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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	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
YARS	8565	broad.mit.edu	37	1	33244985	33244985	+	Nonsense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:33244985G>A	uc001bvy.1	-	12	2262	c.1474C>T	c.(1474-1476)CAG>TAG	p.Q492*	YARS_uc001bvw.1_Nonsense_Mutation_p.Q152*|YARS_uc001bvx.1_Nonsense_Mutation_p.Q143*	NM_003680	NP_003671	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	492					apoptosis|tyrosyl-tRNA aminoacylation	cytosol|extracellular space|nucleus|soluble fraction	ATP binding|interleukin-8 receptor binding|signal transducer activity|tRNA binding|tyrosine-tRNA ligase activity			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)	CTTTTTACCTGCAACTTCTCG	0.532													5	218	---	---	---	---	PASS
C1orf216	127703	broad.mit.edu	37	1	36181874	36181874	+	Missense_Mutation	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:36181874C>A	uc001bzh.1	-	2	537	c.49G>T	c.(49-51)GAC>TAC	p.D17Y		NM_152374	NP_689587	Q8TAB5	CA216_HUMAN	hypothetical protein LOC127703	17										skin(1)	1		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				GGAGGTGGGTCCCCCAGGAAT	0.577											OREG0013357	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	69	---	---	---	---	PASS
ZC3H12A	80149	broad.mit.edu	37	1	37948064	37948064	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:37948064G>A	uc001cbb.3	+	5	998	c.848G>A	c.(847-849)CGG>CAG	p.R283Q	ZC3H12A_uc001cbc.1_Missense_Mutation_p.G13S	NM_025079	NP_079355	Q5D1E8	ZC12A_HUMAN	zinc finger CCCH-type containing 12A	283					angiogenesis|apoptosis|cell differentiation	cytoplasm|nucleus|plasma membrane	endonuclease activity|metal ion binding			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCACTGGGCCGGCACGGGCCC	0.602													15	264	---	---	---	---	PASS
HIVEP3	59269	broad.mit.edu	37	1	42047570	42047570	+	Missense_Mutation	SNP	G	A	A	rs141506685	byFrequency	TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:42047570G>A	uc001cgz.3	-	4	4112	c.2899C>T	c.(2899-2901)CGC>TGC	p.R967C	HIVEP3_uc001cha.3_Missense_Mutation_p.R967C|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	967	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN (By similarity).				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GGTTTGGGGCGCATGTCAGAT	0.612													4	151	---	---	---	---	PASS
SPATA6	54558	broad.mit.edu	37	1	48771547	48771547	+	Nonsense_Mutation	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:48771547C>A	uc001crr.1	-	12	1363	c.1198G>T	c.(1198-1200)GAG>TAG	p.E400*	SPATA6_uc001crs.1_Nonsense_Mutation_p.E384*|SPATA6_uc010omv.1_Nonsense_Mutation_p.E386*	NM_019073	NP_061946	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6 precursor	400					cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1						AGGTCTCTCTCATCCTGAAAA	0.368													6	75	---	---	---	---	PASS
C1orf175	374977	broad.mit.edu	37	1	55175632	55175632	+	Missense_Mutation	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:55175632G>C	uc010ooe.1	+	24	4068	c.3744G>C	c.(3742-3744)TTG>TTC	p.L1248F	C1orf175_uc001cxq.2_Intron|C1orf175_uc001cxs.2_RNA|C1orf175_uc010ood.1_Missense_Mutation_p.L766F|C1orf175_uc010oof.1_RNA|C1orf175_uc001cxr.1_RNA|C1orf175_uc009vzq.1_RNA|C1orf175_uc001cxt.1_RNA|C1orf175_uc009vzr.1_Missense_Mutation_p.L449F	NM_001039464	NP_001034553	Q68CQ1	HEAT8_HUMAN	hypothetical protein LOC374977	1248						integral to membrane	binding				0						TGGATAACTTGAGACATGACC	0.512													4	172	---	---	---	---	PASS
BSND	7809	broad.mit.edu	37	1	55464936	55464936	+	Missense_Mutation	SNP	T	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:55464936T>A	uc001cye.2	+	1	320	c.77T>A	c.(76-78)ATG>AAG	p.M26K		NM_057176	NP_476517	Q8WZ55	BSND_HUMAN	barttin	26	Helical; (Potential).					basolateral plasma membrane|cytoplasm|integral to plasma membrane|protein complex				ovary(1)|skin(1)	2						ACGTTCCTCATGAGCCATGAT	0.612													42	117	---	---	---	---	PASS
HFM1	164045	broad.mit.edu	37	1	91818104	91818104	+	Missense_Mutation	SNP	T	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:91818104T>A	uc001doa.3	-	16	2036	c.1936A>T	c.(1936-1938)ACA>TCA	p.T646S	HFM1_uc009wdb.2_RNA|HFM1_uc010osu.1_Missense_Mutation_p.T325S|HFM1_uc010osv.1_Missense_Mutation_p.T330S	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	646	Helicase C-terminal.						ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AGAATATCTGTTTCACTGTAC	0.328													4	25	---	---	---	---	PASS
AGL	178	broad.mit.edu	37	1	100327202	100327202	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:100327202G>A	uc001dsi.1	+	3	626	c.226G>A	c.(226-228)GAT>AAT	p.D76N	AGL_uc001dsj.1_Missense_Mutation_p.D76N|AGL_uc001dsk.1_Missense_Mutation_p.D76N|AGL_uc001dsl.1_Missense_Mutation_p.D76N|AGL_uc001dsm.1_Missense_Mutation_p.D60N|AGL_uc001dsn.1_Missense_Mutation_p.D59N	NM_000642	NP_000633	P35573	GDE_HUMAN	amylo-1,6-glucosidase,	76	4-alpha-glucanotransferase.				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		AAGAGAAGATGATTCTGATAA	0.338													4	56	---	---	---	---	PASS
GPSM2	29899	broad.mit.edu	37	1	109439595	109439595	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:109439595G>A	uc010ovc.1	+	3	662	c.166G>A	c.(166-168)GAA>AAA	p.E56K	AKNAD1_uc010ovb.1_Intron|GPSM2_uc010ovd.1_Missense_Mutation_p.E56K|GPSM2_uc010ove.1_Missense_Mutation_p.E56K	NM_013296	NP_037428	P81274	GPSM2_HUMAN	LGN protein	56	TPR 1.				G-protein coupled receptor protein signaling pathway	cell cortex|nucleus	GTPase activator activity|identical protein binding			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		AGTTGGAACTGAAGACCTAAA	0.433													5	105	---	---	---	---	PASS
ITGA10	8515	broad.mit.edu	37	1	145537822	145537822	+	Missense_Mutation	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:145537822G>C	uc001eoa.2	+	21	2736	c.2660G>C	c.(2659-2661)GGA>GCA	p.G887A	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Missense_Mutation_p.G756A|ITGA10_uc009wiw.2_Missense_Mutation_p.G744A|ITGA10_uc010oyw.1_Missense_Mutation_p.G832A	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	887	Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TTCCAGACTGGAGCCAAGGTG	0.612													18	126	---	---	---	---	PASS
FLG2	388698	broad.mit.edu	37	1	152323611	152323611	+	Silent	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:152323611C>T	uc001ezw.3	-	3	6724	c.6651G>A	c.(6649-6651)GGG>GGA	p.G2217G	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	2217							calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTCCCTGTCTCCCATGACCTG	0.522													9	861	---	---	---	---	PASS
FLG2	388698	broad.mit.edu	37	1	152326558	152326558	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:152326558C>G	uc001ezw.3	-	3	3777	c.3704G>C	c.(3703-3705)AGA>ACA	p.R1235T	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1235	Ser-rich.						calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGTTTCCTGTCTCCCATGAAC	0.483													7	355	---	---	---	---	PASS
TMEM79	84283	broad.mit.edu	37	1	156255757	156255757	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:156255757C>G	uc010phi.1	+	2	936	c.740C>G	c.(739-741)ACC>AGC	p.T247S	TMEM79_uc001fod.2_Missense_Mutation_p.T88S|TMEM79_uc009wrw.2_Missense_Mutation_p.T247S	NM_032323	NP_115699	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	247	Helical; (Potential).					integral to membrane				central_nervous_system(1)	1	Hepatocellular(266;0.158)					GTCTTTGCCACCTTCCCCATT	0.602													11	463	---	---	---	---	PASS
