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
S100PBP	64766	broad.mit.edu	37	1	33291705	33291705	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr1:33291705T>C	uc001bvz.2	+	3	282	c.5T>C	c.(4-6)ATG>ACG	p.M2T	S100PBP_uc001bwa.1_Missense_Mutation_p.M2T|S100PBP_uc001bwb.1_Missense_Mutation_p.M2T|S100PBP_uc001bwc.2_Missense_Mutation_p.M2T|S100PBP_uc001bwd.2_RNA	NM_022753	NP_073590	Q96BU1	S1PBP_HUMAN	S100P binding protein isoform a	2						nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				CCAGAAATGATGTGCTCACGG	0.428													48	106	---	---	---	---	PASS
NT5C1A	84618	broad.mit.edu	37	1	40126776	40126776	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr1:40126776G>T	uc001cdq.1	-	5	716	c.716C>A	c.(715-717)GCC>GAC	p.A239D		NM_032526	NP_115915	Q9BXI3	5NT1A_HUMAN	5'-nucleotidase, cytosolic IA	239					purine base metabolic process|purine nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			ovary(1)	1	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GTTCTCGTGGGCCTTCTCATG	0.637													10	251	---	---	---	---	PASS
YBX1	4904	broad.mit.edu	37	1	43161928	43161928	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr1:43161928C>T	uc001chs.2	+	4	494	c.323C>T	c.(322-324)ACT>ATT	p.T108I		NM_004559	NP_004550	P67809	YBOX1_HUMAN	nuclease sensitive element binding protein 1	108	CSD.				CRD-mediated mRNA stabilization|negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|positive regulation of cell division|transcription from RNA polymerase II promoter	CRD-mediated mRNA stability complex|extracellular region|histone pre-mRNA 3'end processing complex|nucleoplasm|stress granule|U12-type spliceosomal complex	double-stranded DNA binding|protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(4)|upper_aerodigestive_tract(1)	5	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GATGGAGAGACTGTGGAGTTT	0.393													4	171	---	---	---	---	PASS
C1orf177	163747	broad.mit.edu	37	1	55280637	55280637	+	Silent	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr1:55280637C>T	uc001cyb.3	+	8	1029	c.975C>T	c.(973-975)CCC>CCT	p.P325P	C1orf177_uc001cya.3_Silent_p.P325P	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN	hypothetical protein LOC163747 isoform 2	325											0						AATGCAAACCCGTCAACCAGC	0.547													41	140	---	---	---	---	PASS
LRIG2	9860	broad.mit.edu	37	1	113636959	113636959	+	Splice_Site	SNP	A	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr1:113636959A>T	uc001edf.1	+	5	714	c.516_splice	c.e5-2	p.L172_splice	LRIG2_uc009wgn.1_Splice_Site_p.L69_splice	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like							cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		TGTTTATTTTAGGAATTTAAG	0.289													4	80	---	---	---	---	PASS
PBXIP1	57326	broad.mit.edu	37	1	154918697	154918697	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr1:154918697G>A	uc001ffr.2	-	10	1512	c.1453C>T	c.(1453-1455)CGG>TGG	p.R485W	PBXIP1_uc001ffs.2_Missense_Mutation_p.R456W|PBXIP1_uc010pep.1_Missense_Mutation_p.R330W	NM_020524	NP_065385	Q96AQ6	PBIP1_HUMAN	pre-B-cell leukemia homeobox interacting protein	485	Nuclear localization signal (Potential).				cell differentiation|multicellular organismal development|negative regulation of transcription, DNA-dependent	cytosol|microtubule|nucleus	protein binding|transcription corepressor activity			large_intestine(1)	1	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TCAGCCTTCCGGTCTCTCTGC	0.552													17	546	---	---	---	---	PASS
NBAS	51594	broad.mit.edu	37	2	15468434	15468434	+	Silent	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr2:15468434C>T	uc002rcc.1	-	37	4376	c.4350G>A	c.(4348-4350)GGG>GGA	p.G1450G	NBAS_uc010exl.1_Silent_p.G522G|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	1450										ovary(2)|liver(1)|skin(1)	4						CACATTTTTGCCCCTaaaaag	0.209													5	303	---	---	---	---	PASS
WDR43	23160	broad.mit.edu	37	2	29148007	29148007	+	Silent	SNP	T	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr2:29148007T>G	uc002rmo.2	+	8	1106	c.1074T>G	c.(1072-1074)ACT>ACG	p.T358T	SNORD53_uc002rmq.1_5'Flank	NM_015131	NP_055946	Q15061	WDR43_HUMAN	WD repeat domain 43	358						nucleolus				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					TTCAGCCTACTATTGAGCGAG	0.413													12	39	---	---	---	---	PASS
