc002jnc.2_Intron|HN1_uc002jnd.2_Intron	NM_016185	NP_057269	Q9UK76	HN1_HUMAN	hematological and neurological expressed 1	105						nucleus					0	all_lung(278;0.14)|Lung NSC(278;0.168)					TACTTACCATGAATATCACCT	0.358													6	5	---	---	---	---	PASS
FSCN2	25794	broad.mit.edu	37	17	79496338	79496338	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79496338G>T	uc010wup.1	+	1	922	c.781G>T	c.(781-783)GTG>TTG	p.V261L	FSCN2_uc010wuo.1_Missense_Mutation_p.V261L	NM_012418	NP_036550	O14926	FSCN2_HUMAN	fascin 2 isoform 1	261					actin filament bundle assembly|anatomical structure morphogenesis|visual perception	actin cytoskeleton|cytoplasm|stereocilium	actin filament binding|protein binding, bridging				0	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			TCACCCACAGGTGGTGCTGGT	0.662													4	7	---	---	---	---	PASS
CXADRP3	440224	broad.mit.edu	37	18	14479261	14479261	+	RNA	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14479261C>T	uc010xai.1	-	3		c.303G>A				NR_024076				Homo sapiens cDNA clone IMAGE:30390722, containing frame-shift errors.												0						GCAGCAGGAGCGCCATGGTGG	0.582													4	17	---	---	---	---	PASS
PIP5K1C	23396	broad.mit.edu	37	19	3641788	3641788	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3641788C>T	uc002lyj.1	-	15	1759	c.1702G>A	c.(1702-1704)GCG>ACG	p.A568T	PIP5K1C_uc010xhq.1_Missense_Mutation_p.A568T|PIP5K1C_uc010xhr.1_Missense_Mutation_p.A568T	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	568					axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		TCCTCTTCCGCGGGTGGCTCC	0.637													28	44	---	---	---	---	PASS
UNC13A	23025	broad.mit.edu	37	19	17780382	17780382	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17780382G>A	uc002nhd.2	-	6	638	c.638C>T	c.(637-639)ACG>ATG	p.T213M		NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A	125					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						CTCAAAGCGCGTGTCCAGGAG	0.612													3	64	---	---	---	---	PASS
ZNF676	163223	broad.mit.edu	37	19	22364321	22364321	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22364321C>T	uc002nqs.1	-	3	516	c.198G>A	c.(196-198)ATG>ATA	p.M66I		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	66					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TTCTCAATATCATTTTTTGGA	0.303													5	148	---	---	---	---	PASS
ZNF98	148198	broad.mit.edu	37	19	22585674	22585674	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22585674G>T	uc002nqt.2	-	3	292	c.170C>A	c.(169-171)TCT>TAT	p.S57Y		NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98	57	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				GTCTGGCTTAGAGGCAGCAAT	0.393													34	130	---	---	---	---	PASS
ZNF492	57615	broad.mit.edu	37	19	22836734	22836734	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22836734C>A	uc002nqw.3	+	3	291	c.47C>A	c.(46-48)TCT>TAT	p.S16Y		NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492	16	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				ATTGCTGCCTCTAAGCCAGAC	0.398													14	151	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	31039026	31039026	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31039026A>G	uc002nsu.1	+	4	2638	c.2500A>G	c.(2500-2502)AGG>GGG	p.R834G	ZNF536_uc010edd.1_Missense_Mutation_p.R834G	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	834					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					TCTGTTCATCAGGCCAGACAT	0.587													5	225	---	---	---	---	PASS
SUPT5H	6829	broad.mit.edu	37	19	39959750	39959750	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39959750A>G	uc002olo.3	+	15	1354	c.1175A>G	c.(1174-1176)GAG>GGG	p.E392G	SUPT5H_uc002olp.3_Missense_Mutation_p.E392G|SUPT5H_uc002olq.3_Missense_Mutation_p.E388G|SUPT5H_uc002oln.3_Missense_Mutation_p.E392G|SUPT5H_uc002olr.3_Missense_Mutation_p.E392G|SUPT5H_uc002ols.1_Missense_Mutation_p.E15G|SUPT5H_uc010egp.1_5'Flank	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	392	Interaction with RNA polymerase II.				cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			ACACTCTCTGAGCTGGAAAAG	0.567													17	115	---	---	---	---	PASS
SPTBN4	57731	broad.mit.edu	37	19	41009977	41009977	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41009977C>A	uc002ony.2	+	12	1689	c.1603C>A	c.(1603-1605)CTT>ATT	p.L535I	SPTBN4_uc002onx.2_Missense_Mutation_p.L535I|SPTBN4_uc002onz.2_Missense_Mutation_p.L535I	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	535	Spectrin 4.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TGAGCAGAACCTTGCCCTGCA	0.667													4	121	---	---	---	---	PASS
PSG8	440533	broad.mit.edu	37	19	43259290	43259290	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43259290G>T	uc002ouo.2	-	4	936	c.838C>A	c.(838-840)CTC>ATC	p.L280I	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG8_uc010eim.2_Intron|PSG8_uc002oui.2_Missense_Mutation_p.L119I|PSG8_uc002ouh.2_Missense_Mutation_p.L280I|PSG8_uc010ein.2_Missense_Mutation_p.L158I|PSG8_uc002ouj.3_Missense_Mutation_p.L62I|PSG8_uc002ouk.3_Missense_Mutation_p.L119I|PSG8_uc002oul.3_Missense_Mutation_p.L280I|PSG8_uc002oum.3_Missense_Mutation_p.L187I|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Missense_Mutation_p.L187I	NM_182707	NP_874366	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8 isoform	280	Ig-like C2-type 2.					extracellular region					0		Prostate(69;0.00899)				CTGACCGGGAGGCTCTGACCA	0.448													75	469	---	---	---	---	PASS
