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
PIK3CD	5293	broad.mit.edu	37	1	9777092	9777092	+	Missense_Mutation	SNP	C	T	T	rs146796121		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9777092C>T	uc001aqb.3	+	7	1064	c.856C>T	c.(856-858)CGG>TGG	p.R286W	PIK3CD_uc010oaf.1_Missense_Mutation_p.R286W|PIK3CD_uc001aqe.3_Intron	NM_005026	NP_005017	O00329	PK3CD_HUMAN	catalytic phosphatidylinositol 3-kinase delta	286					phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(4)|skin(2)|central_nervous_system(1)	7	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)		CCTCGCCATGCGGGATGAGCA	0.632													4	191	---	---	---	---	PASS
PTCHD2	57540	broad.mit.edu	37	1	11562935	11562935	+	Silent	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11562935C>T	uc001ash.3	+	3	1435	c.1297C>T	c.(1297-1299)CTG>TTG	p.L433L	PTCHD2_uc001asi.1_Silent_p.L433L	NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	433	Extracellular (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CGTGGCCATGCTGGCCAAGCA	0.522													3	79	---	---	---	---	PASS
VPS13D	55187	broad.mit.edu	37	1	12423192	12423192	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12423192C>G	uc001atv.2	+	52	10478	c.10337C>G	c.(10336-10338)CCT>CGT	p.P3446R	VPS13D_uc001atw.2_Missense_Mutation_p.P3421R|VPS13D_uc001atx.2_Missense_Mutation_p.P2633R	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	3445					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TTCCACTGGCCTCGGAATGAC	0.453													77	306	---	---	---	---	PASS
MYOM3	127294	broad.mit.edu	37	1	24408528	24408528	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24408528G>A	uc001bin.3	-	18	2406	c.2243C>T	c.(2242-2244)GCG>GTG	p.A748V	MYOM3_uc001bim.3_Missense_Mutation_p.A405V|MYOM3_uc001bio.2_Missense_Mutation_p.A748V|MYOM3_uc001bip.1_3'UTR	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3	748	Fibronectin type-III 4.									skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		CTGATTGACCGCATGCCAGTC	0.602													3	40	---	---	---	---	PASS
NFYC	4802	broad.mit.edu	37	1	41218906	41218906	+	Silent	SNP	T	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41218906T>G	uc001cge.2	+	4	383	c.375T>G	c.(373-375)CCT>CCG	p.P125P	NFYC_uc010ojm.1_Intron|NFYC_uc001cfx.3_Silent_p.P125P|NFYC_uc009vwd.2_Silent_p.P125P|NFYC_uc001cfz.2_Silent_p.P125P|NFYC_uc010ojn.1_Silent_p.P87P|NFYC_uc001cfy.3_Silent_p.P125P|NFYC_uc001cgc.2_Silent_p.P125P|NFYC_uc001cgb.2_Silent_p.P125P|NFYC_uc001cgd.3_Silent_p.P125P|MIR30E_hsa-mir-30e|MI0000749_5'Flank|uc001cgf.1_5'Flank	NM_001142588	NP_001136060	Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma isoform 1	125					protein folding|regulation of transcription from RNA polymerase II promoter	CCAAT-binding factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|kidney(1)	3	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)			AACTGAAACCTCCAAAGCGTC	0.428													15	88	---	---	---	---	PASS
FUBP1	8880	broad.mit.edu	37	1	78414330	78414330	+	3'UTR	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78414330G>A	uc001dii.2	-	20					FUBP1_uc001dih.3_Intron|FUBP1_uc010orm.1_3'UTR	NM_003902	NP_003893	Q96AE4	FUBP1_HUMAN	far upstream element-binding protein						transcription from RNA polymerase II promoter	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			central_nervous_system(2)|lung(1)	3						AAAAAAAAAGGAAACACTATT	0.264													5	16	---	---	---	---	PASS
FNBP1L	54874	broad.mit.edu	37	1	93987691	93987691	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93987691C>T	uc001dpw.2	+	3	193	c.193C>T	c.(193-195)CGG>TGG	p.R65W	FNBP1L_uc001dpv.2_Missense_Mutation_p.R65W	NM_001024948	NP_001020119	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like isoform 1	65	FCH.|Induction of membrane tubulation (By similarity).				endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	lipid binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		TGAAGAGCCACGGTAAATTAC	0.204													6	30	---	---	---	---	PASS
GNAI3	2773	broad.mit.edu	37	1	110129422	110129422	+	Silent	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110129422C>T	uc001dxz.2	+	7	949	c.792C>T	c.(790-792)ATC>ATT	p.I264I		NM_006496	NP_006487	P08754	GNAI3_HUMAN	guanine nucleotide binding protein (G protein),	264					cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			ovary(1)	1		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.046)|Colorectal(144;0.119)|Epithelial(280;0.139)|all cancers(265;0.147)|LUSC - Lung squamous cell carcinoma(189;0.237)		AAACTTCAATCATTCTCTTCC	0.338													28	133	---	---	---	---	PASS
RBM15	64783	broad.mit.edu	37	1	110883213	110883213	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110883213C>T	uc001dzl.1	+	1	1269	c.1186C>T	c.(1186-1188)CGC>TGC	p.R396C	RBM15_uc001dzm.1_Missense_Mutation_p.R396C|uc001dzj.2_5'Flank	NM_022768	NP_073605	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	396	RRM 2.				interspecies interaction between organisms	nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		GGCGTTTGATCGCTTTGGAGT	0.473			T	MKL1	acute megakaryocytic leukemia								21	69	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	145039633	145039633	+	5'UTR	SNP	C	T	T	rs2762750		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145039633C>T	uc001elx.3	-	1					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_5'UTR|PDE4DIP_uc001eln.3_5'UTR|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCCTTAGTCTCAGGACGCTCC	0.597			T	PDGFRB	MPD								4	66	---	---	---	---	PASS
DUSP27	92235	broad.mit.edu	37	1	167095901	167095901	+	Silent	SNP	A	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167095901A>C	uc001geb.1	+	5	1533	c.1533A>C	c.(1531-1533)GCA>GCC	p.A511A		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27	511					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3						GCTCAGAAGCAGGGAGCAGGG	0.597													28	146	---	---	---	---	PASS
NR5A2	2494	broad.mit.edu	37	1	200089975	200089975	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200089975C>A	uc001gvb.2	+	7	1476	c.1270C>A	c.(1270-1272)CTC>ATC	p.L424I	NR5A2_uc001gvc.2_Missense_Mutation_p.L378I|NR5A2_uc009wzh.2_Missense_Mutation_p.L384I|NR5A2_uc010pph.1_Missense_Mutation_p.L352I	NM_205860	NP_995582	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	424	Lipid binding.				embryo development|positive regulation of viral genome replication|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	lipid binding|protein binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Prostate(682;0.19)					CGGAGCCACCCTCAACAACCT	0.428													5	241	---	---	---	---	PASS
ZNF124	7678	broad.mit.edu	37	1	247322364	247322364	+	Silent	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247322364G>A	uc001ick.2	-	3	301	c.162C>T	c.(160-162)AAC>AAT	p.N54N	ZNF124_uc001ici.2_RNA|ZNF124_uc001icj.1_Silent_p.N54N	NM_003431	NP_003422	Q15973	ZN124_HUMAN	zinc finger protein 124	54	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)			CTTCCCCTTTGTTTCCTAAAA	0.303													18	132	---	---	---	---	PASS
VN1R5	317705	broad.mit.edu	37	1	247420345	247420345	+	Silent	SNP	T	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247420345T>C	uc010pyu.1	+	2	972	c.972T>C	c.(970-972)GAT>GAC	p.D324D		NM_173858	NP_776257	Q7Z5H4	VN1R5_HUMAN	vomeronasal 1 receptor 5	324	Cytoplasmic (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0	all_cancers(71;5.7e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)	all_cancers(173;0.0314)	OV - Ovarian serous cystadenocarcinoma(106;0.00854)			TTTATGCTGATAACCAAATAT	0.254													3	128	---	---	---	---	PASS
OTX1	5013	broad.mit.edu	37	2	63282664	63282664	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63282664G>C	uc002scd.2	+	5	526	c.278G>C	c.(277-279)TGC>TCC	p.C93S	OTX1_uc010ypt.1_Missense_Mutation_p.C27S	NM_014562	NP_055377	P32242	OTX1_HUMAN	orthodenticle homeobox 1	93	Homeobox.					nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(2)	2	Lung NSC(7;0.121)|all_lung(7;0.211)					CGCGCCAAATGCCGCCAGCAG	0.657													6	35	---	---	---	---	PASS
C2orf89	129293	broad.mit.edu	37	2	85097390	85097390	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85097390C>T	uc010ysl.1	-	2	717	c.628G>A	c.(628-630)GAA>AAA	p.E210K	C2orf89_uc002sou.3_Missense_Mutation_p.E210K|C2orf89_uc010fgc.1_Missense_Mutation_p.E210K	NM_001080824	NP_001074293	Q86V40	CB089_HUMAN	hypothetical protein LOC129293 precursor	210	Extracellular (Potential).					integral to membrane				ovary(1)	1						CACTGCTCTTCCACCTTTTCC	0.488													97	304	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89986884	89986884	+	Intron	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89986884G>A	uc010fhm.2	+						uc002stn.1_RNA					Parts of antibodies, mostly variable regions.																		GTGATGGAAAGACCTATTTGT	0.537													17	52	---	---	---	---	PASS
GCC2	9648	broad.mit.edu	37	2	109100728	109100728	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109100728A>G	uc002tec.2	+	13	3728	c.3574A>G	c.(3574-3576)ATT>GTT	p.I1192V	GCC2_uc002ted.2_Missense_Mutation_p.I1091V	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	1192	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1						AGAAATAAAAATTCAAAAACA	0.259													15	59	---	---	---	---	PASS
SLC35F5	80255	broad.mit.edu	37	2	114512805	114512805	+	Silent	SNP	A	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114512805A>C	uc002tku.1	-	3	634	c.210T>G	c.(208-210)GCT>GCG	p.A70A	SLC35F5_uc002tkt.2_RNA|SLC35F5_uc002tkv.2_Silent_p.A64A|SLC35F5_uc002tkw.2_Silent_p.A70A	NM_025181	NP_079457	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	70	Helical; (Potential).				transport	integral to membrane					0						CAATCCCAAGAGCCATTCGCC	0.408													35	74	---	---	---	---	PASS
PROC	5624	broad.mit.edu	37	2	128186505	128186505	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128186505A>C	uc002tok.2	+	9	1442	c.1369A>C	c.(1369-1371)AAG>CAG	p.K457Q	PROC_uc002tol.2_Missense_Mutation_p.K478Q|PROC_uc010yzi.1_Missense_Mutation_p.K513Q|PROC_uc010yzj.1_Missense_Mutation_p.K352Q|PROC_uc010yzk.1_Missense_Mutation_p.K512Q|PROC_uc002tom.2_Missense_Mutation_p.K491Q	NM_000312	NP_000303	P04070	PROC_HUMAN	protein C	457					blood coagulation|leukocyte migration|negative regulation of apoptosis|negative regulation of blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|Golgi lumen|plasma membrane	calcium ion binding|protein binding|serine-type endopeptidase activity				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	AGCCCCCCAGAAGAGCTGGGC	0.572													23	95	---	---	---	---	PASS
KCNH7	90134	broad.mit.edu	37	2	163241431	163241431	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163241431G>C	uc002uch.1	-	13	2941	c.2729C>G	c.(2728-2730)CCT>CGT	p.P910R		NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,	910	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	AGAGTCTTCAGGATCATTTGT	0.343													39	196	---	---	---	---	PASS
CYBRD1	79901	broad.mit.edu	37	2	172411334	172411334	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172411334G>A	uc002ugy.3	+	4	1048	c.858G>A	c.(856-858)ATG>ATA	p.M286I	CYBRD1_uc002ugz.3_3'UTR	NM_024843	NP_079119	Q53TN4	CYBR1_HUMAN	cytochrome b reductase 1 isoform 1	286					cellular iron ion homeostasis|electron transport chain|transmembrane transport	integral to membrane	ferric-chelate reductase activity|metal ion binding				0						GATCTACCATGTAAAATGTTG	0.398													11	72	---	---	---	---	PASS