FCRL2	79368	broad.mit.edu	37	1	157738319	157738319	+	Silent	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:157738319C>G	uc001fre.2	-	5	827	c.768G>C	c.(766-768)CTG>CTC	p.L256L	FCRL2_uc001frd.2_5'Flank|FCRL2_uc010phz.1_Silent_p.L256L|FCRL2_uc009wsp.2_Intron	NM_030764	NP_110391	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2 precursor	256	Ig-like C2-type 3.|Extracellular (Potential).				cell-cell signaling	integral to membrane|plasma membrane|soluble fraction	receptor activity|SH3/SH2 adaptor activity			ovary(1)|pancreas(1)	2	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GCTCTGCTGACAGGGAACGCT	0.532													148	222	---	---	---	---	PASS
SMG7	9887	broad.mit.edu	37	1	183520990	183520990	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:183520990C>T	uc001gqg.2	+	22	3460	c.3338C>T	c.(3337-3339)TCT>TTT	p.S1113F	SMG7_uc001gqf.2_Intron|SMG7_uc001gqh.2_Missense_Mutation_p.S1067F|SMG7_uc001gqi.2_Missense_Mutation_p.S1025F|SMG7_uc010poc.1_Missense_Mutation_p.S1121F	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1	1113					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						CCTGGACCTTCTGCTCTGGAG	0.498													6	68	---	---	---	---	PASS
C1orf107	27042	broad.mit.edu	37	1	210010489	210010489	+	Missense_Mutation	SNP	G	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:210010489G>T	uc001hhr.1	+	6	1071	c.995G>T	c.(994-996)CGC>CTC	p.R332L	C1orf107_uc009xcu.1_Missense_Mutation_p.R47L	NM_014388	NP_055203	Q68CQ4	DIEXF_HUMAN	digestive-organ expansion factor homolog	332					multicellular organismal development	nucleus					0				OV - Ovarian serous cystadenocarcinoma(81;0.0367)		AATAGCAGACGCCGAAGCCAG	0.512													10	36	---	---	---	---	PASS
MTR	4548	broad.mit.edu	37	1	237048463	237048463	+	Missense_Mutation	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:237048463G>C	uc001hyi.3	+	26	3142	c.2719G>C	c.(2719-2721)GAG>CAG	p.E907Q	MTR_uc010pxw.1_Missense_Mutation_p.E500Q|MTR_uc010pxx.1_Missense_Mutation_p.E856Q|MTR_uc010pxy.1_Missense_Mutation_p.E761Q	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine	907	B12-binding.				nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	TGAATACTTTGAGGAAATCAT	0.348													3	71	---	---	---	---	PASS
OR11L1	391189	broad.mit.edu	37	1	248004586	248004586	+	Missense_Mutation	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:248004586C>A	uc001idn.1	-	1	613	c.613G>T	c.(613-615)GCC>TCC	p.A205S		NM_001001959	NP_001001959	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L,	205	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			CACAGCACGGCAATTGACAGG	0.478													91	127	---	---	---	---	PASS
ADCY3	109	broad.mit.edu	37	2	25048948	25048948	+	Missense_Mutation	SNP	A	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr2:25048948A>G	uc002rfs.3	-	15	2742	c.2543T>C	c.(2542-2544)CTC>CCC	p.L848P	ADCY3_uc002rfr.3_Missense_Mutation_p.L435P|ADCY3_uc010ykm.1_Missense_Mutation_p.L849P	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3	848	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					GAGCATCATGAGGAACACCAT	0.617													25	40	---	---	---	---	PASS
ADCY3	109	broad.mit.edu	37	2	25061355	25061355	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr2:25061355C>G	uc002rfs.3	-	7	1691	c.1492G>C	c.(1492-1494)GAG>CAG	p.E498Q	ADCY3_uc002rfr.3_Missense_Mutation_p.E131Q|ADCY3_uc010ykm.1_Missense_Mutation_p.E498Q	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3	498	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					TTCTTCACCTCTGGCTTGGAG	0.433													4	198	---	---	---	---	PASS
ERLEC1	27248	broad.mit.edu	37	2	54024926	54024926	+	Missense_Mutation	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr2:54024926G>C	uc002rxl.2	+	5	764	c.484G>C	c.(484-486)GAA>CAA	p.E162Q	ASB3_uc002rxi.3_Intron|ERLEC1_uc002rxm.2_Missense_Mutation_p.E162Q|ERLEC1_uc002rxn.2_Missense_Mutation_p.E162Q	NM_015701	NP_056516	Q96DZ1	ERLEC_HUMAN	erlectin isoform 1	162	PRKCSH 1.				ER-associated protein catabolic process	endoplasmic reticulum lumen	glycoprotein binding|protein binding			ovary(2)	2						CCTTCTATTTGAAAAAGGTTG	0.289													3	160	---	---	---	---	PASS
SNRNP200	23020	broad.mit.edu	37	2	96969005	96969005	+	Silent	SNP	C	A	A	rs115907254	byFrequency	TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr2:96969005C>A	uc002svu.2	-	3	359	c.273G>T	c.(271-273)TCG>TCT	p.S91S		NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit	91						catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10						CAATGCCCTCCGACAGCAGAG	0.488													5	818	---	---	---	---	PASS
CNGA3	1261	broad.mit.edu	37	2	99013095	99013095	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr2:99013095G>A	uc002syt.2	+	8	1879	c.1462G>A	c.(1462-1464)GCA>ACA	p.A488T	CNGA3_uc002syu.2_Missense_Mutation_p.A470T|CNGA3_uc010fij.2_Missense_Mutation_p.A492T	NM_001298	NP_001289	Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3 isoform	488	cGMP.				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(5)|upper_aerodigestive_tract(1)	6						GGACTGTGAGGCAGGGCTGCT	0.557													6	53	---	---	---	---	PASS
IHH	3549	broad.mit.edu	37	2	219920495	219920495	+	Missense_Mutation	SNP	T	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr2:219920495T>C	uc002vjo.1	-	3	670	c.670A>G	c.(670-672)AGG>GGG	p.R224G		NM_002181	NP_002172	Q14623	IHH_HUMAN	Indian hedgehog homolog precursor	224					cell-cell signaling|intein-mediated protein splicing|proteolysis	extracellular space|plasma membrane	cholesterol binding|patched binding|peptidase activity			breast(1)	1		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000188)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCTCCCGGCCTCACGGCTGAC	0.677													4	104	---	---	---	---	PASS
FAM134A	79137	broad.mit.edu	37	2	220047043	220047043	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr2:220047043C>G	uc002vjw.3	+	9	1460	c.1324C>G	c.(1324-1326)CTC>GTC	p.L442V	FAM134A_uc010fwc.2_Missense_Mutation_p.L235V|FAM134A_uc002vjx.2_Intron	NM_024293	NP_077269	Q8NC44	F134A_HUMAN	hypothetical protein LOC79137	442						endoplasmic reticulum|integral to membrane				ovary(1)|central_nervous_system(1)	2		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GAGTGGTGGCCTCACTGCTCT	0.622													94	176	---	---	---	---	PASS
PTPRN	5798	broad.mit.edu	37	2	220164096	220164096	+	Missense_Mutation	SNP	G	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr2:220164096G>T	uc002vkz.2	-	11	1623	c.1534C>A	c.(1534-1536)CCA>ACA	p.P512T	PTPRN_uc010zlc.1_Missense_Mutation_p.P422T|PTPRN_uc002vla.2_Missense_Mutation_p.P483T	NM_002846	NP_002837	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	512	Extracellular (Potential).				response to reactive oxygen species	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|lung(1)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		GTGAGGGCTGGTCCCACCACA	0.557											OREG0015221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	164	---	---	---	---	PASS
COL4A4	1286	broad.mit.edu	37	2	227985759	227985759	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr2:227985759G>A	uc010zlt.1	-	5	952	c.298C>T	c.(298-300)CCT>TCT	p.P100S		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	100	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GCTGCTCCAGGAGGGCCGCGG	0.532													16	96	---	---	---	---	PASS