ZC3H4	23211	broad.mit.edu	37	19	47589711	47589711	+	Missense_Mutation	SNP	C	T	T	rs653615		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47589711C>T	uc002pga.3	-	6	838	c.800G>A	c.(799-801)GGC>GAC	p.G267D	ZC3H4_uc002pgb.1_Intron	NM_015168	NP_055983	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	267	Gly-rich.						nucleic acid binding|zinc ion binding			skin(4)|ovary(2)	6		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		TCTGCCCCTGCCTCGGCTGCC	0.667													4	81	---	---	---	---	PASS
C20orf194	25943	broad.mit.edu	37	20	3251194	3251194	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3251194C>T	uc002wii.2	-	30	2716	c.2665G>A	c.(2665-2667)GTG>ATG	p.V889M	C20orf194_uc002wij.3_Missense_Mutation_p.V628M|C20orf194_uc002wik.2_Missense_Mutation_p.V563M	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943	889											0						GTGAATACCACGTTACTCACC	0.557													11	103	---	---	---	---	PASS
MCM8	84515	broad.mit.edu	37	20	5965622	5965622	+	Silent	SNP	G	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5965622G>A	uc002wmi.2	+	15	2306	c.1929G>A	c.(1927-1929)GAG>GAA	p.E643E	MCM8_uc002wmj.2_Silent_p.E627E|MCM8_uc002wmk.2_Silent_p.E683E|MCM8_uc002wml.2_Silent_p.E643E|MCM8_uc010gbp.2_Silent_p.E596E|MCM8_uc002wmm.2_Silent_p.E181E	NM_032485	NP_115874	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	643					cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1						TAGTTTCTGAGAAGCCATTAT	0.378													11	78	---	---	---	---	PASS
DDX27	55661	broad.mit.edu	37	20	47845307	47845307	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47845307C>T	uc002xuh.2	+	8	916	c.855C>T	c.(853-855)CGC>CGT	p.R285R		NM_017895	NP_060365	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	285	Helicase ATP-binding.					nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ATAAACCCCGCCAGGCTCCAG	0.572													109	226	---	---	---	---	PASS
KCNG1	3755	broad.mit.edu	37	20	49620929	49620929	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49620929C>T	uc002xwa.3	-	3	1484	c.1189G>A	c.(1189-1191)GTC>ATC	p.V397I		NM_002237	NP_002228	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G,	397	Helical; Name=Segment S5; (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2						TTCTCGATGACGTAGAGCAGG	0.662													4	72	---	---	---	---	PASS
CTCFL	140690	broad.mit.edu	37	20	56099193	56099193	+	Silent	SNP	C	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56099193C>T	uc010gix.1	-	1	731	c.69G>A	c.(67-69)CCG>CCA	p.P23P	CTCFL_uc010giw.1_Silent_p.P23P|CTCFL_uc002xym.2_Silent_p.P23P|CTCFL_uc010giz.1_Intron|CTCFL_uc010giy.1_Intron|CTCFL_uc010gja.1_Silent_p.P23P|CTCFL_uc010gjb.1_Silent_p.P23P|CTCFL_uc010gjc.1_Silent_p.P23P|CTCFL_uc010gjd.1_Silent_p.P23P|CTCFL_uc010gje.2_Silent_p.P23P|CTCFL_uc010gjf.2_Intron|CTCFL_uc010gjg.2_Intron|CTCFL_uc010gjh.1_Silent_p.P23P|CTCFL_uc010gji.1_Intron|CTCFL_uc010gjj.1_Silent_p.P23P|CTCFL_uc010gjk.1_Silent_p.P23P|CTCFL_uc010gjl.1_Silent_p.P23P	NM_080618	NP_542185	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor-like protein	23					cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GGCCTTTTTCCGGCATCAACT	0.507													241	498	---	---	---	---	PASS
ZNF512B	57473	broad.mit.edu	37	20	62597694	62597694	+	Silent	SNP	T	G	G	rs817329	byFrequency	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62597694T>G	uc002yhl.1	-	5	888	c.834A>C	c.(832-834)GTA>GTC	p.V278V		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	278					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CAAGCTTTGTTACCGTAATGG	0.577													7	624	---	---	---	---	PASS
DYRK1A	1859	broad.mit.edu	37	21	38884778	38884778	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38884778G>C	uc002ywk.2	+	11	2311	c.2236G>C	c.(2236-2238)GAA>CAA	p.E746Q	DYRK1A_uc002ywi.2_3'UTR|DYRK1A_uc002ywj.2_Missense_Mutation_p.E737Q|DYRK1A_uc002ywl.2_3'UTR|DYRK1A_uc002ywm.2_3'UTR|DYRK1A_uc011aei.1_Missense_Mutation_p.E507Q	NM_001396	NP_001387	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	746					nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4						GGCTGATAGAGAAGAGTCCCC	0.438													7	178	---	---	---	---	PASS
PLXNB2	23654	broad.mit.edu	37	22	50716066	50716066	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50716066T>C	uc003bkv.3	-	33	5256	c.5150A>G	c.(5149-5151)CAG>CGG	p.Q1717R	PLXNB2_uc003bkt.1_Missense_Mutation_p.Q509R|PLXNB2_uc003bku.1_Missense_Mutation_p.Q702R	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor	1717	Cytoplasmic (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CATGAAGGTCTGCGCGATGAC	0.627													3	119	---	---	---	---	PASS