TTC30B	150737	broad.mit.edu	37	2	178416809	178416809	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178416809C>T	uc002uln.2	-	1	716	c.683G>A	c.(682-684)GGC>GAC	p.G228D	TTC30B_uc010zfc.1_5'UTR	NM_152517	NP_689730	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	228					cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			AGTGGTCATGCCCACACCTAG	0.522													4	135	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179417031	179417031	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179417031C>T	uc010zfg.1	-	284	83116	c.82892G>A	c.(82891-82893)GGA>GAA	p.G27631E	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.G21326E|TTN_uc010zfi.1_Missense_Mutation_p.G21259E|TTN_uc010zfj.1_Missense_Mutation_p.G21134E	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	28558							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTATTTTCCTCCATGCTCCTT	0.403													44	134	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179587903	179587903	+	Silent	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179587903G>A	uc010zfg.1	-	72	18323	c.18099C>T	c.(18097-18099)AAC>AAT	p.N6033N	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.N2694N	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6960							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGTGACTATGTTACATTTTT	0.403													23	63	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179614567	179614567	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179614567T>C	uc002unb.2	-	46	12784	c.12560A>G	c.(12559-12561)CAG>CGG	p.Q4187R	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACAACTGGCTGGGGCTCACC	0.373													4	169	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179665198	179665198	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179665198C>G	uc002und.2	-	4	732	c.507G>C	c.(505-507)GAG>GAC	p.E169D	TTN_uc010zfg.1_Missense_Mutation_p.E169D|TTN_uc010zfh.1_Missense_Mutation_p.E169D|TTN_uc010zfi.1_Missense_Mutation_p.E169D|TTN_uc010zfj.1_Missense_Mutation_p.E169D|TTN_uc002unb.2_Missense_Mutation_p.E169D			Q8WZ42	TITIN_HUMAN	Homo sapiens cDNA FLJ32040 fis, clone NTONG2000858, highly similar to H.sapiens mRNA for titin protein.	169							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCCTGAGTCCTCAGGGTATG	0.483													71	325	---	---	---	---	PASS
TMEFF2	23671	broad.mit.edu	37	2	192815127	192815127	+	Silent	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192815127G>A	uc002utc.2	-	10	1429	c.1035C>T	c.(1033-1035)TGC>TGT	p.C345C		NM_016192	NP_057276	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two	345	Cytoplasmic (Potential).					extracellular region|integral to membrane				lung(2)|pancreas(1)|breast(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			TGCTTCTGGGGCATTTCCTGG	0.408													4	219	---	---	---	---	PASS
SLC39A10	57181	broad.mit.edu	37	2	196545178	196545178	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196545178G>T	uc002utg.3	+	2	626	c.412G>T	c.(412-414)GAA>TAA	p.E138*	SLC39A10_uc002uth.3_Nonsense_Mutation_p.E138*|SLC39A10_uc010zgp.1_Intron	NM_001127257	NP_001120729	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter),	138	His-rich.				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			pancreas(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.221)			TTTAAATTCAGAAAATCAAAC	0.353													42	122	---	---	---	---	PASS
FN1	2335	broad.mit.edu	37	2	216257812	216257812	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216257812G>A	uc002vfa.2	-	25	4177	c.3911C>T	c.(3910-3912)GCG>GTG	p.A1304V	FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Missense_Mutation_p.A1304V|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Missense_Mutation_p.A1304V|FN1_uc002vfj.2_Missense_Mutation_p.A1304V|FN1_uc002vez.2_5'Flank|FN1_uc010zjp.1_5'UTR	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	1304	Fibronectin type-III 8.|Cell-attachment.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TTCTCCTGCCGCAACTACTGT	0.483													4	122	---	---	---	---	PASS
USP40	55230	broad.mit.edu	37	2	234431845	234431845	+	Silent	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234431845A>G	uc010zmr.1	-	15	2205	c.2205T>C	c.(2203-2205)ATT>ATC	p.I735I	USP40_uc010zmt.1_Silent_p.I379I	NM_018218	NP_060688	Q9NVE5	UBP40_HUMAN	ubiquitin thioesterase 40	723					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)|breast(1)	3		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CCTGAATTAAAATTGAGCTTC	0.448													72	274	---	---	---	---	PASS
UGT1A9	54600	broad.mit.edu	37	2	234580748	234580748	+	Silent	SNP	T	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234580748T>C	uc002vus.2	+	1	205	c.168T>C	c.(166-168)GTT>GTC	p.V56V	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Silent_p.V56V	NM_021027	NP_066307	O60656	UD19_HUMAN	UDP glycosyltransferase 1 family, polypeptide A9	56					drug metabolic process|flavone metabolic process|negative regulation of fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|retinoic acid binding			ovary(3)|breast(1)|skin(1)	5		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Entacapone(DB00494)|Etodolac(DB00749)|Indomethacin(DB00328)|Irinotecan(DB00762)|Mycophenolic acid(DB01024)|Oxyphenonium(DB00219)|Propofol(DB00818)|Sorafenib(DB00398)	ATGAGGTGGTTGTAGTCATGC	0.532													3	162	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188197	10188197	+	Splice_Site	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188197G>T	uc003bvc.2	+	2	554	c.341_splice	c.e2-1	p.G114_splice	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(7)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TGTCCCGATAGGTCACCTTTG	0.333		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				60	174	---	---	---	---	PASS
AMT	275	broad.mit.edu	37	3	49456775	49456775	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49456775A>G	uc003cww.2	-	6	743	c.614T>C	c.(613-615)ATG>ACG	p.M205T	AMT_uc011bcn.1_Missense_Mutation_p.M113T|AMT_uc003cwx.2_Missense_Mutation_p.M205T|AMT_uc011bco.1_Missense_Mutation_p.M161T|AMT_uc003cwy.2_Missense_Mutation_p.M157T|AMT_uc011bcp.1_Missense_Mutation_p.M108T|AMT_uc011bcq.1_Missense_Mutation_p.M149T	NM_000481	NP_000472	P48728	GCST_HUMAN	aminomethyltransferase isoform 1 precursor	205					glycine catabolic process	mitochondrion	aminomethyltransferase activity|transaminase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)	AGCACTGGTCATGAAGGGCAG	0.617													3	41	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52443894	52443894	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52443894T>C	uc003ddx.2	-	1	116	c.1A>G	c.(1-3)ATG>GTG	p.M1V	PHF7_uc003ddy.2_5'Flank|PHF7_uc003ddz.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	1					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CCCTTATTCATCTTCCCGCGG	0.766			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								11	38	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52651339	52651339	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52651339A>T	uc003des.2	-	14	1769	c.1757T>A	c.(1756-1758)ATG>AAG	p.M586K	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.M586K|PBRM1_uc003der.2_Missense_Mutation_p.M554K|PBRM1_uc003det.2_Missense_Mutation_p.M601K|PBRM1_uc003deu.2_Missense_Mutation_p.M601K|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.M586K|PBRM1_uc010hmk.1_Missense_Mutation_p.M586K|PBRM1_uc003dey.2_Missense_Mutation_p.M586K|PBRM1_uc003dez.1_Missense_Mutation_p.M586K|PBRM1_uc003dfb.1_Missense_Mutation_p.M499K|PBRM1_uc003dfc.2_5'Flank	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	586	Bromo 4.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GTCTTCTATCATTCCCTCTTC	0.443			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								48	81	---	---	---	---	PASS
ATXN7	6314	broad.mit.edu	37	3	63981632	63981632	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63981632C>A	uc003dlw.3	+	12	2687	c.2134C>A	c.(2134-2136)CCA>ACA	p.P712T	ATXN7_uc003dlv.2_Missense_Mutation_p.P712T|ATXN7_uc010hnv.2_Missense_Mutation_p.P712T|ATXN7_uc011bfn.1_Missense_Mutation_p.P567T	NM_000333	NP_000324	O15265	ATX7_HUMAN	ataxin 7 isoform a	712	Ser-rich.				cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		AAACAGTTCCCCACTGTTGGT	0.398													3	57	---	---	---	---	PASS
ZNF654	55279	broad.mit.edu	37	3	88190108	88190108	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88190108C>A	uc003dqv.2	+	1	1847	c.1648C>A	c.(1648-1650)CTG>ATG	p.L550M	CGGBP1_uc003dqu.2_Intron	NM_018293	NP_060763	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	550					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		TGGCAAATGCCTGACCACCTA	0.383													4	128	---	---	---	---	PASS
MORC1	27136	broad.mit.edu	37	3	108788593	108788593	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108788593C>T	uc003dxl.2	-	9	788	c.701G>A	c.(700-702)AGG>AAG	p.R234K	MORC1_uc011bhn.1_Missense_Mutation_p.R234K	NM_014429	NP_055244	Q86VD1	MORC1_HUMAN	MORC family CW-type zinc finger 1	234					cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8						GAATGACCACCTCGCTGGGAA	0.358													16	108	---	---	---	---	PASS
DNAJC13	23317	broad.mit.edu	37	3	132245126	132245126	+	Splice_Site	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132245126G>A	uc003eor.2	+	53	6446	c.6381_splice	c.e53+1	p.Q2127_splice		NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2						AGTAGCACAAGTAAGTGACTT	0.368													32	116	---	---	---	---	PASS
A4GNT	51146	broad.mit.edu	37	3	137843327	137843327	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137843327A>C	uc003ers.2	-	3	1004	c.802T>G	c.(802-804)TGG>GGG	p.W268G		NM_016161	NP_057245	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	268	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	acetylglucosaminyltransferase activity|galactosyltransferase activity			central_nervous_system(1)	1						TAGCGCCTCCACTCTCGATAG	0.498													39	120	---	---	---	---	PASS
XRN1	54464	broad.mit.edu	37	3	142030531	142030531	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142030531T>C	uc003eus.2	-	42	5010	c.4943A>G	c.(4942-4944)GAG>GGG	p.E1648G	XRN1_uc010huu.2_Missense_Mutation_p.E1102G|XRN1_uc003eut.2_Missense_Mutation_p.E1635G|XRN1_uc003euu.2_Missense_Mutation_p.E1636G	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a	1648					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						TGATGAGCTCTCCCGTGGACT	0.443													8	214	---	---	---	---	PASS
SLC9A9	285195	broad.mit.edu	37	3	142987800	142987800	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142987800G>T	uc003evn.2	-	15	1809	c.1627C>A	c.(1627-1629)CAC>AAC	p.H543N		NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen	543					regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						GGACCAGAGTGGGTTAAAATT	0.468													32	112	---	---	---	---	PASS
OPA1	4976	broad.mit.edu	37	3	193355797	193355797	+	Silent	SNP	C	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193355797C>G	uc003ftm.2	+	9	1161	c.927C>G	c.(925-927)GCC>GCG	p.A309A	OPA1_uc003ftg.2_Silent_p.A364A|OPA1_uc003fth.2_Silent_p.A328A|OPA1_uc003fti.2_Silent_p.A346A|OPA1_uc003ftj.2_Silent_p.A327A|OPA1_uc003ftk.2_Silent_p.A310A|OPA1_uc003ftl.2_Silent_p.A291A|OPA1_uc003ftn.2_Silent_p.A273A	NM_015560	NP_056375	O60313	OPA1_HUMAN	optic atrophy 1 isoform 1	309	Mitochondrial intermembrane (By similarity).				apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		AAATGATTGCCCAAGCTCGAA	0.433													6	61	---	---	---	---	PASS
WHSC1	7468	broad.mit.edu	37	4	1920240	1920240	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1920240G>C	uc003gdz.3	+	5	1476	c.1300G>C	c.(1300-1302)GGA>CGA	p.G434R	WHSC1_uc003geb.3_Missense_Mutation_p.G434R|WHSC1_uc003gec.3_Missense_Mutation_p.G434R|WHSC1_uc003ged.3_Missense_Mutation_p.G434R|WHSC1_uc003gee.3_RNA|WHSC1_uc003gef.3_RNA|WHSC1_uc003gdx.2_Missense_Mutation_p.G434R|WHSC1_uc003gdy.1_Missense_Mutation_p.G434R|WHSC1_uc010icd.1_Missense_Mutation_p.G434R|WHSC1_uc003gea.1_Missense_Mutation_p.G434R|WHSC1_uc010ice.1_Missense_Mutation_p.G434R|WHSC1_uc003geh.1_Missense_Mutation_p.G434R	NM_001042424	NP_001035889	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1 protein	434					anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		CCCCAGAAGAGGAGTAGGGTC	0.552			T	IGH@	MM								9	30	---	---	---	---	PASS
PSAPL1	768239	broad.mit.edu	37	4	7436245	7436245	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7436245A>G	uc011bwj.1	-	1	456	c.362T>C	c.(361-363)ATG>ACG	p.M121T	SORCS2_uc003gkb.3_Intron|SORCS2_uc011bwi.1_Intron	NM_001085382	NP_001078851	Q6NUJ1	SAPL1_HUMAN	prosaposin-like protein 1	121	Saposin B-type 1.				sphingolipid metabolic process	extracellular region|lysosome					0						CCCACGGAGCATGCTCAGGAT	0.652													4	15	---	---	---	---	PASS