MLPH	79083	broad.mit.edu	37	2	238443205	238443205	+	Splice_Site	SNP	A	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr2:238443205A>C	uc002vwt.2	+	9	1248	c.1021_splice	c.e9-2	p.I341_splice	MLPH_uc002vws.2_Intron|MLPH_uc010fyt.1_Intron|MLPH_uc002vwu.2_Intron|MLPH_uc002vwv.2_Intron|MLPH_uc002vww.2_Intron|MLPH_uc002vwx.2_Intron|MLPH_uc010fyu.2_Splice_Site_p.I93_splice	NM_024101	NP_077006	Q9BV36	MELPH_HUMAN	melanophilin isoform 1								metal ion binding			ovary(1)	1		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		CTTCTGCTGCAGATCTTTGAG	0.537													41	118	---	---	---	---	PASS
CEP63	80254	broad.mit.edu	37	3	134278014	134278014	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr3:134278014C>T	uc003eqo.1	+	15	2145	c.1696C>T	c.(1696-1698)CAT>TAT	p.H566Y	CEP63_uc003eql.1_Intron|CEP63_uc003eqm.2_Intron|CEP63_uc003eqn.1_Intron	NM_025180	NP_079456	Q96MT8	CEP63_HUMAN	centrosomal protein 63 isoform a	566					cell division|DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitosis|signal transduction in response to DNA damage|spindle assembly	centrosome|cytosol|spindle pole	protein binding			ovary(1)	1						CCAGCACAGACATGATGGAAT	0.408													12	231	---	---	---	---	PASS
ZNF718	255403	broad.mit.edu	37	4	155125	155125	+	Missense_Mutation	SNP	A	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr4:155125A>G	uc003fzt.3	+	8	783	c.650A>G	c.(649-651)CAT>CGT	p.H217R	ZNF595_uc003fzu.1_Intron|ZNF718_uc010iaz.2_RNA|ZNF718_uc003fzw.3_5'UTR	NM_001039127	NP_001034216	Q3SXZ3	ZN718_HUMAN	zinc finger protein 718	217	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)		CTTACTAAACATAAGAGAATT	0.383													10	4	---	---	---	---	PASS
CNO	55330	broad.mit.edu	37	4	6718352	6718352	+	Missense_Mutation	SNP	A	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr4:6718352A>G	uc003gjp.1	+	1	511	c.416A>G	c.(415-417)GAG>GGG	p.E139G		NM_018366	NP_060836	Q9NUP1	CNO_HUMAN	cappuccino	139	Potential.				cellular membrane organization|post-Golgi vesicle-mediated transport	cytosol					0				Colorectal(103;0.0523)		GACCGGCTGGAGGCCTTCGTG	0.697													3	8	---	---	---	---	PASS
NCAPG	64151	broad.mit.edu	37	4	17829940	17829940	+	Missense_Mutation	SNP	T	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr4:17829940T>C	uc003gpp.2	+	12	1869	c.1693T>C	c.(1693-1695)TAT>CAT	p.Y565H	NCAPG_uc011bxj.1_Missense_Mutation_p.Y74H	NM_022346	NP_071741	Q9BPX3	CND3_HUMAN	chromosome condensation protein G	565					cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	protein binding			large_intestine(1)	1				STAD - Stomach adenocarcinoma(129;0.18)		TATTTTATGCTATGAACTGTT	0.348													3	52	---	---	---	---	PASS
PRMT10	90826	broad.mit.edu	37	4	148582038	148582038	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr4:148582038C>G	uc003ilc.2	-	7	1247	c.1105G>C	c.(1105-1107)GAG>CAG	p.E369Q	PRMT10_uc003ilb.2_Missense_Mutation_p.E13Q|PRMT10_uc003ild.2_Missense_Mutation_p.E256Q	NM_138364	NP_612373	Q6P2P2	ANM10_HUMAN	protein arginine methyltransferase 10	369						cytoplasm	binding|protein methyltransferase activity			ovary(1)|central_nervous_system(1)	2						TCAAAGCACTCTGTCAAAGCC	0.328													3	48	---	---	---	---	PASS
PIK3R1	5295	broad.mit.edu	37	5	67569222	67569222	+	Missense_Mutation	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr5:67569222G>C	uc003jva.2	+	3	899	c.339G>C	c.(337-339)TTG>TTC	p.L113F	PIK3R1_uc003jvb.2_Missense_Mutation_p.L113F	NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1	113	Rho-GAP.				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.?(2)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)	TTGCAGCTTTGACTCTCCCGG	0.423			Mis|F|O		gliobastoma|ovarian|colorectal					TCGA GBM(4;<1E-08)			12	222	---	---	---	---	PASS
TNPO1	3842	broad.mit.edu	37	5	72183038	72183038	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr5:72183038C>T	uc003kck.3	+	12	1439	c.1292C>T	c.(1291-1293)GCA>GTA	p.A431V	TNPO1_uc011csj.1_Missense_Mutation_p.A381V|TNPO1_uc003kch.2_Missense_Mutation_p.A423V|TNPO1_uc003kci.3_Missense_Mutation_p.A423V|TNPO1_uc003kcg.3_Missense_Mutation_p.A423V	NM_002270	NP_002261	Q92973	TNPO1_HUMAN	transportin 1 isoform 1	431	HEAT 4.				interspecies interaction between organisms|mRNA metabolic process|protein import into nucleus, translocation	cytosol|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			skin(3)|urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)	7		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		GTTTTAGGAGCAATTGCTGAA	0.353													26	42	---	---	---	---	PASS
MSH3	4437	broad.mit.edu	37	5	80074605	80074605	+	Silent	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr5:80074605C>G	uc003kgz.2	+	17	2638	c.2385C>G	c.(2383-2385)CTC>CTG	p.L795L		NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3	795					maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		TGAATCAGCTCCGGGAGCAGC	0.393								MMR					9	71	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	89921057	89921057	+	Silent	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr5:89921057C>T	uc003kju.2	+	6	765	c.669C>T	c.(667-669)GAC>GAT	p.D223D	GPR98_uc003kjt.2_Translation_Start_Site	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	223	Calx-beta 2.|Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TACTCGATGACGAGGTTGGCT	0.453													4	14	---	---	---	---	PASS
AFF4	27125	broad.mit.edu	37	5	132228778	132228778	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr5:132228778C>G	uc003kyd.2	-	12	2748	c.2340G>C	c.(2338-2340)AAG>AAC	p.K780N	AFF4_uc011cxk.1_Missense_Mutation_p.K458N|AFF4_uc003kye.1_Missense_Mutation_p.K780N	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31	780					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)			TTTTGGGTTTCTTGCTCTCAC	0.423													15	214	---	---	---	---	PASS
PTTG1	9232	broad.mit.edu	37	5	159854787	159854787	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr5:159854787C>T	uc003lyj.2	+	5	481	c.436C>T	c.(436-438)CTC>TTC	p.L146F	PTTG1_uc003lyk.2_Missense_Mutation_p.L146F	NM_004219	NP_004210	O95997	PTTG1_HUMAN	pituitary tumor-transforming protein 1	146					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|chromosome organization|chromosome segregation|DNA repair|mitosis|spermatogenesis|transcription from RNA polymerase II promoter	cytosol|nucleus	cysteine-type endopeptidase inhibitor activity|sequence-specific DNA binding transcription factor activity|SH3 domain binding				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.00219)|Epithelial(171;0.00348)|all cancers(165;0.0104)		TGGAGTGCCTCTCATGATCCT	0.512													5	69	---	---	---	---	PASS
BAT2	7916	broad.mit.edu	37	6	31600358	31600358	+	Missense_Mutation	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr6:31600358C>A	uc003nvb.3	+	16	4157	c.3908C>A	c.(3907-3909)GCT>GAT	p.A1303D	BAT2_uc011dnv.1_Intron|BAT2_uc003nvc.3_Missense_Mutation_p.A1303D	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	1303	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0						CGCCGGGCAGCTGCCAAGTCT	0.612													4	128	---	---	---	---	PASS
TSPO2	222642	broad.mit.edu	37	6	41010825	41010825	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr6:41010825C>T	uc003opj.2	+	2	402	c.101C>T	c.(100-102)CCG>CTG	p.P34L	UNC5CL_uc010jxe.1_Intron|TSPO2_uc003opk.2_Nonsense_Mutation_p.R44*|TSPO2_uc011dub.1_Missense_Mutation_p.P34L	NM_001010873	NP_001010873	Q5TGU0	TSPO2_HUMAN	benzodiazapine receptor (peripheral)-like 1	34					transport	endoplasmic reticulum membrane|integral to membrane	cholesterol binding|receptor activity				0						TGTGAGGGCCCGAGGATGCTG	0.552													5	297	---	---	---	---	PASS