TSPAN7	7102	broad.mit.edu	37	X	38540490	38540490	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38540490G>C	uc004deg.3	+	6	699	c.630G>C	c.(628-630)GAG>GAC	p.E210D	TSPAN7_uc011mkj.1_Missense_Mutation_p.E236D|TSPAN7_uc011mkk.1_Missense_Mutation_p.E227D|TSPAN7_uc004deh.2_Missense_Mutation_p.E118D	NM_004615	NP_004606	P41732	TSN7_HUMAN	tetraspanin 7	210	Extracellular (Potential).				interspecies interaction between organisms	integral to plasma membrane				ovary(1)	1						GTTTCATGGAGACTAACATGG	0.478													59	105	---	---	---	---	PASS
ABCB7	22	broad.mit.edu	37	X	74318818	74318818	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74318818C>A	uc004eca.2	-	4	437	c.412G>T	c.(412-414)GCT>TCT	p.A138S	ABCB7_uc004ebz.2_Missense_Mutation_p.A139S|ABCB7_uc011mqn.1_Missense_Mutation_p.A112S|ABCB7_uc010nls.2_Intron|ABCB7_uc010nlt.2_Intron	NM_004299	NP_004290	O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B, member 7	138					cellular iron ion homeostasis	integral to membrane|mitochondrial inner membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|heme transporter activity			ovary(1)	1						GCAACTCTAGCTCGTAGATCT	0.363													55	70	---	---	---	---	PASS
CDK11B	984	broad.mit.edu	37	1	1600092	1600093	+	Intron	DEL	TG	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1600092_1600093delTG	uc001agv.1	-						CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc009vkl.1_Intron|SLC35E2B_uc001ahe.3_Intron|SLC35E2B_uc001ahf.3_Intron|SLC35E2B_uc001ahg.3_Intron|SLC35E2B_uc001ahh.3_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						CTGTTTTTTTTGTTTGTTTGTT	0.317													10	10	---	---	---	---	
SLC6A9	6536	broad.mit.edu	37	1	44489938	44489938	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44489938delT	uc001cln.2	-	2	254	c.12delA	c.(10-12)AAAfs	p.K4fs	SLC6A9_uc010okm.1_Frame_Shift_Del_p.K4fs|SLC6A9_uc010oko.1_5'UTR|SLC6A9_uc010okp.1_RNA	NM_001024845	NP_001020016	P48067	SC6A9_HUMAN	solute carrier family 6 member 9 isoform 3	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						integral to plasma membrane|membrane fraction	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity				0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	CTTTGGCACCTTTTCCTACCA	0.627													759	7	---	---	---	---	
ZCCHC11	23318	broad.mit.edu	37	1	52991038	52991038	+	Intron	DEL	T	-	-	rs112941788		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52991038delT	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron|ZCCHC11_uc009vze.1_Intron|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Intron|ZCCHC11_uc001cuc.2_Intron|ZCCHC11_uc001cud.2_Intron	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3						ATGAAAAGGCTTTTTTTTTTT	0.318													4	2	---	---	---	---	
GBP5	115362	broad.mit.edu	37	1	89732536	89732537	+	Intron	DEL	AT	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89732536_89732537delAT	uc001dnc.2	-						GBP5_uc001dnd.2_Intron|GBP5_uc001dne.1_Intron	NM_052942	NP_443174	Q96PP8	GBP5_HUMAN	guanylate-binding protein 5							plasma membrane	GTP binding|GTPase activity			ovary(1)	1				all cancers(265;0.00784)|Epithelial(280;0.0286)		AGCTGGGTGAATATATATATAT	0.218													23	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116891725	116891725	+	IGR	DEL	A	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116891725delA								C1orf161 (213864 upstream) : ATP1A1 (23279 downstream)																							taaggagcttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
RABGAP1L	9910	broad.mit.edu	37	1	174671596	174671596	+	Intron	DEL	A	-	-	rs11296570		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174671596delA	uc001gjx.2	+						RABGAP1L_uc001gkb.3_Intron|RABGAP1L_uc001gkc.3_Intron|RABGAP1L_uc001gkd.3_Intron	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						TAAGGCATATATAATTCCTAC	0.229													4	2	---	---	---	---	
DDX1	1653	broad.mit.edu	37	2	15742621	15742621	+	Intron	DEL	T	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15742621delT	uc002rce.2	+						DDX1_uc010yjq.1_Intron	NM_004939	NP_004930	Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1						DNA duplex unwinding|double-strand break repair|multicellular organismal development|regulation of transcription, DNA-dependent|regulation of translational initiation|spliceosome assembly|transcription, DNA-dependent	cleavage body|stress granule|tRNA-splicing ligase complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|DNA/RNA helicase activity|exonuclease activity|poly(A) RNA binding|protein binding|RNA helicase activity|transcription cofactor activity			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		GAATGTATGATTTATAAAACC	0.383													61	20	---	---	---	---	
AFTPH	54812	broad.mit.edu	37	2	64777812	64777829	+	5'Flank	DEL	CACACACACACACACACA	-	-	rs10553905	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64777812_64777829delCACACACACACACACACA	uc002sdc.2	+						AFTPH_uc002scz.2_Intron|AFTPH_uc002sda.2_Intron|AFTPH_uc002sdb.2_Intron	NM_203437	NP_982261	Q6ULP2	AFTIN_HUMAN	aftiphilin protein isoform a						protein transport	AP-1 adaptor complex|cytosol|nucleus	clathrin binding			ovary(2)	2						tgtacgcatgcacacacacacacacacacacacacaca	0.000													4	2	---	---	---	---	