ALB	213	broad.mit.edu	37	4	74283985	74283985	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74283985A>G	uc003hgs.3	+	12	1682	c.1609A>G	c.(1609-1611)ATA>GTA	p.I537V	ALB_uc003hgw.3_Missense_Mutation_p.I345V|ALB_uc011cbe.1_Missense_Mutation_p.I216V|ALB_uc003hgt.3_Missense_Mutation_p.I537V|ALB_uc010iii.2_Missense_Mutation_p.I422V|ALB_uc003hgu.3_Missense_Mutation_p.I387V|ALB_uc003hgv.3_Missense_Mutation_p.I216V|ALB_uc011cbf.1_Missense_Mutation_p.I427V|ALB_uc010iij.2_RNA|ALB_uc003hgx.3_Missense_Mutation_p.I216V	NM_000477	NP_000468	P02768	ALBU_HUMAN	albumin preproprotein	537	Albumin 3.				bile acid and bile salt transport|bile acid metabolic process|cellular response to starvation|hemolysis by symbiont of host erythrocytes|lipoprotein metabolic process|maintenance of mitochondrion location|negative regulation of apoptosis|platelet activation|platelet degranulation|sodium-independent organic anion transport|transmembrane transport	extracellular space|platelet alpha granule lumen|protein complex	antioxidant activity|chaperone binding|copper ion binding|DNA binding|drug binding|fatty acid binding|pyridoxal phosphate binding|toxin binding			ovary(3)|skin(3)	6	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)		Acenocoumarol(DB01418)|Acitretin(DB00459)|Alfentanil(DB00802)|Aluminium(DB01370)|Auranofin(DB00995)|Bismuth(DB01402)|Captopril(DB01197)|Carboplatin(DB00958)|Cefalotin(DB00456)|Cefazolin(DB01327)|Cefonicid(DB01328)|Cefoperazone(DB01329)|Chlorpheniramine(DB01114)|Chlorpromazine(DB00477)|Ciprofloxacin(DB00537)|Clonazepam(DB01068)|Cloxacillin(DB01147)|Cytarabine(DB00987)|Dantrolene(DB01219)|Diclofenac(DB00586)|Diflunisal(DB00861)|Digitoxin(DB01396)|Estrone(DB00655)|Ethacrynic acid(DB00903)|Etodolac(DB00749)|Flurbiprofen(DB00712)|Gadobenate Dimeglumine(DB00743)|Gatifloxacin(DB01044)|Gliclazide(DB01120)|Halothane(DB01159)|Human Serum Albumin(DB00062)|Hyaluronidase(DB00070)|Ibuprofen(DB01050)|Insulin-detemir(DB01307)|Insulin-glargine(DB01308)|Iodipamide(DB04711)|Ketoprofen(DB01009)|Levamisole(DB00848)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Mefenamic acid(DB00784)|Mephenytoin(DB00532)|Methotrexate(DB00563)|Nortriptyline(DB00540)|Oxazepam(DB00842)|Paclitaxel(DB01229)|Phenprocoumon(DB00946)|Probenecid(DB01032)|Propofol(DB00818)|Pyridoxine(DB00165)|Salicyclic acid(DB00936)|Saquinavir(DB01232)|Serum albumin(DB00096)|Serum albumin iodonated(DB00064)|Sodium lauryl sulfate(DB00815)|Sucralfate(DB00364)|Sulfamethizole(DB00576)|Sulindac(DB00605)|Suprofen(DB00870)|Testosterone(DB00624)|Xanthophyll(DB00137)	CCATGCAGATATATGCACACT	0.403													34	151	---	---	---	---	PASS
CCNI	10983	broad.mit.edu	37	4	77969663	77969663	+	Silent	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77969663G>T	uc003hkm.2	-	7	1387	c.843C>A	c.(841-843)CCC>CCA	p.P281P	CCNI_uc011ccb.1_Silent_p.P267P	NM_006835	NP_006826	Q14094	CCNI_HUMAN	cyclin I	281					spermatogenesis					ovary(1)	1						GGACAGAGGAGGGATGTAATC	0.537													50	182	---	---	---	---	PASS
ABCG2	9429	broad.mit.edu	37	4	89016750	89016750	+	Silent	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89016750A>G	uc003hrg.2	-	14	2152	c.1659T>C	c.(1657-1659)GGT>GGC	p.G553G	ABCG2_uc003hrh.2_Missense_Mutation_p.V550A|ABCG2_uc003hrf.2_Silent_p.G421G	NM_004827	NP_004818	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G, member 2	553	ABC transmembrane type-2.|Helical; (Potential).				cellular iron ion homeostasis|urate metabolic process	integral to membrane|plasma membrane	ATP binding|heme transporter activity|protein homodimerization activity|xenobiotic-transporting ATPase activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Imatinib(DB00619)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nitrendipine(DB01054)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Topotecan(DB01030)	TGACCAACAGACCTGAAAAAA	0.408													15	48	---	---	---	---	PASS
RPL34	6164	broad.mit.edu	37	4	109543342	109543342	+	Silent	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109543342C>T	uc003hyz.2	+	3	191	c.147C>T	c.(145-147)TGC>TGT	p.C49C	LOC285456_uc003hyy.2_5'Flank|LOC285456_uc011cfl.1_5'Flank|RPL34_uc003hza.2_Silent_p.C49C	NM_000995	NP_000986	P49207	RL34_HUMAN	ribosomal protein L34	49					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000286)		GTGGTGTGTGCCCAGGCAGAC	0.448													4	143	---	---	---	---	PASS
FHDC1	85462	broad.mit.edu	37	4	153897676	153897676	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153897676C>T	uc003inf.2	+	11	3308	c.3233C>T	c.(3232-3234)GCC>GTC	p.A1078V		NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	1078					actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)					CCCGAGGATGCCGCTCCCAAG	0.662													3	52	---	---	---	---	PASS
GPX8	493869	broad.mit.edu	37	5	54459987	54459987	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54459987A>G	uc003jpq.2	+	3	608	c.571A>G	c.(571-573)AGG>GGG	p.R191G	CDC20B_uc003jpn.1_Intron|CDC20B_uc010ivu.1_Intron|CDC20B_uc003jpo.1_Intron|CDC20B_uc010ivv.1_Intron|CDC20B_uc003jpp.2_Intron|GPX8_uc003jpr.2_3'UTR|GPX8_uc003jps.2_RNA|GPX8_uc003jpt.2_Missense_Mutation_p.R140G	NM_001008397	NP_001008398	Q8TED1	GPX8_HUMAN	glutathione peroxidase 8	191					response to oxidative stress	integral to membrane	glutathione peroxidase activity				0					Glutathione(DB00143)	TGAAGTCATCAGGCCTGACAT	0.423													42	106	---	---	---	---	PASS
RAPGEF6	51735	broad.mit.edu	37	5	130799538	130799538	+	Intron	SNP	A	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130799538A>C	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvq.2_Intron|RAPGEF6_uc003kvr.2_Intron|RAPGEF6_uc011cxe.1_Intron|RAPGEF6_uc010jdk.2_3'UTR	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		CTCTATAAAAAAACAGGAACT	0.299													2	2	---	---	---	---	PASS
LARS	51520	broad.mit.edu	37	5	145557190	145557190	+	Silent	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145557190C>T	uc003lnx.1	-	2	283	c.45G>A	c.(43-45)AAG>AAA	p.K15K	LARS_uc011dbq.1_Silent_p.K15K|LARS_uc011dbr.1_Intron|LARS_uc011dbs.1_Silent_p.K15K	NM_020117	NP_064502	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	15					leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	CTTTCTCAATCTTCTTCAAAA	0.363													36	130	---	---	---	---	PASS
THOC3	84321	broad.mit.edu	37	5	175387036	175387036	+	Missense_Mutation	SNP	C	T	T	rs139761351		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175387036C>T	uc003mdg.3	-	6	1326	c.992G>A	c.(991-993)GGC>GAC	p.G331D		NM_032361	NP_115737	Q96J01	THOC3_HUMAN	THO complex 3	331					intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	transcription export complex	RNA binding				0	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		GTCATATTTGCCGTCTTTGTC	0.557													11	77	---	---	---	---	PASS
SNRNP48	154007	broad.mit.edu	37	6	7605680	7605680	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7605680G>A	uc003mxr.2	+	7	826	c.767G>A	c.(766-768)TGG>TAG	p.W256*	SNRNP48_uc003mxs.2_RNA|SNRNP48_uc003mxt.1_Nonsense_Mutation_p.W8*	NM_152551	NP_689764	Q6IEG0	SNR48_HUMAN	U11/U12 snRNP 48K	256					mRNA processing	cytoplasm|U12-type spliceosomal complex	metal ion binding				0						AGCAATCATTGGCAAGAAGAG	0.383													29	110	---	---	---	---	PASS
HIST1H2AJ	8331	broad.mit.edu	37	6	27782114	27782114	+	3'UTR	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27782114C>T	uc003njn.1	-	1					HIST1H2BM_uc003njo.2_5'Flank	NM_021066	NP_066544	Q99878	H2A1J_HUMAN	histone cluster 1, H2aj						nucleosome assembly	nucleosome|nucleus	DNA binding				0						TGTTTTTATGCGCTTTTCAAC	0.478													5	299	---	---	---	---	PASS
OR12D3	81797	broad.mit.edu	37	6	29342284	29342284	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29342284G>A	uc003nme.2	-	1	785	c.781C>T	c.(781-783)CCT>TCT	p.P261S		NM_030959	NP_112221	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D,	261	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|breast(1)	3						GCTGAAGCAGGACGAATATAT	0.488													23	108	---	---	---	---	PASS
VARS2	57176	broad.mit.edu	37	6	30884693	30884693	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30884693G>A	uc003nsc.1	+	7	1342	c.710G>A	c.(709-711)GGT>GAT	p.G237D	VARS2_uc003nsd.2_Missense_Mutation_p.G237D|VARS2_uc011dmx.1_Missense_Mutation_p.G237D|VARS2_uc011dmy.1_Missense_Mutation_p.G97D|VARS2_uc011dmz.1_Missense_Mutation_p.G267D|VARS2_uc011dna.1_Missense_Mutation_p.G237D|VARS2_uc011dnb.1_RNA|VARS2_uc011dnc.1_RNA|VARS2_uc011dnd.1_5'Flank|VARS2_uc010jsg.1_5'Flank	NM_020442	NP_065175	Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	237					valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4						CGAGCTCTGGGTGCCTCCCTG	0.433													60	200	---	---	---	---	PASS
VARS2	57176	broad.mit.edu	37	6	30884694	30884694	+	Silent	SNP	T	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30884694T>C	uc003nsc.1	+	7	1343	c.711T>C	c.(709-711)GGT>GGC	p.G237G	VARS2_uc003nsd.2_Silent_p.G237G|VARS2_uc011dmx.1_Silent_p.G237G|VARS2_uc011dmy.1_Silent_p.G97G|VARS2_uc011dmz.1_Silent_p.G267G|VARS2_uc011dna.1_Silent_p.G237G|VARS2_uc011dnb.1_RNA|VARS2_uc011dnc.1_RNA|VARS2_uc011dnd.1_5'Flank|VARS2_uc010jsg.1_5'Flank	NM_020442	NP_065175	Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	237					valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4						GAGCTCTGGGTGCCTCCCTGG	0.438													61	203	---	---	---	---	PASS
EHMT2	10919	broad.mit.edu	37	6	31855386	31855386	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31855386T>C	uc003nxz.1	-	15	1989	c.1979A>G	c.(1978-1980)CAG>CGG	p.Q660R	EHMT2_uc003nxv.1_5'Flank|EHMT2_uc003nxw.1_5'Flank|EHMT2_uc003nxx.1_5'Flank|EHMT2_uc003nxy.1_Missense_Mutation_p.Q451R|EHMT2_uc011don.1_Missense_Mutation_p.Q683R|EHMT2_uc003nya.1_Missense_Mutation_p.Q626R	NM_006709	NP_006700	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	660	ANK 1.				DNA methylation|peptidyl-lysine dimethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			ovary(1)	1						CAGCTCGCCCTGCTTCACGGA	0.448													12	58	---	---	---	---	PASS
NOTCH4	4855	broad.mit.edu	37	6	32170158	32170158	+	Silent	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32170158C>T	uc003obb.2	-	21	3589	c.3450G>A	c.(3448-3450)ACG>ACA	p.T1150T	NOTCH4_uc003oba.2_5'UTR|NOTCH4_uc011dpu.1_Intron|NOTCH4_uc011dpv.1_Intron	NM_004557	NP_004548	Q99466	NOTC4_HUMAN	notch4 preproprotein	1150	Extracellular (Potential).|EGF-like 29.				cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|protein heterodimerization activity|receptor activity			lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1)	22						CCCCCAAGCCCGTGGTCTCTG	0.642													8	31	---	---	---	---	PASS
HSD17B8	7923	broad.mit.edu	37	6	33174459	33174459	+	3'UTR	SNP	A	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33174459A>C	uc003odi.1	+	9					uc003odj.1_5'Flank|MIR219-1_hsa-mir-219-1|MI0000296_5'Flank|RING1_uc011dqw.1_5'Flank|RING1_uc011dqx.1_5'Flank|RING1_uc003odk.2_5'Flank|RING1_uc003odl.2_5'Flank	NM_014234	NP_055049	Q92506	DHB8_HUMAN	estradiol 17 beta-dehydrogenase 8						estrogen biosynthetic process|fatty acid biosynthetic process	mitochondrial matrix	3-hydroxyacyl-CoA dehydrogenase activity|estradiol 17-beta-dehydrogenase activity|protein binding|testosterone 17-beta-dehydrogenase (NAD+) activity			breast(1)|central_nervous_system(1)	2					NADH(DB00157)	GACTCTGCTCACCCCCCCACC	0.537													7	84	---	---	---	---	PASS
BTBD9	114781	broad.mit.edu	37	6	38545497	38545497	+	Splice_Site	SNP	T	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38545497T>A	uc003ooa.3	-	7	1611	c.1035_splice	c.e7-1	p.R345_splice	BTBD9_uc003ony.3_Splice_Site_p.R277_splice|BTBD9_uc010jwv.2_Splice_Site_p.R277_splice|BTBD9_uc010jww.2_Splice_Site|BTBD9_uc010jwx.2_Splice_Site_p.R345_splice	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a						cell adhesion						0						GAGTAAGACCTGTGAATCAAA	0.308													3	138	---	---	---	---	PASS
FOXP4	116113	broad.mit.edu	37	6	41554889	41554889	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41554889C>T	uc003oql.2	+	6	1111	c.653C>T	c.(652-654)CCG>CTG	p.P218L	FOXP4_uc003oqm.2_Missense_Mutation_p.P216L|FOXP4_uc003oqn.2_Missense_Mutation_p.P218L	NM_001012426	NP_001012426	Q8IVH2	FOXP4_HUMAN	forkhead box P4 isoform 1	218	Gln-rich.				embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)					CAGACCCTTCCGCAAGGTGAG	0.652											OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	6	14	---	---	---	---	PASS
KLHL32	114792	broad.mit.edu	37	6	97533087	97533087	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97533087T>G	uc010kcm.1	+	6	969	c.497T>G	c.(496-498)TTC>TGC	p.F166C	KLHL32_uc003poy.2_Missense_Mutation_p.F166C|KLHL32_uc011ead.1_Missense_Mutation_p.F130C|KLHL32_uc003poz.2_Intron|KLHL32_uc011eae.1_Missense_Mutation_p.F97C|KLHL32_uc003ppa.2_RNA	NM_052904	NP_443136	Q96NJ5	KLH32_HUMAN	kelch-like 32	166										ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		GTGATCGATTTCTTAGTGAAA	0.458													4	294	---	---	---	---	PASS