PTPRK	5796	broad.mit.edu	37	6	128540114	128540114	+	Nonsense_Mutation	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr6:128540114G>C	uc003qbk.2	-	6	1188	c.821C>G	c.(820-822)TCA>TGA	p.S274*	PTPRK_uc003qbj.2_Nonsense_Mutation_p.S274*|PTPRK_uc010kfc.2_Nonsense_Mutation_p.S274*|PTPRK_uc011ebu.1_Nonsense_Mutation_p.S274*|PTPRK_uc003qbl.1_Nonsense_Mutation_p.S144*|PTPRK_uc011ebv.1_Nonsense_Mutation_p.S274*	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	274	Extracellular (Potential).|Ig-like C2-type.				cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		ACCTCGTTCTGACTGAGTTAC	0.408													34	46	---	---	---	---	PASS
NFE2L3	9603	broad.mit.edu	37	7	26225048	26225048	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr7:26225048C>T	uc003sxq.2	+	4	2002	c.1730C>T	c.(1729-1731)TCA>TTA	p.S577L		NM_004289	NP_004280	Q9Y4A8	NF2L3_HUMAN	nuclear factor erythroid 2-like 3	577					transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			skin(3)|ovary(1)	4						CTACAAGTCTCACTTATCCGT	0.373													15	42	---	---	---	---	PASS
NT5C3	51251	broad.mit.edu	37	7	33059302	33059302	+	Missense_Mutation	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr7:33059302C>A	uc003tdk.2	-	6	567	c.490G>T	c.(490-492)GCT>TCT	p.A164S	AVL9_uc011kai.1_Intron|NT5C3_uc003tdi.2_Missense_Mutation_p.A125S|NT5C3_uc003tdj.2_Missense_Mutation_p.A125S	NM_001002010	NP_001002010	Q9H0P0	5NT3_HUMAN	5'-nucleotidase, cytosolic III isoform 1	164					nucleotide metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol|endoplasmic reticulum	2'-phosphotransferase activity|5'-nucleotidase activity|magnesium ion binding|nucleotide binding			ovary(1)	1			GBM - Glioblastoma multiforme(11;0.0894)			TTTGGTAAAGCTTGCTGAACA	0.313													4	108	---	---	---	---	PASS
AGAP3	116988	broad.mit.edu	37	7	150840549	150840549	+	Silent	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr7:150840549C>A	uc003wjg.1	+	17	2398	c.2395C>A	c.(2395-2397)CGG>AGG	p.R799R	AGAP3_uc003wje.1_Silent_p.R468R|AGAP3_uc003wjj.1_Silent_p.R298R|AGAP3_uc003wjk.1_Silent_p.R217R	NM_031946	NP_114152	Q96P47	AGAP3_HUMAN	centaurin, gamma 3 isoform a	763	ANK 1.				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3						AGATGACCTGCGGCTGTTGGT	0.612													4	68	---	---	---	---	PASS
CYC1	1537	broad.mit.edu	37	8	145150845	145150845	+	Nonsense_Mutation	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr8:145150845C>A	uc003zaz.3	+	2	282	c.239C>A	c.(238-240)TCG>TAG	p.S80*	CYC1_uc003zay.2_Nonsense_Mutation_p.S21*	NM_001916	NP_001907	P08574	CY1_HUMAN	cytochrome c-1	80					respiratory electron transport chain|transport	cell junction|integral to membrane|mitochondrial inner membrane|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding				0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCTCTGCATTCGGCTGTGAGT	0.652											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	25	88	---	---	---	---	PASS
RPL8	6132	broad.mit.edu	37	8	146017203	146017203	+	Missense_Mutation	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr8:146017203C>A	uc003zeb.2	-	3	346	c.235G>T	c.(235-237)GCC>TCC	p.A79S	RPL8_uc003zdz.2_RNA|RPL8_uc003zea.2_Intron|RPL8_uc003zec.2_Missense_Mutation_p.A79S|RPL8_uc010mgc.2_Missense_Mutation_p.A79S	NM_033301	NP_150644	P62917	RL8_HUMAN	ribosomal protein L8	79					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	rRNA binding|structural constituent of ribosome				0	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.191)		ATGCCCTCGGCGGCAATGAAC	0.642													4	195	---	---	---	---	PASS
SLC34A3	142680	broad.mit.edu	37	9	140130450	140130450	+	Missense_Mutation	SNP	G	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr9:140130450G>T	uc004cmf.1	+	13	1568	c.1382G>T	c.(1381-1383)TGG>TTG	p.W461L	SLC34A3_uc011met.1_Missense_Mutation_p.W461L	NM_080877	NP_543153	Q8N130	NPT2C_HUMAN	solute carrier family 34 (sodium phosphate),	461	Helical; Name=M6; (Potential).				cellular phosphate ion homeostasis	apical plasma membrane|integral to membrane	sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity				0	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		ATCCTGCTGTGGTACCTGGTG	0.692											OREG0019630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	105	---	---	---	---	PASS
AKR1C4	1109	broad.mit.edu	37	10	5242169	5242169	+	Missense_Mutation	SNP	T	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr10:5242169T>A	uc001ihw.2	+	2	143	c.110T>A	c.(109-111)GTC>GAC	p.V37D		NM_001818	NP_001809	P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	37					androgen metabolic process|bile acid biosynthetic process	cytosol	aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid transmembrane transporter activity|chlordecone reductase activity|electron carrier activity			ovary(1)	1					NADH(DB00157)	GCTGTAGAGGTCACCAAATTA	0.398													5	82	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	16982213	16982213	+	Missense_Mutation	SNP	T	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr10:16982213T>A	uc001ioo.2	-	37	5418	c.5366A>T	c.(5365-5367)CAG>CTG	p.Q1789L		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1789	CUB 12.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GCTGCAGTCCTGAGAGTCTTC	0.438													4	195	---	---	---	---	PASS
CACNB2	783	broad.mit.edu	37	10	18823121	18823121	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr10:18823121C>T	uc001ipr.2	+	11	1231	c.1171C>T	c.(1171-1173)CCT>TCT	p.P391S	CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Missense_Mutation_p.P367S|CACNB2_uc001ipt.2_Missense_Mutation_p.P353S|CACNB2_uc001ipu.2_Missense_Mutation_p.P363S|CACNB2_uc001ipv.2_Missense_Mutation_p.P339S|CACNB2_uc009xka.1_Missense_Mutation_p.P325S|CACNB2_uc001ipw.2_Missense_Mutation_p.P298S|CACNB2_uc001ipx.2_Missense_Mutation_p.P336S|CACNB2_uc001ipz.2_Missense_Mutation_p.P313S|CACNB2_uc001ipy.2_Missense_Mutation_p.P337S|CACNB2_uc010qco.1_Missense_Mutation_p.P305S|CACNB2_uc001iqa.2_Missense_Mutation_p.P343S|NSUN6_uc001iqb.2_Intron	NM_201596	NP_963890	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2	391					axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	CTCCTTGGCCCCTATTATAGT	0.368													35	121	---	---	---	---	PASS
GPAM	57678	broad.mit.edu	37	10	113928283	113928283	+	Splice_Site	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr10:113928283C>A	uc009xxy.1	-	11	1093	c.895_splice	c.e11-1	p.H299_splice	GPAM_uc001kzp.2_Splice_Site_p.H299_splice|GPAM_uc001kzq.1_Splice_Site_p.H299_splice	NM_020918	NP_065969	Q9HCL2	GPAT1_HUMAN	mitochondrial glycerol 3-phosphate						phospholipid biosynthetic process|triglyceride biosynthetic process	integral to membrane|mitochondrial outer membrane	glycerol-3-phosphate O-acyltransferase activity			ovary(1)|skin(1)	2				Epithelial(162;0.0306)|all cancers(201;0.123)		CAACTATATGCTGGGATATAA	0.373													13	35	---	---	---	---	PASS
TRUB1	142940	broad.mit.edu	37	10	116732013	116732013	+	Missense_Mutation	SNP	A	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr10:116732013A>G	uc001lcd.2	+	6	777	c.716A>G	c.(715-717)CAG>CGG	p.Q239R	TRUB1_uc010qsl.1_Missense_Mutation_p.Q141R	NM_139169	NP_631908	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase homolog 1	239					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding				0		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		CAAAAATTCCAGCCACCATTT	0.353													3	48	---	---	---	---	PASS
KCNJ11	3767	broad.mit.edu	37	11	17409221	17409221	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr11:17409221C>T	uc001mna.2	-	1	986	c.418G>A	c.(418-420)GAG>AAG	p.E140K	KCNJ11_uc001mnb.3_Missense_Mutation_p.E53K	NM_000525	NP_000516	B4DWI4	B4DWI4_HUMAN	potassium inwardly-rectifying channel J11	140						integral to membrane	ATP-activated inward rectifier potassium channel activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0276)|Colorectal(2;0.0633)		GGGCACTCCTCAGTCACCATG	0.552											OREG0020810	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	40	---	---	---	---	PASS