DPP4	1803	broad.mit.edu	37	2	162903818	162903819	+	Intron	INS	-	G	G			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162903818_162903819insG	uc002ubz.2	-						DPP4_uc010fpb.2_Intron|DPP4_uc002uca.1_Intron|DPP4_uc002ucb.1_Intron	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	TTTAAAAACAAGGATTACCTCT	0.337													33	22	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	229212590	229212593	+	IGR	DEL	TTCC	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229212590_229212593delTTCC								SPHKAP (166229 upstream) : PID1 (676097 downstream)																							ccttccccttttccttccttcctt	0.044													4	3	---	---	---	---	
PTPRG	5793	broad.mit.edu	37	3	61644712	61644717	+	Intron	DEL	CCTGCC	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61644712_61644717delCCTGCC	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|PTPRG_uc003dla.3_Intron	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		GCTGTTTTCTcctgcccctgcccctg	0.427													4	2	---	---	---	---	
PDZRN3	23024	broad.mit.edu	37	3	73437147	73437148	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73437147_73437148insA	uc003dpl.1	-	8	1585_1586	c.1489_1490insT	c.(1489-1491)TCAfs	p.S497fs	PDZRN3_uc011bgh.1_Frame_Shift_Ins_p.S154fs|PDZRN3_uc010hoe.1_Frame_Shift_Ins_p.S195fs|PDZRN3_uc011bgf.1_Frame_Shift_Ins_p.S214fs|PDZRN3_uc011bgg.1_Frame_Shift_Ins_p.S217fs	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	497	PDZ 2.						ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		AATCAGCAATGAAAAGTTTTTA	0.421													502	265	---	---	---	---	
MYLK	4638	broad.mit.edu	37	3	123456059	123456060	+	Intron	INS	-	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123456059_123456060insT	uc003ego.2	-						MYLK_uc011bjw.1_Intron|MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		gagcaagactctgtctgaagag	0.233													5	3	---	---	---	---	
XRN1	54464	broad.mit.edu	37	3	142142545	142142546	+	Intron	DEL	AA	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142142545_142142546delAA	uc003eus.2	-						XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron|XRN1_uc003euv.1_Intron|XRN1_uc003euw.2_Intron|XRN1_uc011bnh.1_Intron	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3						TTAGGTTCACAAAAGCAATTAA	0.248													33	13	---	---	---	---	
PKD2	5311	broad.mit.edu	37	4	88940482	88940482	+	Intron	DEL	A	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88940482delA	uc003hre.2	+							NM_000297	NP_000288	Q13563	PKD2_HUMAN	polycystin 2							basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body	calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity			skin(1)	1		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		AAATGTGATTAAAAAAAAAAA	0.308													4	2	---	---	---	---	
TRIM2	23321	broad.mit.edu	37	4	154215279	154215280	+	Intron	INS	-	A	A	rs148467106	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154215279_154215280insA	uc003ing.2	+						TRIM2_uc003inh.2_Intron	NM_001130067	NP_001123539	Q9C040	TRIM2_HUMAN	tripartite motif-containing 2 isoform 2							cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		TCTGAAGAGACAAAATCTCTTC	0.282													3	3	---	---	---	---	
FAT2	2196	broad.mit.edu	37	5	150886733	150886733	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150886733delA	uc003lue.3	-	22	12512	c.12499delT	c.(12499-12501)TGGfs	p.W4167fs	GM2A_uc011dcs.1_Intron|FAT2_uc003lud.3_Frame_Shift_Del_p.W774fs	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	4167	Cytoplasmic (Potential).				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCGCTGGACCAGGTTCTCTTA	0.557													163	57	---	---	---	---	
EYA4	2070	broad.mit.edu	37	6	133836761	133836762	+	Intron	DEL	GT	-	-	rs145450874		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133836761_133836762delGT	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron|uc003qeg.1_Intron	NM_004100	NP_004091	O95677	EYA4_HUMAN	eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		gtgtgtgtgagtgtgtgtgtgt	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	82982561	82982562	+	IGR	DEL	TG	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82982561_82982562delTG								PCLO (190364 upstream) : SEMA3E (10660 downstream)																							catagttacctgtgtgtgtgtg	0.000													3	6	---	---	---	---	
SLC26A3	1811	broad.mit.edu	37	7	107427059	107427059	+	Intron	DEL	A	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107427059delA	uc003ver.2	-						SLC26A3_uc003ves.2_Intron	NM_000111	NP_000102	P40879	S26A3_HUMAN	solute carrier family 26, member 3						excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)|skin(1)	4						TGGGGAGGCGAAAAAAAAAAA	0.463													5	3	---	---	---	---	
LAMB1	3912	broad.mit.edu	37	7	107603171	107603171	+	Intron	DEL	G	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107603171delG	uc003vew.2	-						LAMB1_uc003vev.2_Intron|LAMB1_uc003vex.2_Intron	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor						axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	aaaaaaaaaagaaagaaagaa	0.149													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	131275575	131275575	+	IGR	DEL	C	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131275575delC								PODXL (34199 upstream) : PLXNA4 (532517 downstream)																							ttccttccttccttccttcct	0.070													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	143816457	143816457	+	IGR	DEL	T	-	-	rs67586979		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143816457delT								OR2A2 (8827 upstream) : OR2A14 (9749 downstream)																							ATCCCATTTCTTTTTTTTTTt	0.244													7	4	---	---	---	---	