ZNF680	340252	broad.mit.edu	37	7	63982840	63982840	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63982840G>T	uc003tta.2	-	4	465	c.292C>A	c.(292-294)CAT>AAT	p.H98N	ZNF680_uc010kzr.2_Missense_Mutation_p.H25N	NM_178558	NP_848653	Q8NEM1	ZN680_HUMAN	zinc finger protein 680 isoform 1	98					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.118)|all_lung(88;0.243)				TTTATGCTATGCTCTGGCCAA	0.308													4	148	---	---	---	---	PASS
MLXIPL	51085	broad.mit.edu	37	7	73011232	73011232	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73011232A>G	uc003tyn.1	-	10	1682	c.1634T>C	c.(1633-1635)CTT>CCT	p.L545P	MLXIPL_uc003tyj.1_5'UTR|MLXIPL_uc003tyk.1_Missense_Mutation_p.L545P|MLXIPL_uc003tyl.1_Missense_Mutation_p.L545P|MLXIPL_uc003tym.1_Missense_Mutation_p.L545P|MLXIPL_uc003tyo.1_RNA|MLXIPL_uc003typ.1_Missense_Mutation_p.L452P|MLXIPL_uc003tyq.1_Missense_Mutation_p.L287P	NM_032951	NP_116569	Q9NP71	WBS14_HUMAN	Williams Beuren syndrome chromosome region 14	545					anatomical structure morphogenesis|energy reserve metabolic process|glucose mediated signaling pathway|intracellular protein kinase cascade|negative regulation of cell cycle arrest|negative regulation of oxidative phosphorylation|negative regulation of peptidyl-serine phosphorylation|positive regulation of cell proliferation|positive regulation of fatty acid biosynthetic process|positive regulation of glycolysis|positive regulation of transcription from RNA polymerase II promoter|triglyceride homeostasis	cytosol|transcription factor complex	carbohydrate response element binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)				GCTGGATACAAGTGGTGGCTC	0.672													5	21	---	---	---	---	PASS
LAMB1	3912	broad.mit.edu	37	7	107596066	107596066	+	Silent	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107596066A>G	uc003vew.2	-	21	3035	c.2700T>C	c.(2698-2700)GCT>GCC	p.A900A	LAMB1_uc003vev.2_Silent_p.A924A	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	900	Laminin EGF-like 8.				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)	CATAGTAACCAGCCAAGCACC	0.522													25	35	---	---	---	---	PASS
LAMB4	22798	broad.mit.edu	37	7	107720165	107720165	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107720165G>A	uc010ljo.1	-	15	1852	c.1768C>T	c.(1768-1770)CCT>TCT	p.P590S	LAMB4_uc003vey.2_Missense_Mutation_p.P590S	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	590	Laminin IV type B.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						CATGTAACAGGGTTCCCAGGA	0.512													11	63	---	---	---	---	PASS
CAPZA2	830	broad.mit.edu	37	7	116533094	116533094	+	Silent	SNP	A	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116533094A>T	uc003vil.2	+	3	253	c.150A>T	c.(148-150)GCA>GCT	p.A50A	CAPZA2_uc003vik.1_RNA|CAPZA2_uc011knk.1_RNA	NM_006136	NP_006127	P47755	CAZA2_HUMAN	capping protein (actin filament) muscle Z-line,	50					actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex	actin binding				0	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)			GGGAAGGAGCAGCCCAGTAAG	0.323													26	166	---	---	---	---	PASS
ZC3HC1	51530	broad.mit.edu	37	7	129666109	129666109	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129666109T>A	uc003vpi.2	-	6	692	c.665A>T	c.(664-666)GAA>GTA	p.E222V	ZC3HC1_uc003vph.2_Missense_Mutation_p.E109V|ZC3HC1_uc010lma.2_Missense_Mutation_p.E109V	NM_016478	NP_057562	Q86WB0	NIPA_HUMAN	zinc finger, C3HC type 1	222					cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)					AAGTTCATCTTCAAGCAAGTG	0.408													32	166	---	---	---	---	PASS
ZC3HC1	51530	broad.mit.edu	37	7	129666110	129666110	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129666110C>A	uc003vpi.2	-	6	691	c.664G>T	c.(664-666)GAA>TAA	p.E222*	ZC3HC1_uc003vph.2_Nonsense_Mutation_p.E109*|ZC3HC1_uc010lma.2_Nonsense_Mutation_p.E109*	NM_016478	NP_057562	Q86WB0	NIPA_HUMAN	zinc finger, C3HC type 1	222					cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)					AGTTCATCTTCAAGCAAGTGT	0.408													32	167	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142032050	142032050	+	Intron	SNP	G	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142032050G>C	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc011krs.1_Missense_Mutation_p.R4S					SubName: Full=V_segment translation product; Flags: Fragment;																		TGGGCACAAGGCTCCTCTGCT	0.483													4	69	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151859848	151859848	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151859848T>A	uc003wla.2	-	43	11033	c.10814A>T	c.(10813-10815)AAA>ATA	p.K3605I	MLL3_uc003wkz.2_Missense_Mutation_p.K2666I|MLL3_uc003wky.2_Missense_Mutation_p.K1114I	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	3605					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		tcttgttcttttctttttccc	0.353			N		medulloblastoma								12	203	---	---	---	---	PASS
ERICH1	157697	broad.mit.edu	37	8	623372	623372	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:623372T>A	uc003wph.2	-	4	1045	c.980A>T	c.(979-981)GAG>GTG	p.E327V	ERICH1_uc011kwh.1_Missense_Mutation_p.E327V|ERICH1_uc003wpe.1_Missense_Mutation_p.E233V|ERICH1_uc003wpi.2_Missense_Mutation_p.E139V	NM_207332	NP_997215	Q86X53	ERIC1_HUMAN	glutamate-rich 1	327	Glu-rich.									large_intestine(2)	2		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		ATCATCTTCCTCGCTGGCGTC	0.498													68	251	---	---	---	---	PASS
LZTS1	11178	broad.mit.edu	37	8	20107281	20107281	+	Silent	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20107281C>T	uc003wzr.2	-	3	1854	c.1743G>A	c.(1741-1743)CTG>CTA	p.L581L	LZTS1_uc010ltg.1_Silent_p.L522L	NM_021020	NP_066300	Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	581					cell cycle|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	cell junction|dendritic spine|Golgi apparatus|nucleolus|nucleoplasm|postsynaptic density|postsynaptic membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		CAGCCCCTTCCAGGTCAACCT	0.657													44	113	---	---	---	---	PASS
CDCA2	157313	broad.mit.edu	37	8	25364407	25364407	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25364407G>T	uc003xep.1	+	15	2704	c.2225G>T	c.(2224-2226)GGT>GTT	p.G742V	PPP2R2A_uc003xek.2_Intron|CDCA2_uc011lae.1_3'UTR|CDCA2_uc003xeq.1_Missense_Mutation_p.G727V|CDCA2_uc003xer.1_Missense_Mutation_p.G405V	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	742					cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		TTTTCTGCTGGTGGTCAAAAT	0.423													10	104	---	---	---	---	PASS
ASH2L	9070	broad.mit.edu	37	8	37967896	37967896	+	Splice_Site	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37967896G>T	uc003xkt.3	+	4	460	c.402_splice	c.e4-1	p.S134_splice	ASH2L_uc011lbk.1_Splice_Site|ASH2L_uc003xku.3_Splice_Site_p.S40_splice|ASH2L_uc010lwa.2_Splice_Site_p.S40_splice	NM_004674	NP_004665	Q9UBL3	ASH2L_HUMAN	ash2-like isoform a						hemopoiesis|histone H3-K4 methylation|positive regulation of cell proliferation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription from RNA polymerase II promoter	Set1C/COMPASS complex	metal ion binding|protein binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)				CTCTTCGGCAGATCCTGTCTA	0.318													29	134	---	---	---	---	PASS
STAR	6770	broad.mit.edu	37	8	38008507	38008507	+	5'UTR	SNP	C	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38008507C>G	uc003xkv.1	-	1					STAR_uc010lwc.1_5'UTR	NM_001007243	NP_001007244	P49675	STAR_HUMAN	steroidogenic acute regulatory protein isoform						C21-steroid hormone biosynthetic process	mitochondrial intermembrane space	cholesterol transporter activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.0151)|Lung NSC(58;0.0295)		READ - Rectum adenocarcinoma(644;0.188)		AAATGTCCCCCGCTGAAGGCT	0.547													2	6	---	---	---	---	PASS
SNAI2	6591	broad.mit.edu	37	8	49833919	49833919	+	5'UTR	SNP	A	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49833919A>T	uc003xqp.2	-	1						NM_003068	NP_003059	O43623	SNAI2_HUMAN	snail 2						canonical Wnt receptor signaling pathway|ectoderm and mesoderm interaction|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_cancers(86;0.0368)|all_epithelial(80;0.000624)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				AGGCTCGGGCAGGGGCCGTGC	0.697													9	36	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77768068	77768068	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77768068C>T	uc003yav.2	+	10	9163	c.8776C>T	c.(8776-8778)CGC>TGC	p.R2926C	ZFHX4_uc003yau.1_Missense_Mutation_p.R2971C|ZFHX4_uc003yaw.1_Missense_Mutation_p.R2926C	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2926	Homeobox 4.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TCTGCCCAAACGCGTAGTCCA	0.433										HNSCC(33;0.089)			15	49	---	---	---	---	PASS
ZHX2	22882	broad.mit.edu	37	8	123963970	123963970	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123963970C>G	uc003ypk.1	+	3	787	c.220C>G	c.(220-222)CTC>GTC	p.L74V		NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	74						cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			GTCCAAAAAACTCCAAGGTGG	0.478													17	43	---	---	---	---	PASS
TOR1A	1861	broad.mit.edu	37	9	132584984	132584984	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132584984C>T	uc004byl.2	-	2	397	c.320G>A	c.(319-321)GGC>GAC	p.G107D	TOR1A_uc004bym.2_RNA|TOR1A_uc004byn.2_Missense_Mutation_p.G107D	NM_000113	NP_000104	O14656	TOR1A_HUMAN	torsin A precursor	107	ATP.				chaperone mediated protein folding requiring cofactor|response to unfolded protein	endoplasmic reticulum lumen|nuclear membrane	ATP binding|serine-type endopeptidase activity|unfolded protein binding			central_nervous_system(1)	1		Ovarian(14;0.00556)				GAAATTTTTGCCGGTGCCTGT	0.468													5	334	---	---	---	---	PASS
C9orf139	401563	broad.mit.edu	37	9	139929522	139929522	+	3'UTR	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139929522C>T	uc004ckp.1	+	3					FUT7_uc004ckq.2_5'Flank	NM_207511	NP_997394	Q6ZV77	CI139_HUMAN	hypothetical protein LOC401563												0	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.99e-05)|Epithelial(140;0.000493)		TGGGTTTGTGCGGACCCAGGC	0.612													3	70	---	---	---	---	PASS
TAF3	83860	broad.mit.edu	37	10	8051125	8051125	+	Silent	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8051125G>T	uc010qbd.1	+	5	2400	c.2400G>T	c.(2398-2400)GCG>GCT	p.A800A		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	800	Pro-rich.				maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						cggcccccgcgcccgcccccg	0.249													4	6	---	---	---	---	PASS
POLL	27343	broad.mit.edu	37	10	103339507	103339507	+	Silent	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103339507G>A	uc001ktg.1	-	8	2197	c.1431C>T	c.(1429-1431)TGC>TGT	p.C477C	DPCD_uc010qpz.1_Intron|POLL_uc001ktd.1_Silent_p.C150C|POLL_uc001kte.1_Silent_p.C169C|POLL_uc001kth.1_Silent_p.C202C|POLL_uc001kti.1_Silent_p.C477C|POLL_uc001ktj.1_Silent_p.C477C|POLL_uc001ktf.2_Silent_p.C385C|POLL_uc001ktk.1_Silent_p.C216C|POLL_uc010qqa.1_Silent_p.C216C|POLL_uc010qqb.1_RNA|POLL_uc001ktm.2_Silent_p.C477C|POLL_uc001ktl.2_Silent_p.C389C|POLL_uc010qqc.1_Silent_p.C169C	NM_013274	NP_037406	Q9UGP5	DPOLL_HUMAN	DNA-directed DNA polymerase lambda	477	DNA binding.				DNA replication|nucleotide-excision repair|somatic hypermutation of immunoglobulin genes	nucleus	DNA binding|DNA-directed DNA polymerase activity|lyase activity|metal ion binding				0		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		CTGGGAGCCGGCACACCCCCA	0.632								DNA_polymerases_(catalytic_subunits)					4	85	---	---	---	---	PASS
RPL13AP6	644511	broad.mit.edu	37	10	112696573	112696573	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112696573T>C	uc010qrh.1	-	1	441	c.419A>G	c.(418-420)CAC>CGC	p.H140R	SHOC2_uc001kzl.3_Intron|SHOC2_uc009xxx.2_Intron|SHOC2_uc010qrg.1_Intron	NR_026715				SubName: Full=cDNA FLJ51256, highly similar to 60S ribosomal protein L13a;												0						GTGAGCCAGGTGCCCCAGATA	0.537													3	26	---	---	---	---	PASS