MAPK8IP1	9479	broad.mit.edu	37	11	45924235	45924235	+	Missense_Mutation	SNP	G	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr11:45924235G>T	uc001nbr.2	+	5	1087	c.917G>T	c.(916-918)CGG>CTG	p.R306L		NM_005456	NP_005447	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting	306					vesicle-mediated transport	nucleus|perinuclear region of cytoplasm	kinesin binding|MAP-kinase scaffold activity|protein kinase inhibitor activity			ovary(2)|breast(1)|skin(1)	4				GBM - Glioblastoma multiforme(35;0.231)		ACTGAGAGCCGGATGTCAGTC	0.667													13	37	---	---	---	---	PASS
OR5L1	219437	broad.mit.edu	37	11	55579660	55579660	+	Missense_Mutation	SNP	A	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr11:55579660A>T	uc001nhw.1	+	1	718	c.718A>T	c.(718-720)ACC>TCC	p.T240S		NM_001004738	NP_001004738	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L,	240	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(2)	5		all_epithelial(135;0.208)				AGCCTTCTCCACCTGTGCTTC	0.502													29	74	---	---	---	---	PASS
LGALS12	85329	broad.mit.edu	37	11	63278578	63278578	+	Splice_Site	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr11:63278578G>C	uc001nxa.2	+	6	965	c.624_splice	c.e6+1	p.L208_splice	LGALS12_uc001nxb.2_Intron|LGALS12_uc001nxc.2_Splice_Site_p.L209_splice|LGALS12_uc001nxd.2_Splice_Site_p.L147_splice|LGALS12_uc001nxe.2_Intron|LGALS12_uc009yot.2_Splice_Site_p.L168_splice	NM_033101	NP_149092	Q96DT0	LEG12_HUMAN	lectin, galactoside-binding, soluble, 12 isoform						apoptosis|induction of apoptosis by intracellular signals	nucleus	lactose binding			ovary(2)	2						CCCCAGGCTGGTGAGTGAACC	0.557													8	78	---	---	---	---	PASS
MEN1	4221	broad.mit.edu	37	11	64572634	64572634	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr11:64572634C>G	uc001obj.2	-	9	1310	c.1237G>C	c.(1237-1239)GAG>CAG	p.E413Q	MAP4K2_uc001obh.2_5'Flank|MAP4K2_uc001obi.2_5'Flank|MAP4K2_uc010rnp.1_5'Flank|MEN1_uc001obk.2_Missense_Mutation_p.E413Q|MEN1_uc001obl.2_Missense_Mutation_p.E373Q|MEN1_uc001obm.2_Missense_Mutation_p.E408Q|MEN1_uc001obn.2_Missense_Mutation_p.E413Q|MEN1_uc001obo.2_Missense_Mutation_p.E413Q|MEN1_uc001obp.2_Missense_Mutation_p.E408Q|MEN1_uc001obq.2_Missense_Mutation_p.E413Q|MEN1_uc001obr.2_Missense_Mutation_p.E413Q	NM_130800	NP_570712	O00255	MEN1_HUMAN	menin isoform 1	413					DNA repair|histone lysine methylation|MAPKKK cascade|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of JNK cascade|negative regulation of osteoblast differentiation|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of telomerase activity|negative regulation of transcription from RNA polymerase II promoter|osteoblast development|positive regulation of protein binding|positive regulation of transforming growth factor beta receptor signaling pathway|response to gamma radiation|response to UV|transcription, DNA-dependent	chromatin|cleavage furrow|cytosol|histone methyltransferase complex|nuclear matrix|soluble fraction	double-stranded DNA binding|four-way junction DNA binding|protein binding, bridging|protein N-terminus binding|R-SMAD binding|transcription regulatory region DNA binding|Y-form DNA binding			parathyroid(105)|pancreas(64)|gastrointestinal_tract_(site_indeterminate)(15)|small_intestine(13)|lung(9)|pituitary(7)|NS(7)|adrenal_gland(5)|soft_tissue(4)|central_nervous_system(4)|thymus(2)|stomach(1)|retroperitoneum(1)|skin(1)	238						GCGAAGCACTCAGGGTCCTGG	0.627			D|Mis|N|F|S		parathyroid tumors|Pancreatic neuroendocrine tumors	parathyroid adenoma|pituitary adenoma|pancreatic islet cell|carcinoid			Hyperparathyroidism_Familial_Isolated|Multiple_Endocrine_Neoplasia_type_1				16	97	---	---	---	---	PASS
RPS6KB2	6199	broad.mit.edu	37	11	67201893	67201893	+	Nonsense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr11:67201893C>T	uc001old.2	+	13	1175	c.1093C>T	c.(1093-1095)CAG>TAG	p.Q365*	RPS6KB2_uc001olf.2_Nonsense_Mutation_p.Q165*|RPS6KB2_uc001olg.2_Nonsense_Mutation_p.Q365*|RPS6KB2_uc009yrq.2_Nonsense_Mutation_p.Q165*|RPS6KB2_uc001ole.2_RNA|RPS6KB2_uc001olh.2_RNA|RPS6KB2_uc009yrr.2_Nonsense_Mutation_p.Q196*	NM_003952	NP_003943	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide	365	AGC-kinase C-terminal.				nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of translational initiation|translation	nucleoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|stomach(1)|lung(1)|salivary_gland(1)	7			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			CTTCACACGGCAGACGCCGGT	0.647													35	72	---	---	---	---	PASS
NPAT	4863	broad.mit.edu	37	11	108043367	108043367	+	Missense_Mutation	SNP	T	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr11:108043367T>C	uc001pjz.3	-	13	2446	c.2344A>G	c.(2344-2346)AAA>GAA	p.K782E	NPAT_uc010rvv.1_5'Flank|NPAT_uc001pka.2_Missense_Mutation_p.K577E	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	782					positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		TCTGCATTTTTAGTAGGTGAT	0.378													28	56	---	---	---	---	PASS
ZW10	9183	broad.mit.edu	37	11	113608372	113608372	+	Silent	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr11:113608372C>T	uc001poe.2	-	14	1975	c.1938G>A	c.(1936-1938)GTG>GTA	p.V646V	ZW10_uc009yyv.2_RNA	NM_004724	NP_004715	O43264	ZW10_HUMAN	centromere/kinetochore protein zw10	646					cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		AATATATATTCACTGGCAGGA	0.418													14	98	---	---	---	---	PASS
CADM1	23705	broad.mit.edu	37	11	115080343	115080343	+	Silent	SNP	G	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr11:115080343G>T	uc001ppi.3	-	8	1158	c.1029C>A	c.(1027-1029)ACC>ACA	p.T343T	CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001pph.3_Silent_p.T95T	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1	343	Extracellular (Potential).			PPTTIPPPTTTTTTTTTTTTTILTIIT -> TTATTEPAVH GLTQLPNSAEELDSEDLS (in Ref. 3; BAC11657).	adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		tggtggtggtggttgttgtgg	0.269													3	39	---	---	---	---	PASS
ERC1	23085	broad.mit.edu	37	12	1192740	1192740	+	Silent	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr12:1192740G>A	uc001qjb.2	+	3	1321	c.1080G>A	c.(1078-1080)TTG>TTA	p.L360L	ERC1_uc001qiz.2_RNA|ERC1_uc001qjc.2_Silent_p.L360L|ERC1_uc001qja.2_RNA|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Silent_p.L360L|ERC1_uc010sdv.1_Silent_p.L136L	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon	360	Potential.				I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			ACAGTATGTTGAGAGAGGTAT	0.413													7	128	---	---	---	---	PASS
TMTC1	83857	broad.mit.edu	37	12	29669355	29669355	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr12:29669355G>A	uc001rjb.2	-	15	2384	c.1910C>T	c.(1909-1911)TCA>TTA	p.S637L	TMTC1_uc001riz.2_Missense_Mutation_p.S394L|TMTC1_uc001rja.2_Missense_Mutation_p.S481L|TMTC1_uc001riy.2_Missense_Mutation_p.S90L	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	745						integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					GGTCTCCTCTGACACAATGTG	0.468													4	79	---	---	---	---	PASS