WDR60	55112	broad.mit.edu	37	7	158679944	158679947	+	Intron	DEL	ATTG	-	-	rs137953229		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158679944_158679947delATTG	uc003woe.3	+						WDR60_uc010lqv.2_Intron|WDR60_uc010lqw.2_Intron	NM_018051	NP_060521	Q8WVS4	WDR60_HUMAN	WD repeat domain 60											ovary(2)|breast(1)|central_nervous_system(1)	4	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		gaagatgcaaattgattgaaagta	0.015													4	3	---	---	---	---	
GDAP1	54332	broad.mit.edu	37	8	75275006	75275007	+	Intron	INS	-	CT	CT	rs140955331	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75275006_75275007insCT	uc003yah.2	+						GDAP1_uc011lfj.1_Intron|GDAP1_uc003yai.2_Intron	NM_018972	NP_061845	Q8TB36	GDAP1_HUMAN	ganglioside-induced differentiation-associated							cytoplasm					0	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			CTTCAACTTAGCTCTCTCTCTC	0.411													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68430364	68430365	+	IGR	INS	-	A	A	rs140332329		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68430364_68430365insA								FAM27B (636175 upstream) : MIR1299 (571874 downstream)																							TTATGCAGAAGAAAAAATTAAC	0.322													9	4	---	---	---	---	
TRPM6	140803	broad.mit.edu	37	9	77457044	77457044	+	Intron	DEL	G	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77457044delG	uc004ajl.1	-						TRPM6_uc004ajk.1_Intron|TRPM6_uc010mpb.1_Intron|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajn.1_Intron	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,						response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						aaaaaaaaaagaaagaaaCCA	0.199													144	7	---	---	---	---	
PCSK5	5125	broad.mit.edu	37	9	78790207	78790208	+	Intron	INS	-	GAATA	GAATA	rs10124596		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78790207_78790208insGAATA	uc004ajz.2	+						PCSK5_uc004ajy.2_Frame_Shift_Ins_p.R688fs|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						cgaatcgaatcgaatagaatag	0.099													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90436742	90436744	+	IGR	DEL	ACA	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90436742_90436744delACA								CTSL3 (34943 upstream) : C9orf79 (60997 downstream)																							CCAGTTAGTGACAACAACAACAA	0.409													4	2	---	---	---	---	
EPB41L4B	54566	broad.mit.edu	37	9	112018049	112018049	+	Intron	DEL	C	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112018049delC	uc004bdz.1	-						EPB41L4B_uc004bea.2_Intron	NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|skin(1)	3						GGGAGCCAGGCCTACCTGATC	0.463													172	87	---	---	---	---	
TRUB2	26995	broad.mit.edu	37	9	131075834	131075834	+	Intron	DEL	G	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131075834delG	uc004buq.1	-							NM_015679	NP_056494	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase homolog 2						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(1)	1						aaaaaaaaaagaaaagaaaaG	0.209													5	3	---	---	---	---	
C9orf114	51490	broad.mit.edu	37	9	131586559	131586560	+	Intron	DEL	GT	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131586559_131586560delGT	uc004bwd.2	-						C9orf114_uc004bwe.2_Intron|C9orf114_uc010mym.2_Intron	NM_016390	NP_057474	Q5T280	CI114_HUMAN	hypothetical protein LOC51490												0						GAGCtgtgtggtgtgtgtgtgt	0.500													9	4	---	---	---	---	
CUBN	8029	broad.mit.edu	37	10	17168718	17168718	+	Intron	DEL	T	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17168718delT	uc001ioo.2	-							NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTCTAGTATGTTTTCTGTGAA	0.353													141	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42386982	42386983	+	IGR	DEL	GA	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42386982_42386983delGA								None (None upstream) : LOC441666 (440332 downstream)																							gaatggaatggaatggaatagt	0.030													4	2	---	---	---	---	
HERC4	26091	broad.mit.edu	37	10	69798110	69798110	+	Intron	DEL	A	-	-	rs35054670		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69798110delA	uc001jng.3	-						HERC4_uc001jnf.3_Intron|HERC4_uc001jnh.3_Intron|HERC4_uc009xpr.2_Intron|HERC4_uc001jni.3_Intron|HERC4_uc001jnj.2_Intron	NM_022079	NP_071362	Q5GLZ8	HERC4_HUMAN	hect domain and RLD 4 isoform a						cell differentiation|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	cytosol	ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3						AGCTAGATACAAAAAAAAAAA	0.323													4	2	---	---	---	---	