MUC6	4588	broad.mit.edu	37	11	1016334	1016334	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1016334G>C	uc001lsw.2	-	31	6518	c.6467C>G	c.(6466-6468)TCG>TGG	p.S2156W		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	2156	Ser-rich.|Thr-rich.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AACAGAAGGCGATGAAGTCTG	0.552													5	25	---	---	---	---	PASS
TRIM5	85363	broad.mit.edu	37	11	5700397	5700397	+	Silent	SNP	C	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5700397C>A	uc001mbm.1	-	3	677	c.420G>T	c.(418-420)GTG>GTT	p.V140V	TRIM5_uc001mbq.1_Silent_p.V140V|TRIM5_uc001mbl.1_RNA|TRIM5_uc001mbn.2_Silent_p.V140V|TRIM5_uc001mbo.2_Silent_p.V140V|TRIM5_uc001mbp.2_Silent_p.V140V	NM_033034	NP_149023	Q9C035	TRIM5_HUMAN	tripartite motif protein TRIM5 isoform alpha	140	Potential.				interspecies interaction between organisms|protein trimerization|response to virus	cytoplasm|cytoplasmic mRNA processing body	ligase activity|protein binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		CCTGGAGCTTCACCTGTGAGA	0.453													6	433	---	---	---	---	PASS
MPPED2	744	broad.mit.edu	37	11	30557623	30557623	+	Silent	SNP	A	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30557623A>T	uc001msr.2	-	2	348	c.228T>A	c.(226-228)CCT>CCA	p.P76P	MPPED2_uc001msq.3_Silent_p.P76P|MPPED2_uc009yji.2_5'UTR	NM_001584	NP_001575	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	76					nervous system development		hydrolase activity|metal ion binding			skin(1)	1						TGTCCCCATAAGGCATCTGGA	0.517													32	95	---	---	---	---	PASS
TNKS1BP1	85456	broad.mit.edu	37	11	57077417	57077417	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57077417G>A	uc001njr.2	-	5	3080	c.2768C>T	c.(2767-2769)GCC>GTC	p.A923V	TNKS1BP1_uc001njs.2_Missense_Mutation_p.A923V|TNKS1BP1_uc009ymd.1_Missense_Mutation_p.A374V	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	923	Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				CTGCTCATCGGCATCCTGGCT	0.572													5	408	---	---	---	---	PASS
CPSF7	79869	broad.mit.edu	37	11	61188976	61188976	+	Silent	SNP	A	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61188976A>C	uc001nrq.2	-	3	293	c.159T>G	c.(157-159)CCT>CCG	p.P53P	CPSF7_uc001nro.2_Silent_p.P53P|CPSF7_uc001nrp.2_Silent_p.P96P|CPSF7_uc001nrr.2_Silent_p.P53P|CPSF7_uc001nrs.1_5'UTR|CPSF7_uc009ynp.2_Silent_p.P53P	NM_001136040	NP_001129512	Q8N684	CPSF7_HUMAN	pre-mRNA cleavage factor I, 59 kDa subunit	53	Poly-Pro.				mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	mRNA cleavage factor complex	nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1						GGCGAACAGGAGGAGGTGGTT	0.517													25	93	---	---	---	---	PASS
NAALAD2	10003	broad.mit.edu	37	11	89907078	89907078	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89907078G>T	uc001pdf.3	+	14	1606	c.1497G>T	c.(1495-1497)TTG>TTT	p.L499F	NAALAD2_uc009yvx.2_Missense_Mutation_p.L466F|NAALAD2_uc009yvy.2_Intron	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	499	Extracellular (Potential).|NAALADase.				proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				ATAAAAATTTGCCTAGGTAAG	0.403													33	201	---	---	---	---	PASS
KRT86	3892	broad.mit.edu	37	12	52646173	52646173	+	Intron	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52646173A>G	uc010snq.1	+						uc010snr.1_Silent_p.G205G	NM_002284	NP_002275	O43790	KRT86_HUMAN	keratin 86						cytoskeleton organization	keratin filament	structural molecule activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCTGCAGGGCACCCTCCAGCT	0.642													5	95	---	---	---	---	PASS
NACA	4666	broad.mit.edu	37	12	57113130	57113130	+	Intron	SNP	A	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57113130A>T	uc001slz.2	-						NACA_uc001sly.2_Intron|NACA_uc009zoy.1_Silent_p.P728P|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Intron|NACA_uc001smb.2_Intron|NACA_uc010squ.1_Intron	NM_001113201	NP_001106672	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha						interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1						TTGGGATTTCAGGGGCCAGCA	0.512			T	BCL6	NHL								3	30	---	---	---	---	PASS
OSBPL8	114882	broad.mit.edu	37	12	76786494	76786494	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76786494A>G	uc001sye.1	-	10	1276	c.796T>C	c.(796-798)TGT>CGT	p.C266R	OSBPL8_uc001syf.1_Missense_Mutation_p.C224R|OSBPL8_uc001syg.1_Missense_Mutation_p.C224R|OSBPL8_uc001syh.1_Missense_Mutation_p.C241R	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform	266					lipid transport		lipid binding			ovary(1)	1						AGACTAGAACATTTCAAAGCC	0.378													27	121	---	---	---	---	PASS
AHSA1	10598	broad.mit.edu	37	14	77935429	77935429	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77935429C>T	uc001xtw.2	+	9	1014	c.854C>T	c.(853-855)GCC>GTC	p.A285V		NM_012111	NP_036243	O95433	AHSA1_HUMAN	activator of heat shock 90kDa protein ATPase	285					protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		GGACACTTTGCCACCATCACC	0.493													4	194	---	---	---	---	PASS
BDKRB1	623	broad.mit.edu	37	14	96730316	96730316	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96730316C>G	uc001yfh.2	+	3	505	c.297C>G	c.(295-297)AAC>AAG	p.N99K	BDKRB1_uc010avn.2_Missense_Mutation_p.N99K	NM_000710	NP_000701	P46663	BKRB1_HUMAN	bradykinin receptor B1	99	Extracellular (Potential).				elevation of cytosolic calcium ion concentration	endoplasmic reticulum|integral to plasma membrane	bradykinin receptor activity			ovary(3)	3		all_cancers(154;0.0677)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.208)|Epithelial(152;0.226)		ATATCTGGAACCAGTTTAACT	0.552													17	105	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	20644461	20644461	+	Intron	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20644461C>T	uc001ytg.2	-						uc010tyx.1_Intron|uc001yth.3_Intron|uc010tyy.1_3'UTR					RecName: Full=Putative HERC2-like protein 3;																		CTCTGAGTGACGGCACTGCGC	0.622													3	9	---	---	---	---	PASS
NIPA2	81614	broad.mit.edu	37	15	23006301	23006301	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23006301C>A	uc001yux.2	-	8	1616	c.1003G>T	c.(1003-1005)GAA>TAA	p.E335*	NIPA2_uc001yuy.2_Nonsense_Mutation_p.E335*|NIPA2_uc001yuz.2_Nonsense_Mutation_p.E335*|NIPA2_uc001yva.2_Nonsense_Mutation_p.E316*|NIPA2_uc001yvb.2_Nonsense_Mutation_p.E335*|NIPA2_uc010ayb.2_Nonsense_Mutation_p.E316*	NM_030922	NP_112184	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome	335	Cytoplasmic (Potential).					early endosome|integral to membrane|plasma membrane				haematopoietic_and_lymphoid_tissue(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		AAGCTTTCTTCATTATTATTA	0.368													5	173	---	---	---	---	PASS
ARHGAP11B	89839	broad.mit.edu	37	15	30919056	30919056	+	Silent	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30919056G>T	uc001zet.1	+	1	178	c.33G>T	c.(31-33)CTG>CTT	p.L11L	ARHGAP11B_uc010azv.1_Intron|ARHGAP11B_uc001zeu.2_RNA	NM_001039841	NP_001034930	Q3KRB8	RHGBB_HUMAN	Rho GTPase activating protein 11B	11					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		AGTTGGCCCTGTTGCAGCATC	0.552													21	62	---	---	---	---	PASS
PLA2G4D	283748	broad.mit.edu	37	15	42363506	42363506	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42363506G>A	uc001zox.2	-	17	1786	c.1691C>T	c.(1690-1692)CCC>CTC	p.P564L		NM_178034	NP_828848	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD	564	PLA2c.				phospholipid catabolic process	cytoplasmic vesicle membrane|cytosol	metal ion binding|phospholipase A2 activity			large_intestine(1)|skin(1)	2		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GGTGGTCAGGGGCTCCTTCTC	0.607													4	27	---	---	---	---	PASS
TP53BP1	7158	broad.mit.edu	37	15	43748161	43748161	+	Nonsense_Mutation	SNP	G	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43748161G>C	uc001zrs.2	-	12	2778	c.2630C>G	c.(2629-2631)TCA>TGA	p.S877*	TP53BP1_uc010udp.1_Nonsense_Mutation_p.S877*|TP53BP1_uc001zrq.3_Nonsense_Mutation_p.S882*|TP53BP1_uc001zrr.3_Nonsense_Mutation_p.S882*|TP53BP1_uc010udq.1_Nonsense_Mutation_p.S882*	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3	877					double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		CTCTGCATCTGAGCTTAGCTG	0.453								Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					23	249	---	---	---	---	PASS
SORD	6652	broad.mit.edu	37	15	45365869	45365869	+	3'UTR	SNP	A	C	C	rs145349248	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45365869A>C	uc001zul.3	+	9					SORD_uc001zum.3_3'UTR|SORD_uc010bdz.2_3'UTR	NM_003104	NP_003095	Q00796	DHSO_HUMAN	sorbitol dehydrogenase						fructose biosynthetic process|glucose metabolic process|L-xylitol catabolic process|sorbitol catabolic process|sperm motility	cilium|extracellular space|flagellum|membrane fraction|mitochondrial membrane|soluble fraction	L-iditol 2-dehydrogenase activity|NAD binding|sugar binding|zinc ion binding				0		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)	NADH(DB00157)	GAAGTCCTTAAGCAGAGGAAT	0.428													3	18	---	---	---	---	PASS
TCF12	6938	broad.mit.edu	37	15	57565320	57565320	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57565320G>A	uc002aec.2	+	18	2050	c.1766G>A	c.(1765-1767)CGC>CAC	p.R589H	TCF12_uc010ugm.1_Missense_Mutation_p.R641H|TCF12_uc010ugn.1_Missense_Mutation_p.R609H|TCF12_uc002aea.2_Missense_Mutation_p.R613H|TCF12_uc010bfs.2_Missense_Mutation_p.R10H|TCF12_uc002aeb.2_Missense_Mutation_p.R613H|TCF12_uc002aed.2_Missense_Mutation_p.R589H|TCF12_uc002aee.2_Missense_Mutation_p.R419H|TCF12_uc010bft.2_Missense_Mutation_p.R443H|TCF12_uc010ugo.1_Missense_Mutation_p.R353H|TCF12_uc010ugp.1_Missense_Mutation_p.R246H|TCF12_uc010ugq.1_Missense_Mutation_p.R223H|TCF12_uc010ugr.1_Missense_Mutation_p.R202H	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b	589	Basic motif.				immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		GAACGCTTACGCGTGCGGGAT	0.428			T	TEC	extraskeletal myxoid chondrosarcoma								23	92	---	---	---	---	PASS
CGNL1	84952	broad.mit.edu	37	15	57836715	57836715	+	Nonsense_Mutation	SNP	C	G	G	rs137878510	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57836715C>G	uc002aeg.2	+	16	3496	c.3420C>G	c.(3418-3420)TAC>TAG	p.Y1140*	CGNL1_uc010bfw.2_Nonsense_Mutation_p.Y1140*	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1	1140	Potential.					myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		AAGGTTCCTACAGGTCCAGCA	0.592													7	36	---	---	---	---	PASS
HERC1	8925	broad.mit.edu	37	15	63970224	63970224	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63970224C>A	uc002amp.2	-	37	7038	c.6890G>T	c.(6889-6891)AGG>ATG	p.R2297M		NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	2297					protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						GCAAAGAGTCCTCAGCTGCAG	0.522													18	80	---	---	---	---	PASS
WASH3P	374666	broad.mit.edu	37	15	102515298	102515298	+	Silent	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102515298C>T	uc002cdi.2	+	9	1942	c.522C>T	c.(520-522)ATC>ATT	p.I174I	WASH3P_uc002cdl.2_Silent_p.I174I|WASH3P_uc002cdk.2_RNA|WASH3P_uc002cdp.2_Silent_p.I174I|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						CTGGGGGCATCGGCAAGGCCA	0.652													3	23	---	---	---	---	PASS
HN1L	90861	broad.mit.edu	37	16	1748907	1748907	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1748907G>A	uc002cmg.2	+	5	517	c.481G>A	c.(481-483)GAC>AAC	p.D161N	HN1L_uc010uvi.1_Missense_Mutation_p.D189N|HN1L_uc010brt.2_RNA|HN1L_uc010bru.2_3'UTR|HN1L_uc010uvj.1_3'UTR|HN1L_uc010uvk.1_Missense_Mutation_p.D148N	NM_144570	NP_653171	Q9H910	HN1L_HUMAN	hematological and neurological expressed 1-like	161						cytoplasm|nucleus				upper_aerodigestive_tract(1)	1						GCCCACAGTCGACAGCCATGA	0.637													33	130	---	---	---	---	PASS
CCNF	899	broad.mit.edu	37	16	2506613	2506613	+	Silent	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2506613G>A	uc002cqd.1	+	17	2041	c.1953G>A	c.(1951-1953)CAG>CAA	p.Q651Q	CCNF_uc002cqe.1_Silent_p.Q343Q	NM_001761	NP_001752	P41002	CCNF_HUMAN	cyclin F	651	PEST.				cell division|mitosis|negative regulation of centrosome duplication|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	centriole|nucleus|SCF ubiquitin ligase complex	protein binding			central_nervous_system(1)|kidney(1)	2		Ovarian(90;0.17)				ATTGCTGCCAGGAATCCAGTG	0.602													11	49	---	---	---	---	PASS