TUBA1C	84790	broad.mit.edu	37	12	49666490	49666490	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr12:49666490C>G	uc001rtt.1	+	4	930	c.830C>G	c.(829-831)TCT>TGT	p.S277C	TUBA1C_uc001rts.2_Missense_Mutation_p.S242C|TUBA1C_uc010smh.1_Missense_Mutation_p.S347C|uc010smi.1_Missense_Mutation_p.R33T	NM_032704	NP_116093	Q9BQE3	TBA1C_HUMAN	tubulin alpha 6	277					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity				0						CCTGTCATCTCTGCTGAGAAA	0.532													5	202	---	---	---	---	PASS
TMEM132D	121256	broad.mit.edu	37	12	129822298	129822298	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr12:129822298G>A	uc009zyl.1	-	4	1508	c.1180C>T	c.(1180-1182)CCA>TCA	p.P394S		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	394	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGTGTGGCTGGCAGGTCACCA	0.572													5	332	---	---	---	---	PASS
SLITRK1	114798	broad.mit.edu	37	13	84454188	84454188	+	Silent	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr13:84454188G>A	uc001vlk.2	-	1	2341	c.1455C>T	c.(1453-1455)TCC>TCT	p.S485S		NM_052910	NP_443142	Q96PX8	SLIK1_HUMAN	slit and trk like 1 protein precursor	485	Extracellular (Potential).|LRR 11.					integral to membrane				ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		CCACAGGCAGGGACCTCAGCA	0.542													27	50	---	---	---	---	PASS
OR4K1	79544	broad.mit.edu	37	14	20403949	20403949	+	Missense_Mutation	SNP	A	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr14:20403949A>T	uc001vwj.1	+	1	124	c.124A>T	c.(124-126)AAT>TAT	p.N42Y		NM_001004063	NP_001004063	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K,	42	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)		AGTGCTAGGCAATGTCTTAAT	0.363													87	166	---	---	---	---	PASS
MAP3K9	4293	broad.mit.edu	37	14	71197217	71197217	+	Silent	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr14:71197217C>T	uc001xmm.2	-	12	3195	c.3195G>A	c.(3193-3195)CGG>CGA	p.R1065R	MAP3K9_uc010ttk.1_Silent_p.R793R|MAP3K9_uc001xmk.2_Silent_p.R798R|MAP3K9_uc001xml.2_Silent_p.R1079R	NM_033141	NP_149132	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase	1065					activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		CCAGGAGCGTCCGCTCAGTCG	0.642													4	89	---	---	---	---	PASS
HEATR4	399671	broad.mit.edu	37	14	73974852	73974852	+	Missense_Mutation	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr14:73974852G>C	uc010tub.1	-	9	2189	c.1867C>G	c.(1867-1869)CTG>GTG	p.L623V	HEATR4_uc010tua.1_Missense_Mutation_p.L576V	NM_203309	NP_976054			HEAT repeat containing 4											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		TTCTCACTCAGATAGCTCAGG	0.448													3	140	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106110410	106110410	+	RNA	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr14:106110410C>T	uc010tyt.1	-	3641		c.60959G>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_RNA					Parts of antibodies, mostly variable regions.												0						CTTACCTGGGCACGGTGGGCA	0.617													13	284	---	---	---	---	PASS
SLC12A6	9990	broad.mit.edu	37	15	34548481	34548481	+	Missense_Mutation	SNP	T	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr15:34548481T>C	uc001zhw.2	-	6	858	c.694A>G	c.(694-696)ATG>GTG	p.M232V	SLC12A6_uc001zhv.2_Missense_Mutation_p.M181V|SLC12A6_uc001zhx.2_Missense_Mutation_p.M217V|SLC12A6_uc001zhy.2_RNA|SLC12A6_uc001zhz.2_RNA|SLC12A6_uc001zia.2_Missense_Mutation_p.M173V|SLC12A6_uc001zib.2_Missense_Mutation_p.M223V|SLC12A6_uc001zic.2_Missense_Mutation_p.M232V|SLC12A6_uc010bau.2_Missense_Mutation_p.M232V|SLC12A6_uc001zid.2_Missense_Mutation_p.M173V|SLC12A6_uc001zhu.2_Missense_Mutation_p.M44V	NM_133647	NP_598408	Q9UHW9	S12A6_HUMAN	solute carrier family 12, member 6 isoform a	232	Cytoplasmic (Potential).				angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity			central_nervous_system(5)|ovary(1)|skin(1)	7		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	GCAGTCAACATTGTCTGCAGA	0.413													15	31	---	---	---	---	PASS
SEMA7A	8482	broad.mit.edu	37	15	74703219	74703219	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr15:74703219C>T	uc002axv.2	-	14	1787	c.1747G>A	c.(1747-1749)GTG>ATG	p.V583M	SEMA7A_uc010ulk.1_Missense_Mutation_p.V418M|SEMA7A_uc010ull.1_Missense_Mutation_p.V569M	NM_003612	NP_003603	O75326	SEM7A_HUMAN	semaphorin 7A isoform 1 preproprotein	583	Ig-like C2-type.				axon guidance|immune response|inflammatory response|integrin-mediated signaling pathway|positive regulation of axon extension|positive regulation of ERK1 and ERK2 cascade|positive regulation of macrophage cytokine production|regulation of inflammatory response	anchored to membrane|external side of plasma membrane	receptor activity			breast(1)|central_nervous_system(1)	2						CTCTGCTCCACGTTCTCCTTG	0.612													62	155	---	---	---	---	PASS
PDIA2	64714	broad.mit.edu	37	16	335012	335012	+	Silent	SNP	G	A	A	rs45591741	by1000genomes	TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr16:335012G>A	uc002cgn.1	+	9	1783	c.675G>A	c.(673-675)AAG>AAA	p.K225K	PDIA2_uc010bqt.1_Silent_p.K70K|PDIA2_uc002cgo.1_Silent_p.K225K	NM_006849	NP_006840	Q13087	PDIA2_HUMAN	protein disulfide isomerase A2 precursor	225					apoptosis|cell redox homeostasis|glycerol ether metabolic process|protein folding|protein retention in ER lumen|response to hypoxia	endoplasmic reticulum lumen	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity|steroid binding			central_nervous_system(1)|skin(1)	2		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				TTCTCTTCAAGAAGGTAGGTC	0.632													4	124	---	---	---	---	PASS
SMPD3	55512	broad.mit.edu	37	16	68398801	68398801	+	Missense_Mutation	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr16:68398801C>A	uc002ewa.2	-	5	1830	c.1408G>T	c.(1408-1410)GCC>TCC	p.A470S	SMPD3_uc010cfe.2_Missense_Mutation_p.A470S|SMPD3_uc010vlh.1_Missense_Mutation_p.A470S	NM_018667	NP_061137	Q9NY59	NSMA2_HUMAN	neutral sphingomyelin phosphodiesterase 3	470	Lumenal (Potential).				cell cycle|multicellular organismal development|sphingomyelin catabolic process	Golgi membrane|integral to membrane|plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity			skin(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	CACCGGATGGCGCTGTCCTCT	0.597													12	31	---	---	---	---	PASS
LDHD	197257	broad.mit.edu	37	16	75149555	75149555	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr16:75149555C>G	uc002fdm.2	-	2	123	c.76G>C	c.(76-78)GAG>CAG	p.E26Q	LDHD_uc002fdn.2_Missense_Mutation_p.E26Q	NM_153486	NP_705690	Q86WU2	LDHD_HUMAN	D-lactate dehydrogenase isoform 1 precursor	26							D-lactate dehydrogenase (cytochrome) activity|flavin adenine dinucleotide binding|protein binding				0						CTGCAGAGCTCTCCCTGCAGG	0.687													3	25	---	---	---	---	PASS
CHST5	23563	broad.mit.edu	37	16	75563756	75563756	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr16:75563756G>A	uc002fei.2	-	3	1922	c.527C>T	c.(526-528)ACG>ATG	p.T176M	CHST5_uc002fej.1_Missense_Mutation_p.T182M	NM_024533	NP_078809	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	176	Lumenal (Potential).				N-acetylglucosamine metabolic process|protein sulfation	integral to membrane|intrinsic to Golgi membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0						TGGCTGCCGCGTGCACAGTGT	0.662													40	244	---	---	---	---	PASS
SPG7	6687	broad.mit.edu	37	16	89623473	89623473	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr16:89623473G>A	uc002fnj.2	+	17	2381	c.2360G>A	c.(2359-2361)GGA>GAA	p.G787E	SPG7_uc002fnl.2_Missense_Mutation_p.G196E	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 isoform 1	787	Mitochondrial matrix (Potential).				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		CCTCCACTTGGAGGCGAAGAG	0.607											OREG0024053	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	61	---	---	---	---	PASS