UNC5B	219699	broad.mit.edu	37	10	73056667	73056715	+	Intron	DEL	CAGATATTCCAGCTGCACACCACGCTGGCGGAGGTGAGGGAAGGGCGGC	-	-	rs11817565	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73056667_73056715delCAGATATTCCAGCTGCACACCACGCTGGCGGAGGTGAGGGAAGGGCGGC	uc001jro.2	+						UNC5B_uc001jrp.2_Intron	NM_170744	NP_734465	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3						AAGGGTGGGGCAGATATTCCAGCTGCACACCACGCTGGCGGAGGTGAGGGAAGGGCGGCCAGATATTCC	0.635													4	5	---	---	---	---	
PIPSL	266971	broad.mit.edu	37	10	95718422	95718422	+	3'UTR	DEL	T	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95718422delT	uc009xuj.2	-	1						NR_002319				RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha;          Short=PtdIns(4)P-5-kinase alpha;          Short=PIP5KIalpha;          EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha;												0						tctttctttcttttttttttG	0.164													4	2	---	---	---	---	
EPS8L2	64787	broad.mit.edu	37	11	725877	725878	+	Intron	INS	-	C	C	rs144060424	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:725877_725878insC	uc001lqt.2	+						EPS8L2_uc001lqu.2_Intron|EPS8L2_uc010qwk.1_Intron|EPS8L2_uc001lqv.2_Intron|EPS8L2_uc001lqw.2_Intron|EPS8L2_uc001lqx.2_Intron|EPS8L2_uc001lqy.2_Intron	NM_022772	NP_073609	Q9H6S3	ES8L2_HUMAN	epidermal growth factor receptor pathway							cytoplasm				pancreas(1)	1		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGGGTCGCAGCCCCCAGCTTC	0.752													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	77811794	77811795	+	IGR	INS	-	T	T	rs146323800	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77811794_77811795insT								NDUFC2 (20529 upstream) : ALG8 (193 downstream)																							GGAAAGGTGAGTTTTTTTCAGA	0.450													2	4	---	---	---	---	
CHEK1	1111	broad.mit.edu	37	11	125525217	125525217	+	3'UTR	DEL	C	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125525217delC	uc009zbo.2	+	13					CHEK1_uc010sbh.1_3'UTR|CHEK1_uc010sbi.1_3'UTR|CHEK1_uc001qcf.3_3'UTR|CHEK1_uc009zbp.2_3'UTR|CHEK1_uc001qcg.3_3'UTR|CHEK1_uc009zbq.2_3'UTR|CHEK1_uc001qci.1_RNA|CHEK1_uc001qcj.2_3'UTR	NM_001114122	NP_001107594	O14757	CHK1_HUMAN	checkpoint kinase 1						cellular response to mechanical stimulus|DNA repair|DNA replication|gamete generation|negative regulation of cell proliferation|reciprocal meiotic recombination|regulation of cyclin-dependent protein kinase activity|replicative senescence	condensed nuclear chromosome|microtubule organizing center|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(3)|lung(2)|skin(1)	6	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		GCCACATGATCGGACCATCGG	0.443								Other_conserved_DNA_damage_response_genes					78	8	---	---	---	---	
GLB1L3	112937	broad.mit.edu	37	11	134178448	134178450	+	Intron	DEL	CAT	-	-	rs140914654	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134178448_134178450delCAT	uc009zdf.2	+						GLB1L3_uc010scu.1_Intron|GLB1L3_uc001qho.3_Intron	NM_001080407	NP_001073876	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		tcaccatcaccatcaccaccacc	0.000													6	3	---	---	---	---	
CELA1	1990	broad.mit.edu	37	12	51736597	51736597	+	Intron	DEL	T	-	-	rs5798169		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51736597delT	uc001ryi.1	-							NM_001971	NP_001962	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			breast(1)	1						ATTTAGGAAAttttttttttt	0.174													4	2	---	---	---	---	
ESYT1	23344	broad.mit.edu	37	12	56528386	56528386	+	Intron	DEL	T	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56528386delT	uc001sjq.2	+						ESYT1_uc001sjr.2_Intron	NM_015292	NP_056107	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1							integral to membrane				ovary(4)|skin(1)	5						CAGAATAATAttttttttttt	0.214													5	3	---	---	---	---	
SLC17A8	246213	broad.mit.edu	37	12	100774908	100774915	+	Intron	DEL	CATCTCAG	-	-	rs68046331		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100774908_100774915delCATCTCAG	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						TAGCTCCTCCcatctcagcatctcagca	0.221													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	110072327	110072328	+	IGR	INS	-	ACC	ACC	rs147833484	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110072327_110072328insACC								MVK (37257 upstream) : C12orf34 (79862 downstream)																							ccaccaccactaccaccaccac	0.020													4	2	---	---	---	---	
RNF31	55072	broad.mit.edu	37	14	24621084	24621085	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24621084_24621085delGA	uc001wmn.1	+	11	2262_2263	c.2013_2014delGA	c.(2011-2016)AGGAACfs	p.R671fs	RNF31_uc001wml.1_Frame_Shift_Del_p.R520fs|RNF31_uc001wmm.1_RNA|RNF31_uc010alg.1_Frame_Shift_Del_p.R430fs|RNF31_uc001wmo.1_Frame_Shift_Del_p.R138fs|RNF31_uc001wmp.2_RNA	NM_017999	NP_060469	Q96EP0	RNF31_HUMAN	ring finger protein 31	671_672					CD40 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein linear polyubiquitination|T cell receptor signaling pathway	CD40 receptor complex|internal side of plasma membrane|LUBAC complex	ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(265;0.00861)		AGACACCCAGGAACTATGAGTT	0.634													213	29	---	---	---	---	