NLRC3	197358	broad.mit.edu	37	16	3614126	3614126	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3614126G>A	uc010btn.2	-	5	1223	c.812C>T	c.(811-813)GCA>GTA	p.A271V		NM_178844	NP_849172	Q7RTR2	NLRC3_HUMAN	NOD3 protein	271	NACHT.				I-kappaB kinase/NF-kappaB cascade|negative regulation of NF-kappaB transcription factor activity|T cell activation	cytoplasm	ATP binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						CTGGCCAGATGCACTGGGACG	0.582													9	68	---	---	---	---	PASS
NLRC3	197358	broad.mit.edu	37	16	3614127	3614127	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3614127C>T	uc010btn.2	-	5	1222	c.811G>A	c.(811-813)GCA>ACA	p.A271T		NM_178844	NP_849172	Q7RTR2	NLRC3_HUMAN	NOD3 protein	271	NACHT.				I-kappaB kinase/NF-kappaB cascade|negative regulation of NF-kappaB transcription factor activity|T cell activation	cytoplasm	ATP binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						TGGCCAGATGCACTGGGACGG	0.582													9	68	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15198590	15198590	+	Intron	SNP	C	T	T	rs113675370		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15198590C>T	uc002ddc.2	+						uc010uzr.1_Missense_Mutation_p.R100H|uc010uzs.1_RNA|uc002ddh.2_3'UTR|uc010bve.1_Intron	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	TGAAGAATGACGATGCTCCGC	0.488													4	136	---	---	---	---	PASS
BBS2	583	broad.mit.edu	37	16	56535341	56535341	+	Silent	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56535341G>A	uc002ejd.2	-	10	1383	c.1149C>T	c.(1147-1149)CTC>CTT	p.L383L	BBS2_uc010ccg.2_3'UTR	NM_031885	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2 protein	383					adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1						GCGTGGTGTGGAGCCTGGTAT	0.517									Bardet-Biedl_syndrome				40	207	---	---	---	---	PASS
GOT2	2806	broad.mit.edu	37	16	58757714	58757714	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58757714T>C	uc002eof.1	-	2	296	c.182A>G	c.(181-183)AAT>AGT	p.N61S	GOT2_uc010vim.1_Missense_Mutation_p.N61S	NM_002080	NP_002071	P00505	AATM_HUMAN	aspartate aminotransferase 2 precursor	61					aspartate catabolic process|fatty acid transport|gluconeogenesis|response to ethanol	mitochondrial matrix|plasma membrane	L-aspartate:2-oxoglutarate aminotransferase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	AACTCCCAGATTCATCTTTTT	0.498													99	422	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90161902	90161902	+	3'UTR	SNP	A	G	G	rs6500471	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90161902A>G	uc002fqp.2	+	3					uc002fqq.2_3'UTR					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		ATATGTTCCAAGACCCTAAAA	0.537													4	58	---	---	---	---	PASS
KRTAP4-7	100132476	broad.mit.edu	37	17	39240627	39240627	+	Missense_Mutation	SNP	T	C	C	rs139671425	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39240627T>C	uc010wfn.1	+	1	169	c.169T>C	c.(169-171)TCT>CCT	p.S57P		NM_033061	NP_149050			keratin associated protein 4-7												0						GTGCTGCCAGTCTGTGTGCTG	0.493													6	32	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45219300	45219300	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45219300A>T	uc002ild.3	-	12	1597	c.1470T>A	c.(1468-1470)CAT>CAA	p.H490Q	CDC27_uc002ile.3_Missense_Mutation_p.H496Q|CDC27_uc002ilf.3_Missense_Mutation_p.H489Q|CDC27_uc010wkp.1_Missense_Mutation_p.H429Q|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	490					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|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|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						GAGAAGGTAGATGGCTCAAAA	0.383													74	440	---	---	---	---	PASS
DLX4	1748	broad.mit.edu	37	17	48050513	48050513	+	Silent	SNP	G	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48050513G>C	uc002ipv.2	+	2	631	c.360G>C	c.(358-360)CCG>CCC	p.P120P	DLX4_uc002ipw.2_Silent_p.P48P	NM_138281	NP_612138	Q92988	DLX4_HUMAN	distal-less homeobox 4 isoform a	120	Homeobox.				multicellular organismal development	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TCCGCAAGCCGAGGACCATCT	0.677													10	41	---	---	---	---	PASS
SEPT9	10801	broad.mit.edu	37	17	75316328	75316328	+	Intron	SNP	A	G	G	rs140915871	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75316328A>G	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_5'UTR	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			TGAGAGAGGGAGGGCGACGGG	0.473													6	32	---	---	---	---	PASS
CELF4	56853	broad.mit.edu	37	18	34855139	34855139	+	Silent	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34855139G>A	uc002lae.2	-	4	912	c.516C>T	c.(514-516)TTC>TTT	p.F172F	CELF4_uc010dnd.1_Silent_p.F171F|CELF4_uc002lag.2_Silent_p.F162F|CELF4_uc002laf.2_Silent_p.F167F|CELF4_uc002lai.2_Silent_p.F157F|CELF4_uc002lah.1_5'Flank|CELF4_uc002laj.1_5'Flank	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1	172	Sufficient for RNA-binding and MSE- dependent splicing activity.|RRM 2.				embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						CAAAGGCCTCGAAAAGGCGGC	0.622													46	153	---	---	---	---	PASS
ZNF516	9658	broad.mit.edu	37	18	74154244	74154244	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74154244G>T	uc010dqx.1	-	2	1002	c.767C>A	c.(766-768)GCC>GAC	p.A256D	ZNF516_uc002lme.2_RNA	NM_014643	NP_055458	Q92618	ZN516_HUMAN	zinc finger protein 516	256	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		CTGGCTGAAGGCCTGGCCACA	0.687													6	38	---	---	---	---	PASS
ADNP2	22850	broad.mit.edu	37	18	77890984	77890984	+	Splice_Site	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77890984A>G	uc002lnw.2	+	3	564	c.109_splice	c.e3-2	p.D37_splice		NM_014913	NP_055728	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2						cellular response to oxidative stress|cellular response to retinoic acid|negative regulation of cell death|neuron differentiation|positive regulation of cell growth	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|breast(3)|central_nervous_system(1)	8		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		CCTTTTTAAAAGGACCTTAAA	0.289													3	194	---	---	---	---	PASS
GAMT	2593	broad.mit.edu	37	19	1398924	1398924	+	Silent	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1398924G>A	uc002lsj.2	-	5	638	c.561C>T	c.(559-561)ATC>ATT	p.I187I	uc002lsi.1_5'Flank|GAMT_uc002lsk.2_Silent_p.I187I	NM_000156	NP_000147	Q14353	GAMT_HUMAN	guanidinoacetate N-methyltransferase isoform a	187					creatine biosynthetic process|muscle contraction	cytosol	guanidinoacetate N-methyltransferase activity				0		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Lung NSC(49;0.000195)|Breast(49;0.000231)|all_lung(49;0.000247)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Creatine(DB00148)	CCTCAAACATGATGGTGATGT	0.612													14	55	---	---	---	---	PASS
EMR1	2015	broad.mit.edu	37	19	6896425	6896425	+	Silent	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6896425C>T	uc002mfw.2	+	3	149	c.111C>T	c.(109-111)GAC>GAT	p.D37D	EMR1_uc010dvc.2_Silent_p.D37D|EMR1_uc010dvb.2_Silent_p.D37D|EMR1_uc010xji.1_Silent_p.D37D|EMR1_uc010xjj.1_Silent_p.D37D	NM_001974	NP_001965	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone	37	Extracellular (Potential).|EGF-like 1.				cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(3)|lung(1)|skin(1)	5	all_hematologic(4;0.166)					ACTGTAGAGACAGTACCTTGT	0.463													52	263	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8167722	8167722	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8167722C>A	uc002mjf.2	-	39	4996	c.4975G>T	c.(4975-4977)GGC>TGC	p.G1659C		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1659	TB 7.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						TGACATGTGCCGTTATAGTGC	0.517													3	145	---	---	---	---	PASS
WIZ	58525	broad.mit.edu	37	19	15533882	15533882	+	3'UTR	SNP	T	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15533882T>A	uc002nbc.2	-	8					WIZ_uc002nba.3_3'UTR|WIZ_uc002nbb.3_3'UTR	NM_021241	NP_067064	O95785	WIZ_HUMAN	widely-interspaced zinc finger motifs							nucleus	zinc ion binding				0						TGGAATGCTTTTGTGTTAGGG	0.378													17	68	---	---	---	---	PASS
ZNF234	10780	broad.mit.edu	37	19	44662288	44662288	+	3'UTR	SNP	C	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44662288C>A	uc002oym.2	+	6					ZNF234_uc002oyl.3_3'UTR	NM_006630	NP_006621	Q14588	ZN234_HUMAN	zinc finger protein 234						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)				AAAAAAAAAACAGAACTCATG	0.328													4	60	---	---	---	---	PASS
DHX34	9704	broad.mit.edu	37	19	47883025	47883025	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47883025C>T	uc010xyn.1	+	14	3106	c.2765C>T	c.(2764-2766)GCC>GTC	p.A922V	DHX34_uc010xyo.1_Missense_Mutation_p.A51V	NM_014681	NP_055496	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	922						intracellular	ATP binding|ATP-dependent helicase activity|RNA binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		CGCCTGGTGGCCGATGGCTGG	0.632													4	107	---	---	---	---	PASS
SIGLEC8	27181	broad.mit.edu	37	19	51961243	51961243	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51961243C>G	uc002pwt.2	-	1	466	c.399G>C	c.(397-399)TGG>TGC	p.W133C	SIGLEC8_uc010yda.1_Missense_Mutation_p.W133C|SIGLEC8_uc002pwu.2_RNA|SIGLEC8_uc010eox.2_Missense_Mutation_p.W133C	NM_014442	NP_055257	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8 precursor	133	Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding|transmembrane receptor activity			ovary(2)|kidney(1)|central_nervous_system(1)|skin(1)	5		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		ATTTGTAACTCCATTTCATGC	0.502													67	281	---	---	---	---	PASS
ZNF578	147660	broad.mit.edu	37	19	53014324	53014324	+	Silent	SNP	T	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53014324T>A	uc002pzp.3	+	6	934	c.690T>A	c.(688-690)TCT>TCA	p.S230S		NM_001099694	NP_001093164	Q96N58	ZN578_HUMAN	zinc finger protein 578	5					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GAGAAAAATCTTTCCAATGTA	0.318													5	189	---	---	---	---	PASS
CNOT3	4849	broad.mit.edu	37	19	54647188	54647188	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54647188C>A	uc002qdj.1	+	4	415	c.104C>A	c.(103-105)GCA>GAA	p.A35E	CNOT3_uc010yel.1_Missense_Mutation_p.A35E|CNOT3_uc002qdi.2_5'UTR|CNOT3_uc002qdk.1_Missense_Mutation_p.A35E|CNOT3_uc010ere.1_5'Flank	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	35					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CTCCACAATGCAGCCAACGCG	0.517													4	125	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57327461	57327461	+	Silent	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57327461G>T	uc002qnu.2	-	7	2700	c.2349C>A	c.(2347-2349)GCC>GCA	p.A783A	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Silent_p.A754A|PEG3_uc002qnv.2_Silent_p.A783A|PEG3_uc002qnw.2_Silent_p.A659A|PEG3_uc002qnx.2_Silent_p.A657A|PEG3_uc010etr.2_Silent_p.A783A	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	783					apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		CTTCCACAGAGGCTAAGCTAT	0.428													127	480	---	---	---	---	PASS
PDYN	5173	broad.mit.edu	37	20	1961113	1961113	+	Nonsense_Mutation	SNP	A	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1961113A>T	uc010gaj.2	-	3	863	c.621T>A	c.(619-621)TAT>TAA	p.Y207*	uc002wfu.1_Intron|PDYN_uc002wfv.2_Nonsense_Mutation_p.Y207*|PDYN_uc010zpt.1_Nonsense_Mutation_p.Y52*	NM_024411	NP_077722	P01213	PDYN_HUMAN	beta-neoendorphin-dynorphin preproprotein	207					cell death|neuropeptide signaling pathway|synaptic transmission	extracellular region|plasma membrane	opioid peptide activity			upper_aerodigestive_tract(1)|ovary(1)	2						AGAAGCCCCCATAGCGTTTGT	0.597													49	202	---	---	---	---	PASS
GSS	2937	broad.mit.edu	37	20	33529582	33529582	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33529582G>T	uc002xbg.2	-	6	622	c.542C>A	c.(541-543)TCT>TAT	p.S181Y	GSS_uc010zun.1_Missense_Mutation_p.S53Y|GSS_uc010zuo.1_Intron|GSS_uc010zup.1_Missense_Mutation_p.S112Y|GSS_uc002xbh.2_RNA|GSS_uc010gez.1_Intron	NM_000178	NP_000169	P48637	GSHB_HUMAN	glutathione synthetase	181					nervous system development|response to oxidative stress|xenobiotic metabolic process	cytosol	ATP binding|glutathione binding|glutathione synthase activity|magnesium ion binding|protein homodimerization activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(18;0.035)		Glutathione(DB00143)|Glycine(DB00145)|L-Cysteine(DB00151)	GGGATTATTAGAGAGGATCTT	0.517													32	135	---	---	---	---	PASS