SERPINF2	5345	broad.mit.edu	37	17	1650617	1650617	+	Missense_Mutation	SNP	G	C	C	rs121965061		TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr17:1650617G>C	uc002ftk.1	+	7	603	c.526G>C	c.(526-528)GAA>CAA	p.E176Q	SERPINF2_uc010vqr.1_Missense_Mutation_p.E112Q	NM_000934	NP_000925	P08697	A2AP_HUMAN	alpha-2-antiplasmin isoform a precursor	176			Missing (in APLID; variant Okinawa; probably blocks intracellular transport of alpha-2-plasmin inhibitor).		acute-phase response|fibrinolysis|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Streptokinase(DB00086)	TCCCATCAAAGAAGATTTCCT	0.567													16	19	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7578403	7578403	+	Missense_Mutation	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr17:7578403C>A	uc002gim.2	-	5	721	c.527G>T	c.(526-528)TGC>TTC	p.C176F	TP53_uc002gig.1_Missense_Mutation_p.C176F|TP53_uc002gih.2_Missense_Mutation_p.C176F|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.C44F|TP53_uc010cng.1_Missense_Mutation_p.C44F|TP53_uc002gii.1_Missense_Mutation_p.C44F|TP53_uc010cnh.1_Missense_Mutation_p.C176F|TP53_uc010cni.1_Missense_Mutation_p.C176F|TP53_uc002gij.2_Missense_Mutation_p.C176F|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.C83F|TP53_uc002gio.2_Missense_Mutation_p.C44F|TP53_uc010vug.1_Missense_Mutation_p.C137F	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	176	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).	Zinc.	CP -> FS (in a sporadic cancer; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in sporadic cancers; somatic mutation).|C -> F (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.C176F(102)|p.C176Y(56)|p.C176S(19)|p.C176W(11)|p.C176R(8)|p.C176fs*71(7)|p.0?(7)|p.C176*(6)|p.C176_R181delCPHHER(3)|p.R174fs*24(3)|p.C176G(3)|p.C176fs*5(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.K164_P219del(1)|p.C176fs*65(1)|p.C176_P177delCP(1)|p.V173fs*69(1)|p.C176fs*68(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.C44Y(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R42fs*24(1)|p.C83Y(1)|p.C176fs*72(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.C176del(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.C176fs*6(1)|p.R174fs*3(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		ATGGTGGGGGCAGCGCCTCAC	0.652		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			26	30	---	---	---	---	PASS
ITGB3	3690	broad.mit.edu	37	17	45367602	45367602	+	Missense_Mutation	SNP	T	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr17:45367602T>A	uc002ilj.2	+	8	1107	c.1087T>A	c.(1087-1089)TCC>ACC	p.S363T	ITGB3_uc002ili.1_Missense_Mutation_p.S363T|ITGB3_uc010wkr.1_RNA	NM_000212	NP_000203	P05106	ITB3_HUMAN	integrin beta chain, beta 3 precursor	363	VWFA.|Extracellular (Potential).				activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)	GTCCATGGATTCCAGCAATGT	0.498													6	270	---	---	---	---	PASS
CUEDC1	404093	broad.mit.edu	37	17	55951058	55951058	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr17:55951058C>G	uc002ivd.1	-	4	1204	c.485G>C	c.(484-486)GGA>GCA	p.G162A	CUEDC1_uc002ive.1_Missense_Mutation_p.G162A	NM_017949	NP_060419	Q9NWM3	CUED1_HUMAN	CUE domain-containing 1	162										skin(2)	2						TGTAGGGGCTCCAGAGCCCAG	0.612													3	115	---	---	---	---	PASS
BZRAP1	9256	broad.mit.edu	37	17	56386399	56386399	+	Missense_Mutation	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr17:56386399G>C	uc002ivx.3	-	22	5105	c.4234C>G	c.(4234-4236)CCT>GCT	p.P1412A	BZRAP1_uc002ivw.2_5'Flank|BZRAP1_uc010dcs.2_Missense_Mutation_p.P1352A|BZRAP1_uc010wnt.1_Missense_Mutation_p.P1412A	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated	1412						mitochondrion	benzodiazepine receptor binding			upper_aerodigestive_tract(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGCTTCTCAGGGGAGCCCCCT	0.647													25	106	---	---	---	---	PASS
MRC2	9902	broad.mit.edu	37	17	60749464	60749464	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr17:60749464C>G	uc002jad.2	+	8	1814	c.1412C>G	c.(1411-1413)CCC>CGC	p.P471R	MRC2_uc002jac.2_Missense_Mutation_p.P471R	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	471	Extracellular (Potential).|C-type lectin 2.				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|skin(1)	3						CCCTTTGAGCCCAACAACTTC	0.562													5	286	---	---	---	---	PASS
KIAA0195	9772	broad.mit.edu	37	17	73492407	73492407	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr17:73492407C>T	uc002jnz.3	+	24	3373	c.3098C>T	c.(3097-3099)ACC>ATC	p.T1033I	KIAA0195_uc010wsa.1_Missense_Mutation_p.T1043I|KIAA0195_uc010wsb.1_Missense_Mutation_p.T673I|KIAA0195_uc002job.3_Missense_Mutation_p.T41I	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	1033					ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TCCTGGGAGACCTTTGGCTAC	0.627													22	148	---	---	---	---	PASS
EMR1	2015	broad.mit.edu	37	19	6913673	6913673	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr19:6913673G>A	uc002mfw.2	+	11	1170	c.1132G>A	c.(1132-1134)GAG>AAG	p.E378K	EMR1_uc010dvc.2_Missense_Mutation_p.E378K|EMR1_uc010dvb.2_Missense_Mutation_p.E326K|EMR1_uc010xji.1_Missense_Mutation_p.E237K|EMR1_uc010xjj.1_Missense_Mutation_p.E201K	NM_001974	NP_001965	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone	378	Ser/Thr-rich.|Extracellular (Potential).				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)					GAATACAACTGAGAGCTTTGT	0.438													21	350	---	---	---	---	PASS
EMR1	2015	broad.mit.edu	37	19	6919644	6919644	+	Missense_Mutation	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr19:6919644G>C	uc002mfw.2	+	13	1544	c.1506G>C	c.(1504-1506)TTG>TTC	p.L502F	EMR1_uc010dvc.2_Missense_Mutation_p.L502F|EMR1_uc010dvb.2_Missense_Mutation_p.L450F|EMR1_uc010xji.1_Missense_Mutation_p.L361F|EMR1_uc010xjj.1_Missense_Mutation_p.L325F	NM_001974	NP_001965	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone	502	Ser/Thr-rich.|Extracellular (Potential).				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)					AGGCTCCCTTGACCACCTCTG	0.493													48	846	---	---	---	---	PASS
EMR1	2015	broad.mit.edu	37	19	6919665	6919665	+	Silent	SNP	G	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr19:6919665G>T	uc002mfw.2	+	13	1565	c.1527G>T	c.(1525-1527)CTG>CTT	p.L509L	EMR1_uc010dvc.2_Silent_p.L509L|EMR1_uc010dvb.2_Silent_p.L457L|EMR1_uc010xji.1_Silent_p.L368L|EMR1_uc010xjj.1_Silent_p.L332L	NM_001974	NP_001965	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone	509	Ser/Thr-rich.|Extracellular (Potential).				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)					AGATCAAGCTGAAGATGAATT	0.478													46	833	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9019622	9019622	+	Silent	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr19:9019622C>T	uc002mkp.2	-	22	37728	c.37524G>A	c.(37522-37524)CGG>CGA	p.R12508R		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12510	Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GCACAGAGGTCCGATGGGTGA	0.507													386	49	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9057251	9057251	+	Silent	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr19:9057251G>A	uc002mkp.2	-	3	30399	c.30195C>T	c.(30193-30195)AGC>AGT	p.S10065S		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	10067	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						CAGGTTCTGTGCTTGTGTCTG	0.468													9	411	---	---	---	---	PASS