FOXA1	3169	broad.mit.edu	37	14	38061220	38061225	+	In_Frame_Del	DEL	CGTTCT	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38061220_38061225delCGTTCT	uc001wuf.2	-	2	1076_1081	c.764_769delAGAACG	c.(763-771)GAGAACGGC>GGC	p.EN255del	FOXA1_uc010tpz.1_In_Frame_Del_p.EN222del	NM_004496	NP_004487	P55317	FOXA1_HUMAN	forkhead box A1	255_256	Fork-head.				chromatin remodeling|embryo development|epithelial cell maturation involved in prostate gland development|epithelial tube branching involved in lung morphogenesis|epithelial-mesenchymal signaling involved in prostate gland development|glucose homeostasis|lung epithelial cell differentiation|negative regulation of survival gene product expression|neuron fate specification|pattern specification process|positive regulation of estrogen receptor signaling pathway|positive regulation of mitotic cell cycle|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|prostate gland epithelium morphogenesis|prostate gland stromal morphogenesis|response to estradiol stimulus|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|protein domain specific binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding				0	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		AAGTAGCAGCCGTTCTCGAACATGTT	0.495													24	12	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106518132	106518133	+	Intron	INS	-	AA	AA			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106518132_106518133insAA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						ACTCCTGTTGCAAAAAAACAAA	0.406													5	3	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	34152708	34152709	+	Intron	INS	-	A	A	rs57641933		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34152708_34152709insA	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						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)		TTTTTTTTTTTAACAGAACAAA	0.322													8	4	---	---	---	---	
DNAH3	55567	broad.mit.edu	37	16	21136284	21136285	+	Intron	INS	-	TG	TG	rs145787563	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21136284_21136285insTG	uc010vbe.1	-						DNAH3_uc002die.2_Intron	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		catttaccatttgtgtgtgtgt	0.079													5	5	---	---	---	---	
SUPT6H	6830	broad.mit.edu	37	17	27010855	27010855	+	Intron	DEL	T	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27010855delT	uc002hby.2	+						SUPT6H_uc010crt.2_Intron	NM_003170	NP_003161	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog						chromatin remodeling|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter	nucleus	hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Lung NSC(42;0.00431)					AGACTCATGAttttttttttt	0.229													32	8	---	---	---	---	
ANAPC11	51529	broad.mit.edu	37	17	79852591	79852591	+	Intron	DEL	C	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79852591delC	uc002kbv.1	+						ANAPC11_uc002kbw.1_Intron|ANAPC11_uc002kbx.1_Intron|ANAPC11_uc002kby.1_Intron|ANAPC11_uc002kbz.1_Intron|ANAPC11_uc002kca.1_Intron|ANAPC11_uc002kcb.1_Intron|ANAPC11_uc002kcc.1_Intron|ANAPC11_uc010dih.1_Intron	NM_016476	NP_057560	Q9NYG5	APC11_HUMAN	APC11 anaphase promoting complex subunit 11						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	zinc ion binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			Gtttcattttctttttttttt	0.259													11	6	---	---	---	---	
TJP3	27134	broad.mit.edu	37	19	3719731	3719733	+	Intron	DEL	AAA	-	-	rs34047272		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3719731_3719733delAAA	uc010xhs.1	+						TJP3_uc010xht.1_Intron|TJP3_uc010xhu.1_5'Flank	NM_014428	NP_055243	O95049	ZO3_HUMAN	tight junction protein 3							tight junction	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		actccgtctcaaaaaaaaaaaaa	0.177											OREG0025089	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
COPE	11316	broad.mit.edu	37	19	19013525	19013526	+	Intron	INS	-	AAGG	AAGG	rs72403201		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19013525_19013526insAAGG	uc002nkk.2	-						COPE_uc002nkl.2_Intron|COPE_uc002nkm.2_Intron|COPE_uc002nkn.2_Intron	NM_007263	NP_009194	O14579	COPE_HUMAN	epsilon subunit of coatomer protein complex						COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	binding|structural molecule activity				0						gaaaggaaggaaaggaaaggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	41375347	41375347	+	IGR	DEL	T	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41375347delT								CYP2A6 (18995 upstream) : CYP2A7 (5998 downstream)																							tcTCCCTCTCttttttttttt	0.025													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42107428	42107431	+	IGR	DEL	CACA	-	-	rs71902951		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42107428_42107431delCACA								CEACAM21 (14232 upstream) : CEACAM4 (17913 downstream)																							cgcgcgcgcgcacacacacacaca	0.221													5	4	---	---	---	---	