TP53TG5	27296	broad.mit.edu	37	20	44004008	44004008	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44004008C>T	uc002xny.2	-	4	520	c.439G>A	c.(439-441)GCA>ACA	p.A147T	SYS1_uc002xnw.1_3'UTR|SYS1-DBNDD2_uc002xnx.2_Intron	NM_014477	NP_055292	Q9Y2B4	T53G5_HUMAN	TP53-target gene 5 protein	147					intracellular signal transduction|negative regulation of cell growth	cytoplasm|nucleus				central_nervous_system(1)	1						CGTGGCATTGCCGCCAATGAC	0.512													5	437	---	---	---	---	PASS
WFDC8	90199	broad.mit.edu	37	20	44190839	44190839	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44190839G>A	uc002xow.2	-	2	125	c.46C>T	c.(46-48)CCC>TCC	p.P16S	WFDC8_uc002xox.2_Missense_Mutation_p.P16S	NM_181510	NP_852611	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8 precursor	16						extracellular region	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)				GAGAAGGTGGGGCTATGGAGA	0.403													4	80	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	11014987	11014987	+	RNA	SNP	A	G	G			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11014987A>G	uc002yis.1	-	7		c.1459T>C						P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			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)		CTATAGTTTCAATAGCAGACT	0.388													3	79	---	---	---	---	PASS
PKNOX1	5316	broad.mit.edu	37	21	44448816	44448816	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44448816A>T	uc002zcq.1	+	10	1119	c.931A>T	c.(931-933)ATC>TTC	p.I311F	PKNOX1_uc002zcp.1_Missense_Mutation_p.I311F|PKNOX1_uc011aex.1_Missense_Mutation_p.I194F	NM_004571	NP_004562	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	311	Homeobox; TALE-type.						sequence-specific DNA binding			large_intestine(2)	2						CTCCAGGTTCATCAATGCCAG	0.428													108	494	---	---	---	---	PASS
TXNRD2	10587	broad.mit.edu	37	22	19883099	19883099	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19883099C>T	uc011ahc.1	-	11	813	c.780G>A	c.(778-780)ATG>ATA	p.M260I	TXNRD2_uc002zql.1_Missense_Mutation_p.M14I|TXNRD2_uc002zqm.1_RNA|TXNRD2_uc002zqn.1_RNA|TXNRD2_uc002zqo.1_RNA|TXNRD2_uc002zqp.1_RNA|TXNRD2_uc002zqr.1_Missense_Mutation_p.M259I|TXNRD2_uc010grv.1_Missense_Mutation_p.M260I|TXNRD2_uc002zqj.1_RNA|TXNRD2_uc002zqs.2_Missense_Mutation_p.M228I	NM_006440	NP_006431	Q9NNW7	TRXR2_HUMAN	thioredoxin reductase 2 precursor	260					cell redox homeostasis|response to oxygen radical	mitochondrion	flavin adenine dinucleotide binding|NADP binding|thioredoxin-disulfide reductase activity			ovary(2)	2	Colorectal(54;0.0993)					CCATGGAGGACATTTGCTGCA	0.627													23	68	---	---	---	---	PASS
CHEK2	11200	broad.mit.edu	37	22	29083962	29083962	+	Missense_Mutation	SNP	G	C	C	rs138839489	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29083962G>C	uc003adu.1	-	15	1627	c.1555C>G	c.(1555-1557)CGA>GGA	p.R519G	CHEK2_uc003ads.1_Missense_Mutation_p.R298G|CHEK2_uc010gvh.1_Missense_Mutation_p.R428G|CHEK2_uc010gvi.1_Missense_Mutation_p.R368G|CHEK2_uc010gvj.1_RNA|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Missense_Mutation_p.R562G|CHEK2_uc003adv.1_Missense_Mutation_p.R490G|CHEK2_uc003adw.1_Missense_Mutation_p.R519G|CHEK2_uc003adx.1_Missense_Mutation_p.R298G|CHEK2_uc003ady.1_Missense_Mutation_p.R508G|CHEK2_uc003adz.1_Missense_Mutation_p.R323G	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a	519					cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20						GGCCGCTTTCGACTAGTAGAA	0.463			F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				3	59	---	---	---	---	PASS
PNPLA4	8228	broad.mit.edu	37	X	7889834	7889834	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7889834G>T	uc011mhq.1	-	4	493	c.331C>A	c.(331-333)CTG>ATG	p.L111M	PNPLA4_uc011mhr.1_Missense_Mutation_p.L111M|PNPLA4_uc011mhs.1_Missense_Mutation_p.L24M	NM_004650	NP_004641	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	111	Patatin.				lipid catabolic process		triglyceride lipase activity				0		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				GATACGTGCAGTCGGTTCTGG	0.453													22	154	---	---	---	---	PASS
FAM9A	171482	broad.mit.edu	37	X	8764374	8764374	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8764374A>T	uc004csg.2	-	6	534	c.423T>A	c.(421-423)GAT>GAA	p.D141E		NM_174951	NP_777611	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	141						nucleolus					0		Hepatocellular(5;0.219)				AAGCTGCTTTATCTATTTTTA	0.294													16	62	---	---	---	---	PASS
MIR222	407007	broad.mit.edu	37	X	45606471	45606471	+	RNA	SNP	C	T	T	rs72631825		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45606471C>T	hsa-mir-222|MI0000299	-			c.60C>T			uc011mle.1_5'Flank|MIR221_hsa-mir-221|MI0000298_5'Flank|uc011mlf.1_RNA																	0						CTGCTGATTACGAAAGACAGG	0.493													6	27	---	---	---	---	PASS
COL4A6	1288	broad.mit.edu	37	X	107431170	107431170	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107431170G>A	uc004enw.3	-	22	1781	c.1678C>T	c.(1678-1680)CGG>TGG	p.R560W	COL4A6_uc004env.3_Missense_Mutation_p.R559W|COL4A6_uc011msn.1_Missense_Mutation_p.R559W|COL4A6_uc010npk.2_Missense_Mutation_p.R559W	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	560	Triple-helical region.|Cell attachment site (Potential).				cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						GAATCACCCCGATCTCCTGGC	0.537									Alport_syndrome_with_Diffuse_Leiomyomatosis				36	285	---	---	---	---	PASS
COL4A5	1287	broad.mit.edu	37	X	107935977	107935977	+	Splice_Site	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107935977G>T	uc004enz.1	+	49	4731	c.4529_splice	c.e49-1	p.G1510_splice	COL4A5_uc011mso.1_Splice_Site_p.G1507_splice|COL4A5_uc011msp.1_Splice_Site_p.G186_splice	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor						axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4						AATCTTTCTAGGGACGGCTGG	0.403									Alport_syndrome_with_Diffuse_Leiomyomatosis				34	127	---	---	---	---	PASS
ATP1B4	23439	broad.mit.edu	37	X	119509282	119509282	+	Silent	SNP	C	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119509282C>T	uc004esr.2	+	5	702	c.618C>T	c.(616-618)TAC>TAT	p.Y206Y	ATP1B4_uc004esq.2_Silent_p.Y202Y|ATP1B4_uc011mtx.1_Silent_p.Y171Y|ATP1B4_uc011mty.1_Silent_p.Y163Y	NM_001142447	NP_001135919	Q9UN42	AT1B4_HUMAN	ATPase, (Na+)/K+ transporting, beta 4	206	Perinuclear space (Potential).				ATP biosynthetic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to plasma membrane|nuclear inner membrane	sodium:potassium-exchanging ATPase activity			ovary(1)|skin(1)	2						CGGGGCAGTACTTCATCCAAG	0.463													58	239	---	---	---	---	PASS
CT47B1	643311	broad.mit.edu	37	X	120009345	120009345	+	Silent	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120009345G>T	uc011muc.1	-	1	435	c.180C>A	c.(178-180)GGC>GGA	p.G60G		NM_001145718	NP_001139190	P0C2W7	CT47B_HUMAN	cancer/testis antigen family 147, member B1	60											0						CCTCCCCGAGGCCTTCCACGG	0.716													19	97	---	---	---	---	PASS
IGSF1	3547	broad.mit.edu	37	X	130411141	130411141	+	Silent	SNP	G	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130411141G>T	uc004ewd.2	-	14	2618	c.2380C>A	c.(2380-2382)CGA>AGA	p.R794R	IGSF1_uc004ewe.3_Silent_p.R788R|IGSF1_uc004ewf.2_Silent_p.R774R	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	794	Extracellular (Potential).|Ig-like C2-type 8.				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5						AAAGTCACTCGGGCACCAGGG	0.433													6	352	---	---	---	---	PASS
MTMR1	8776	broad.mit.edu	37	X	149900042	149900042	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149900042A>C	uc004fei.2	+	8	953	c.818A>C	c.(817-819)GAT>GCT	p.D273A	MTMR1_uc011mya.1_Missense_Mutation_p.D179A|MTMR1_uc004feg.1_Missense_Mutation_p.D273A|MTMR1_uc004feh.1_Missense_Mutation_p.D281A|MTMR1_uc004fej.2_RNA|MTMR1_uc010ntf.2_RNA	NM_003828	NP_003819	Q13613	MTMR1_HUMAN	myotubularin-related protein 1	273	Myotubularin phosphatase.					plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					AGTGTAAAAGATGATGACCTT	0.368													46	187	---	---	---	---	PASS
CNN3	1266	broad.mit.edu	37	1	95365258	95365258	+	Intron	DEL	T	-	-	rs66527009		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95365258delT	uc010otw.1	-						CNN3_uc010otv.1_Intron|CNN3_uc001dqz.3_Intron|CNN3_uc010otx.1_Intron	NM_001839	NP_001830	Q15417	CNN3_HUMAN	calponin 3						actomyosin structure organization|smooth muscle contraction		actin binding|calmodulin binding|tropomyosin binding|troponin C binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)		AAAAAGAAAATTTTAAAGTCA	0.353													6	4	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148349431	148349432	+	5'Flank	INS	-	G	G	rs67020224		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148349431_148349432insG	uc001eqf.2	-						LOC200030_uc001eqe.2_5'Flank|LOC200030_uc001eqg.2_5'Flank|NBPF14_uc009wkf.1_5'Flank|uc001erd.3_5'Flank|uc001erc.3_5'Flank|uc010paj.1_5'Flank|uc010pav.1_5'Flank|uc010paw.1_5'Flank	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						GGGCTGACACTGGGGGGCCAGA	0.559													13	7	---	---	---	---	
GNPAT	8443	broad.mit.edu	37	1	231401975	231401975	+	Intron	DEL	A	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231401975delA	uc001hup.3	+						GNPAT_uc009xfp.2_Intron	NM_014236	NP_055051	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase						ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity			ovary(3)|breast(1)	4	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				ACTAATTTCTAAATTTACTGC	0.393													198	155	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19934791	19934794	+	IGR	DEL	GAAA	-	-	rs72315540	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19934791_19934794delGAAA								OSR1 (376419 upstream) : TTC32 (161724 downstream)																							aggaaggaaggaaagaaggaagga	0.064													0	9	---	---	---	---	
DYNC2LI1	51626	broad.mit.edu	37	2	44032038	44032038	+	Intron	DEL	A	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44032038delA	uc002rtk.2	+						DYNC2LI1_uc002rtj.2_Intron|DYNC2LI1_uc002rtl.2_Intron|DYNC2LI1_uc010ynz.1_Intron	NM_016008	NP_057092	Q8TCX1	DC2L1_HUMAN	dynein 2 light intermediate chain isoform 1							apical part of cell|axonemal dynein complex|cilium axoneme|cytoplasm|microtubule|motile primary cilium	motor activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TGTGGGGGTTAAAAAAAAAAA	0.363													4	2	---	---	---	---	
SNRPG	6637	broad.mit.edu	37	2	70515476	70515480	+	Intron	DEL	TTTAC	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70515476_70515480delTTTAC	uc002sgp.2	-						SNRPG_uc002sgo.2_Intron	NM_003096	NP_003087	P62308	RUXG_HUMAN	small nuclear ribonucleoprotein polypeptide G						histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|RNA binding				0						catttttgtatttacttccacattt	0.117													4	2	---	---	---	---	
PTCD3	55037	broad.mit.edu	37	2	86335250	86335250	+	Intron	DEL	A	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86335250delA	uc002sqw.2	+						POLR1A_uc002sqs.2_5'Flank|POLR1A_uc002sqv.2_5'Flank|PTCD3_uc010ytc.1_Intron	NM_017952	NP_060422	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3 precursor							mitochondrion	protein binding			ovary(1)	1						ccctgtctctaaaaaaaaaaa	0.154													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91764888	91764903	+	IGR	DEL	TGTGTGTGTGTGTGTG	-	-	rs139523492		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91764888_91764903delTGTGTGTGTGTGTGTG								None (None upstream) : LOC654342 (40289 downstream)																							tgtacgtatatgtgtgtgtgtgtgtgtgtgtgtgtg	0.000													5	6	---	---	---	---	
IL1R2	7850	broad.mit.edu	37	2	102632562	102632563	+	Intron	DEL	AC	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102632562_102632563delAC	uc002tbm.2	+						IL1R2_uc002tbn.2_Intron|IL1R2_uc002tbo.1_Intron	NM_004633	NP_004624	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II precursor						immune response	integral to membrane|plasma membrane	interleukin-1, Type II, blocking receptor activity			ovary(1)|breast(1)	2					Anakinra(DB00026)	TTCTTTTTTTACTAGCCATAAA	0.257													19	14	---	---	---	---	