ICAM3	3385	broad.mit.edu	37	19	10449393	10449393	+	Missense_Mutation	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr19:10449393G>C	uc002mob.2	-	2	363	c.308C>G	c.(307-309)TCT>TGT	p.S103C	ICAM3_uc010dxd.1_Missense_Mutation_p.S26C|ICAM3_uc010xlf.1_Missense_Mutation_p.S26C	NM_002162	NP_002153	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3 precursor	103	Extracellular (Potential).|Ig-like C2-type 1.				cell-cell adhesion|regulation of immune response	integral to plasma membrane	integrin binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			TGTTATCTGAGAGCCATTGCA	0.567													17	289	---	---	---	---	PASS
EMR3	84658	broad.mit.edu	37	19	14752416	14752416	+	Missense_Mutation	SNP	C	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr19:14752416C>A	uc002mzi.3	-	10	1211	c.1063G>T	c.(1063-1065)GTG>TTG	p.V355L	EMR3_uc010dzp.2_Missense_Mutation_p.V303L|EMR3_uc010xnv.1_Missense_Mutation_p.V229L	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	355	Extracellular (Potential).				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						ACAGTCAGCACGGGATCCTCC	0.567													3	67	---	---	---	---	PASS
BIRC8	112401	broad.mit.edu	37	19	53793567	53793567	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr19:53793567C>G	uc002qbk.2	-	1	1309	c.61G>C	c.(61-63)GAG>CAG	p.E21Q		NM_033341	NP_203127	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat-containing 8	21	BIR.				apoptosis		zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(134;0.00304)		GCAAGCTGCTCTTTGTTAACG	0.453													41	84	---	---	---	---	PASS
PEG3	5178	broad.mit.edu	37	19	57329195	57329195	+	Missense_Mutation	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr19:57329195C>T	uc002qnu.2	-	6	1132	c.781G>A	c.(781-783)GCT>ACT	p.A261T	ZIM2_uc010ygq.1_5'UTR|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Intron|PEG3_uc002qnv.2_Missense_Mutation_p.A261T|PEG3_uc002qnw.2_Missense_Mutation_p.A137T|PEG3_uc002qnx.2_Missense_Mutation_p.A135T|PEG3_uc010etr.2_Missense_Mutation_p.A261T	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	261					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)		TCGTCTTCAGCAAGCTGCACT	0.502													10	28	---	---	---	---	PASS
PAK7	57144	broad.mit.edu	37	20	9546970	9546970	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr20:9546970G>A	uc002wnl.2	-	6	1597	c.1052C>T	c.(1051-1053)CCC>CTC	p.P351L	PAK7_uc002wnk.2_Missense_Mutation_p.P351L|PAK7_uc002wnj.2_Missense_Mutation_p.P351L|PAK7_uc010gby.1_Missense_Mutation_p.P351L	NM_020341	NP_065074	Q9P286	PAK7_HUMAN	p21-activated kinase 7	351	Linker.						ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)			AGGGCCCCTGGGGTAGGTGTC	0.527													74	192	---	---	---	---	PASS
ZNF337	26152	broad.mit.edu	37	20	25656577	25656577	+	Missense_Mutation	SNP	T	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr20:25656577T>A	uc002wva.2	-	4	1869	c.1347A>T	c.(1345-1347)AAA>AAT	p.K449N	uc002wuz.2_RNA|ZNF337_uc010ztg.1_Missense_Mutation_p.K417N|ZNF337_uc002wvb.2_Missense_Mutation_p.K449N|ZNF337_uc002wvc.2_Missense_Mutation_p.K449N	NM_015655	NP_056470	Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	449	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGATCTGATGTTTCACAAGGG	0.448													9	189	---	---	---	---	PASS
MAPRE1	22919	broad.mit.edu	37	20	31413746	31413746	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr20:31413746G>A	uc002wyh.2	+	2	152	c.13G>A	c.(13-15)GTA>ATA	p.V5I		NM_012325	NP_036457	Q15691	MARE1_HUMAN	microtubule-associated protein, RP/EB family,	5					cell division|cell proliferation|G2/M transition of mitotic cell cycle|mitotic prometaphase|negative regulation of microtubule polymerization|protein localization to microtubule	centrosome|cortical microtubule cytoskeleton|cytosol	microtubule plus-end binding|protein C-terminus binding				0						GGCAGTGAACGTATACTCAAC	0.443													4	109	---	---	---	---	PASS
PACSIN2	11252	broad.mit.edu	37	22	43280505	43280505	+	Silent	SNP	C	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr22:43280505C>T	uc010gzg.2	-	6	894	c.672G>A	c.(670-672)GAG>GAA	p.E224E	PACSIN2_uc003bdg.3_Silent_p.E224E|PACSIN2_uc003bde.3_Silent_p.E224E|PACSIN2_uc003bdf.3_Silent_p.E224E	NM_007229	NP_009160	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in	224					actin cytoskeleton organization|endocytosis	cytoplasmic membrane-bounded vesicle	transporter activity				0		Glioma(61;0.222)				GCTCCATGTTCTCCATGTACT	0.517													13	185	---	---	---	---	PASS
GPR173	54328	broad.mit.edu	37	X	53106311	53106311	+	Missense_Mutation	SNP	G	A	A			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chrX:53106311G>A	uc004dru.2	+	2	766	c.508G>A	c.(508-510)GAG>AAG	p.E170K		NM_018969	NP_061842	Q9NS66	GP173_HUMAN	G protein-coupled receptor 173	170	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1						GTTTATTCGGGAGGAGGACCA	0.557													3	34	---	---	---	---	PASS
TAF1	6872	broad.mit.edu	37	X	70603899	70603899	+	Missense_Mutation	SNP	C	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chrX:70603899C>G	uc004dzu.3	+	13	2083	c.2032C>G	c.(2032-2034)CTT>GTT	p.L678V	BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Missense_Mutation_p.L699V	NM_138923	NP_620278	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 2	678					G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)				AGATGGTGATCTTATTCTTGC	0.443													3	111	---	---	---	---	PASS
MAGT1	84061	broad.mit.edu	37	X	77150833	77150833	+	Silent	SNP	G	C	C			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chrX:77150833G>C	uc004fof.2	-	1	233	c.171C>G	c.(169-171)CCC>CCG	p.P57P	MAGT1_uc004fog.3_RNA|MAGT1_uc004ect.3_Silent_p.P57P	NM_032121	NP_115497	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	25					protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				upper_aerodigestive_tract(1)	1						CAGAGGCTGAGGGAACGTCGC	0.562													14	15	---	---	---	---	PASS
ODZ1	10178	broad.mit.edu	37	X	123775819	123775819	+	Silent	SNP	A	G	G			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chrX:123775819A>G	uc004euj.2	-	11	1963	c.1899T>C	c.(1897-1899)TGT>TGC	p.C633C	ODZ1_uc011muj.1_Silent_p.C632C|ODZ1_uc010nqy.2_Silent_p.C633C	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	633	EGF-like 4.|Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23						CATGGTTGGAACACATTGGGT	0.468													125	90	---	---	---	---	PASS
RAB3GAP2	25782	broad.mit.edu	37	1	220363047	220363048	+	Frame_Shift_Ins	INS	-	T	T			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr1:220363047_220363048insT	uc010puk.1	-	17	1940_1941	c.1776_1777insA	c.(1774-1779)AAACAAfs	p.K592fs	RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_Frame_Shift_Ins_p.K172fs	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	592_593					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)		ACACTTACTTGTTTTTTGGTTG	0.257													4	2	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	48881488	48881489	+	Frame_Shift_Ins	INS	-	AG	AG			TCGA-22-4607-01A-01D-1267-08	TCGA-22-4607-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	d8c6bb83-ebdd-4547-9077-3eba5c8bb9f0	d9a1bd0a-4bcd-4a79-8823-353a62b749fd	g.chr13:48881488_48881489insAG	uc001vcb.2	+	2	376_377	c.210_211insAG	c.(208-213)GTCAGAfs	p.V70fs	RB1_uc010acs.1_Intron	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	70_71					androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.0?(13)|p.?(3)|p.V70fs*39(1)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CAGATCATGTCAGAGAGAGAGC	0.302		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			65	33	---	---	---	---	