FLT3LG	2323	broad.mit.edu	37	19	49982165	49982166	+	Splice_Site	INS	-	C	C			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49982165_49982166insC	uc010yau.1	+	6	433	c.343_splice	c.e6-1	p.P115_splice	FLT3LG_uc002pnv.2_Splice_Site_p.P33_splice|FLT3LG_uc002pnw.2_Splice_Site_p.P33_splice|FLT3LG_uc002pnu.2_Splice_Site_p.P115_splice|FLT3LG_uc002pnx.2_Splice_Site_p.P115_splice|FLT3LG_uc010yav.1_Splice_Site_p.P33_splice	NM_001459	NP_001450	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand precursor						positive regulation of cell proliferation|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity				0		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		CCTGCTCCCAGCCCCCCCCCAG	0.688													4	2	---	---	---	---	
BRSK1	84446	broad.mit.edu	37	19	55813840	55813840	+	Intron	DEL	G	-	-	rs5828617		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55813840delG	uc002qkg.2	+						BRSK1_uc002qkf.2_Intron|BRSK1_uc002qkh.2_Intron	NM_032430	NP_115806	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1						establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV	cell junction|cytoplasm|nucleus	magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1)	6		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		tgaagaaggaggggccggggg	0.000											OREG0025680	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	6	---	---	---	---	
FERMT1	55612	broad.mit.edu	37	20	6078005	6078005	+	Intron	DEL	G	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6078005delG	uc002wmr.2	-						FERMT1_uc010gbt.2_Intron|FERMT1_uc002wms.2_Intron|FERMT1_uc002wmt.2_Intron	NM_017671	NP_060141	Q9BQL6	FERM1_HUMAN	kindlin-1						cell adhesion|establishment of epithelial cell polarity|keratinocyte migration|keratinocyte proliferation	cytosol|focal adhesion|ruffle membrane	binding			ovary(1)|pancreas(1)|skin(1)	3						AATTTGTTCTGGTCTGAAGAA	0.318													5	4	---	---	---	---	
DEFB119	245932	broad.mit.edu	37	20	29965453	29965454	+	Intron	INS	-	TG	TG	rs151207116	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29965453_29965454insTG	uc002wvt.2	-						DEFB119_uc002wvs.2_Intron	NM_153289	NP_695021	Q8N690	DB119_HUMAN	defensin, beta 119 isoform a precursor						defense response to bacterium	extracellular region					0	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			gtgtgtgtatatgtgtgtgtgt	0.020													5	3	---	---	---	---	
C20orf111	51526	broad.mit.edu	37	20	42831694	42831697	+	Frame_Shift_Del	DEL	ACAG	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42831694_42831697delACAG	uc002xlk.2	-	3	232_235	c.95_98delCTGT	c.(94-99)TCTGTTfs	p.S32fs		NM_016470	NP_057554	Q9NX31	CT111_HUMAN	oxidative stress responsive 1	32_33											0		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			GCCTTCTCCAACAGACAGAGATGC	0.417													72	35	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58889651	58889662	+	Intron	DEL	CATTCTCCCATT	-	-	rs114216255	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58889651_58889662delCATTCTCCCATT	uc002ybl.2	+						uc010gjw.1_Intron					Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																		tccatccatccattctcccattcatccatcct	0.000													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11085429	11085470	+	Intron	DEL	ACCACCACCACCACCACCACCACCATCACCACTACCACTACC	-	-	rs28598873	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11085429_11085470delACCACCACCACCACCACCACCACCATCACCACTACCACTACC	uc002yit.1	-						BAGE_uc002yix.2_Intron	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)		caccaccactaccaccaccaccaccaccaccaccatcaccactaccactaccaccaccacca	0.058													9	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11085560	11085560	+	Intron	DEL	T	-	-	rs147223908		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11085560delT	uc002yit.1	-						BAGE_uc002yix.2_Intron	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)		ccaccaccactaccaccacca	0.000													5	3	---	---	---	---	
GABPA	2551	broad.mit.edu	37	21	27130161	27130164	+	Intron	DEL	TTTT	-	-	rs143159574		TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27130161_27130164delTTTT	uc002ylx.3	+						GABPA_uc002yly.3_Intron	NM_002040	NP_002031	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha						positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2						TACAGCATAAtttttttttttttt	0.309													4	2	---	---	---	---	
SEZ6L	23544	broad.mit.edu	37	22	26687981	26688004	+	Intron	DEL	GGAAGGAAGGAAGGAAGGAAGGAT	-	-	rs148991890	by1000genomes	TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26687981_26688004delGGAAGGAAGGAAGGAAGGAAGGAT	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_5'Flank|SEZ6L_uc010gvc.1_5'Flank	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6						aaggaaggaaggaaggaaggaaggaaggaaggatggatggaagg	0.121													3	3	---	---	---	---	
SFI1	9814	broad.mit.edu	37	22	31985765	31985768	+	Intron	DEL	TTTA	-	-			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31985765_31985768delTTTA	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron|SFI1_uc010gwi.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						TTTGTCCATCTTTATTTATTTATT	0.333													4	2	---	---	---	---	
GPC4	2239	broad.mit.edu	37	X	132440258	132440259	+	Intron	INS	-	T	T			TCGA-CH-5737-01A-11D-1576-08	TCGA-CH-5737-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132440258_132440259insT	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)					AATCAATCTGATTTTTTTTTCT	0.391													62	33	---	---	---	---	