ANKAR	150709	broad.mit.edu	37	2	190541861	190541861	+	Intron	DEL	G	-	-	rs56090484		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190541861delG	uc002uqw.1	+						ANKAR_uc002uqu.2_Intron|ANKAR_uc002uqv.1_Intron	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing							integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			ttttttttttggaacagagtc	0.124													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	209777764	209777765	+	IGR	DEL	AC	-	-	rs111770665		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209777764_209777765delAC								PTH2R (72946 upstream) : MAP2 (511006 downstream)																							ttgTGTGTGTacacacacacac	0.020													3	3	---	---	---	---	
DBR1	51163	broad.mit.edu	37	3	137888783	137888783	+	Intron	DEL	A	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137888783delA	uc003erv.2	-						DBR1_uc003eru.2_Intron	NM_016216	NP_057300	Q9UK59	DBR1_HUMAN	debranching enzyme homolog 1							nucleus	metal ion binding|RNA lariat debranching enzyme activity				0						tcaaaaaaagaaaaaaaaaaG	0.149													4	3	---	---	---	---	
HTR3D	200909	broad.mit.edu	37	3	183756837	183756838	+	3'UTR	INS	-	GTCAGTCCAAATT	GTCAGTCCAAATT	rs66883074		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183756837_183756838insGTCAGTCCAAATT	uc011bqv.1	+	8					HTR3D_uc003fmj.2_3'UTR|HTR3D_uc011bqu.1_3'UTR|HTR3D_uc010hxp.2_3'UTR	NM_001163646	NP_001157118	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine receptor 3 subunit D isoform							integral to membrane|plasma membrane	extracellular ligand-gated ion channel activity|receptor activity				0	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			CAGGCTCTCAGTCAGCCTTGTG	0.515													9	15	---	---	---	---	
ZDHHC19	131540	broad.mit.edu	37	3	195937314	195937315	+	Intron	INS	-	TAAAG	TAAAG	rs59406858		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195937314_195937315insTAAAG	uc003fwc.2	-						ZDHHC19_uc010hzz.2_Intron|ZDHHC19_uc010iaa.2_Intron|ZDHHC19_uc010iab.2_Intron	NM_001039617	NP_001034706	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC domain containing 19							integral to membrane	acyltransferase activity|zinc ion binding			ovary(3)	3	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		agagaaagaaagaaagaaaaga	0.233													6	3	---	---	---	---	
FSTL5	56884	broad.mit.edu	37	4	162508449	162508449	+	Intron	DEL	T	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162508449delT	uc003iqh.2	-						FSTL5_uc003iqi.2_Intron|FSTL5_uc010iqv.2_Intron	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a							extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		AAATTTTGTGTTTTTTTTTTT	0.219													7	4	---	---	---	---	
AFF4	27125	broad.mit.edu	37	5	132234183	132234183	+	Intron	DEL	T	-	-	rs67779737		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132234183delT	uc003kyd.2	-						AFF4_uc011cxk.1_Intron|AFF4_uc003kye.1_Intron	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31						transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			tcttcttgtcttttttttttt	0.119													10	5	---	---	---	---	
SPINK6	404203	broad.mit.edu	37	5	147585796	147585803	+	Intron	DEL	ACCTAACC	-	-	rs62388546		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147585796_147585803delACCTAACC	uc003lpa.2	+							NM_205841	NP_995313	Q6UWN8	ISK6_HUMAN	serine protease inhibitor, Kazal type 6							extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTTAAAAGAACCTAACCACACATTCTC	0.216													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	42521030	42521037	+	IGR	DEL	GAAGGAAG	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42521030_42521037delGAAGGAAG								TRERF1 (101165 upstream) : UBR2 (11021 downstream)																							aagaaaaaaCgaaggaaggaaggaagga	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	96734249	96734252	+	IGR	DEL	TGTG	-	-	rs67837506		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96734249_96734252delTGTG								FUT9 (70762 upstream) : KIAA0776 (235450 downstream)																							Tctcactgcttgtgtgtgtgtgtg	0.221													4	2	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	33066270	33066270	+	Intron	DEL	T	-	-	rs34317509		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33066270delT	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						tgcccggccAttttttttttt	0.000													5	3	---	---	---	---	
SLC25A32	81034	broad.mit.edu	37	8	104426906	104426907	+	Intron	DEL	AC	-	-	rs59125759		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104426906_104426907delAC	uc003yll.2	-						SLC25A32_uc011lhr.1_Intron|DCAF13_uc003ylm.1_5'Flank|DCAF13_uc003yln.2_5'Flank|DCAF13_uc003ylo.2_5'Flank	NM_030780	NP_110407	Q9H2D1	MFTC_HUMAN	solute carrier family 25, member 32						folic acid metabolic process|mitochondrial transport	integral to membrane|mitochondrial inner membrane	binding|folic acid transporter activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	GCGGACAGCAACGCTCCCTTCA	0.599													10	10	---	---	---	---	
ARID5B	84159	broad.mit.edu	37	10	63662433	63662434	+	Intron	DEL	TG	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63662433_63662434delTG	uc001jlt.1	+						ARID5B_uc010qil.1_Intron	NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)						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)					TGTTCAAGGAtgtgtgtgtgtg	0.302													4	2	---	---	---	---	
COL17A1	1308	broad.mit.edu	37	10	105800353	105800360	+	Intron	DEL	TGGATAGG	-	-	rs56889497		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105800353_105800360delTGGATAGG	uc001kxr.2	-							NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen						cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		gatggatggatggataggtggatggatg	0.082													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	135455131	135455131	+	IGR	DEL	C	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135455131delC								FRG2B (14832 upstream) : LOC653544 (35148 downstream)																							TACAAAAAAACGATGAGGAAA	0.343													4	3	---	---	---	---	
C2CD3	26005	broad.mit.edu	37	11	73796188	73796188	+	Intron	DEL	T	-	-	rs74787473		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73796188delT	uc001ouu.2	-						C2CD3_uc001out.2_Intron	NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3							centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)					AATGCCTTCAttttttttttt	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31920768	31920775	+	IGR	DEL	AAGGAAGA	-	-	rs12315658	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31920768_31920775delAAGGAAGA								AMN1 (38660 upstream) : H3F3C (23346 downstream)																							ggaaggaaggaaggaagaaaggaaggaa	0.000													3	6	---	---	---	---	
PDS5B	23047	broad.mit.edu	37	13	33344182	33344183	+	Intron	INS	-	T	T			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33344182_33344183insT	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		TAGATAACAGATTTTTTTGTTT	0.272													15	7	---	---	---	---	
SLC7A7	9056	broad.mit.edu	37	14	23244457	23244472	+	Intron	DEL	GTACCATTCCTTAGAG	-	-	rs151185590	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23244457_23244472delGTACCATTCCTTAGAG	uc001wgr.3	-						SLC7A7_uc001wgs.3_Intron|SLC7A7_uc001wgt.3_Intron|SLC7A7_uc001wgu.3_Intron|SLC7A7_uc001wgv.3_Intron	NM_003982	NP_003973	Q9UM01	YLAT1_HUMAN	solute carrier family 7 member 7						blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity			ovary(1)|breast(1)	2	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		GAGCAGAGGTGTACCATTCCTTAGAGCATTTGGATT	0.412													2	4	---	---	---	---	
HHIPL1	84439	broad.mit.edu	37	14	100123116	100123118	+	Intron	DEL	AAG	-	-	rs35577018		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100123116_100123118delAAG	uc010avs.2	+						HHIPL1_uc001ygl.1_Intron	NM_001127258	NP_001120730	Q96JK4	HIPL1_HUMAN	HHIP-like protein 1 isoform a						carbohydrate metabolic process	extracellular region|membrane	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding|scavenger receptor activity			skin(2)	2		Melanoma(154;0.128)				tgtctgcaaaaagaaaagaaaag	0.000													17	8	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106714239	106714240	+	Intron	DEL	AC	-	-	rs112875057		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106714239_106714240delAC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						AGAAAGGAAAACCTTCTCCCGG	0.559													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32177847	32177850	+	IGR	DEL	TTGA	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32177847_32177850delTTGA								HERC2P4 (13973 upstream) : TP53TG3B (506991 downstream)																							GATGCAATTGTTGACTCACCAAGC	0.368													6	5	---	---	---	---	
C16orf46	123775	broad.mit.edu	37	16	81094613	81094614	+	3'UTR	INS	-	A	A	rs148109723	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81094613_81094614insA	uc002fgc.3	-	4					C16orf46_uc010chf.2_Intron|C16orf46_uc010vno.1_3'UTR	NM_152337	NP_689550	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46 isoform 2												0						AGTTGTACTACAAAAAAAAAAT	0.406													4	3	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43893771	43893776	+	Intron	DEL	CTGCCT	-	-	rs10585044		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43893771_43893776delCTGCCT	uc010dap.2	+						CRHR1_uc010wjx.1_Intron|CRHR1_uc002ijp.2_Intron|CRHR1_uc002ijm.2_Intron|CRHR1_uc002ijn.2_Intron|CRHR1_uc010dar.2_Intron|CRHR1_uc010dao.2_Intron|CRHR1_uc010daq.2_Intron|CRHR1_uc010das.1_Intron|CRHR1_uc002ijo.1_Intron	NM_001145146	NP_001138618	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		TGTCCTCTGCCTGCCTGGGGCCTTGG	0.597													16	13	---	---	---	---	
SEC14L1	6397	broad.mit.edu	37	17	75209703	75209704	+	Intron	INS	-	A	A	rs138018754	by1000genomes	TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75209703_75209704insA	uc002jto.2	+						SEC14L1_uc010dhc.2_Intron|SEC14L1_uc010wth.1_Intron|SEC14L1_uc002jtm.2_Intron|SEC14L1_uc010wti.1_Intron|SEC14L1_uc010wtj.1_Intron|SEC14L1_uc002jtr.2_Frame_Shift_Ins_p.G118fs	NM_003003	NP_002994	Q92503	S14L1_HUMAN	SEC14 (S. cerevisiae)-like 1 isoform a						transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2						GGCCAGGAGGGAGTGGCTTTGG	0.619													5	3	---	---	---	---	
SS18L1	26039	broad.mit.edu	37	20	60740585	60740599	+	Intron	DEL	TGCGTGCTGGGCTCG	-	-	rs60919036		TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60740585_60740599delTGCGTGCTGGGCTCG	uc002ycb.2	+						SS18L1_uc011aaa.1_Intron|SS18L1_uc002ybz.1_Intron|SS18L1_uc002yca.1_Intron|SS18L1_uc002ycc.1_Intron	NM_198935	NP_945173	O75177	CREST_HUMAN	SS18-like protein 1						chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore				ovary(2)	2	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			GGAGCACGGCTGCGTGCTGGGCTCGAGCGTAAGCG	0.609			T	SSX1	synovial sarcoma								14	7	---	---	---	---	
GAGE12J	729396	broad.mit.edu	37	X	49199424	49199425	+	Intron	DEL	GT	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49199424_49199425delGT	uc004dnl.3	+						GAGE13_uc004dnn.3_Intron|GAGE8_uc011mne.1_Intron|GAGE8_uc011mnf.1_Intron|GAGE8_uc011mng.1_Intron|GAGE2A_uc004dnr.3_Intron|GAGE8_uc004dnq.3_Intron|GAGE10_uc010nis.2_Intron|GAGE12J_uc004dnk.3_Intron|GAGE2D_uc004dnp.3_Intron|GAGE2C_uc004dno.3_Intron|GAGE2E_uc010njb.2_Intron|GAGE8_uc011mnh.1_Intron	NM_001098406	NP_001465	A6NER3	GG12J_HUMAN	G antigen 12J												0	Ovarian(276;0.236)					TGgtgtgtgcgtgtgtgtgtgt	0.351													4	2	---	---	---	---	
ACSL4	2182	broad.mit.edu	37	X	108911122	108911122	+	Intron	DEL	A	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108911122delA	uc004eoi.2	-						ACSL4_uc004eoj.2_Intron|ACSL4_uc004eok.2_Intron|ACSL4_uc010npp.1_Intron	NM_022977	NP_075266	O60488	ACSL4_HUMAN	acyl-CoA synthetase long-chain family member 4						fatty acid metabolic process|learning or memory|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			large_intestine(1)|lung(1)|ovary(1)	3					Icosapent(DB00159)|Troglitazone(DB00197)	actccatctcaaaaaaaaaaa	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	115853619	115853634	+	IGR	DEL	CCTTCCTTCCTTCCTT	-	-			TCGA-B0-5096-01A-01D-1421-08	TCGA-B0-5096-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115853619_115853634delCCTTCCTTCCTTCCTT								CXorf61 (259482 upstream) : None (None downstream)																							ccttccttccccttccttccttccttccttccttcc	0.000													5	3	---	---	---	---	