ARID5A	10865	broad.mit.edu	37	2	97216909	97216909	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr2:97216909G>A	uc002swe.2	+	7	744	c.644G>A	c.(643-645)AGC>AAC	p.S215N	ARID5A_uc010yuq.1_Missense_Mutation_p.S163N|ARID5A_uc002swf.2_Missense_Mutation_p.S51N|ARID5A_uc002swg.2_Missense_Mutation_p.S163N	NM_212481	NP_997646	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A	215					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding				0						CCCAGGAACAGCACAGAACAG	0.587													4	155	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109382170	109382170	+	Silent	SNP	A	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr2:109382170A>G	uc002tem.3	+	20	5301	c.5175A>G	c.(5173-5175)GAA>GAG	p.E1725E		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	1725	RanBP2-type 7.				carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						CTAAGAAGGAAGGACAGTGGG	0.418													7	241	---	---	---	---	PASS
FIGN	55137	broad.mit.edu	37	2	164466420	164466420	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr2:164466420C>A	uc002uck.1	-	3	2233	c.1922G>T	c.(1921-1923)CGG>CTG	p.R641L		NM_018086	NP_060556	Q5HY92	FIGN_HUMAN	fidgetin	641						nuclear matrix	ATP binding|nucleoside-triphosphatase activity			large_intestine(2)|ovary(1)|skin(1)	4						GAAGTACCTCCGAAGGGATTC	0.433													4	236	---	---	---	---	PASS
PTH2R	5746	broad.mit.edu	37	2	209292995	209292995	+	Nonsense_Mutation	SNP	G	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr2:209292995G>T	uc002vdb.2	+	2	358	c.145G>T	c.(145-147)GAA>TAA	p.E49*	PTH2R_uc010zjb.1_Nonsense_Mutation_p.E60*	NM_005048	NP_005039	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor precursor	49	Extracellular (Potential).					integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)		AGTACAATGTGAACTCAACAT	0.413													3	43	---	---	---	---	PASS
IKZF2	22807	broad.mit.edu	37	2	213886796	213886796	+	Silent	SNP	C	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr2:213886796C>G	uc002vem.2	-	6	802	c.633G>C	c.(631-633)CTG>CTC	p.L211L	IKZF2_uc010fuu.2_Silent_p.L66L|IKZF2_uc002vej.2_Silent_p.L158L|IKZF2_uc002vek.2_RNA|IKZF2_uc010fuv.2_Silent_p.L185L|IKZF2_uc002vel.2_Silent_p.L132L|IKZF2_uc010fuw.2_5'UTR|IKZF2_uc010fux.2_5'UTR|IKZF2_uc010fuy.2_Intron|IKZF2_uc002ven.2_Silent_p.L185L	NM_016260	NP_057344	Q9UKS7	IKZF2_HUMAN	helios isoform 1	211	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		TGTGCTCCTCCAGTGAACTGC	0.507													6	122	---	---	---	---	PASS
FN1	2335	broad.mit.edu	37	2	216236934	216236934	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr2:216236934C>A	uc002vfa.2	-	40	6678	c.6412G>T	c.(6412-6414)GGG>TGG	p.G2138W	FN1_uc002vfb.2_Missense_Mutation_p.G1957W|FN1_uc002vfc.2_Missense_Mutation_p.G1932W|FN1_uc002vfd.2_Missense_Mutation_p.G2113W|FN1_uc002vfe.2_Missense_Mutation_p.G2047W|FN1_uc002vff.2_Missense_Mutation_p.G2022W|FN1_uc002vfg.2_Missense_Mutation_p.G1957W|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Missense_Mutation_p.G2138W|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_Missense_Mutation_p.G332W|FN1_uc010zjp.1_Missense_Mutation_p.G675W|FN1_uc002vfk.1_Intron|FN1_uc010fva.1_Intron|FN1_uc010fvb.1_Intron|FN1_uc010fvc.1_Intron|FN1_uc010fvd.1_Missense_Mutation_p.G229W	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	2047	Connecting strand 3 (CS-3) (V region).				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	ATTTGTTGCCCAACACTGGGT	0.532													4	145	---	---	---	---	PASS
SCN11A	11280	broad.mit.edu	37	3	38949466	38949466	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr3:38949466C>A	uc011ays.1	-	10	1646	c.1447G>T	c.(1447-1449)GAT>TAT	p.D483Y		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	483					response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)	TCATCAGAATCTGACCCAGGA	0.398													4	224	---	---	---	---	PASS
CLSTN2	64084	broad.mit.edu	37	3	140123402	140123402	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr3:140123402C>T	uc003etn.2	+	4	621	c.431C>T	c.(430-432)GCC>GTC	p.A144V	CLSTN2_uc003etm.2_Missense_Mutation_p.A144V	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	144	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						GGTCCCAGGGCCGTGGTCCAT	0.547										HNSCC(16;0.037)			21	91	---	---	---	---	PASS
IGF2BP2	10644	broad.mit.edu	37	3	185542687	185542687	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr3:185542687T>C	uc003fpo.2	-	1	141	c.62A>G	c.(61-63)CAG>CGG	p.Q21R	IGF2BP2_uc003fpp.2_Missense_Mutation_p.Q21R|IGF2BP2_uc003fpq.2_Missense_Mutation_p.Q20R	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding	21	RRM 1.				anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			CCCAAAGAGCTGCCGGAGGTC	0.622													3	14	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195481125	195481125	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr3:195481125G>T	uc011bto.1	-	20	15363	c.14903C>A	c.(14902-14904)GCC>GAC	p.A4968D	MUC4_uc010hzq.2_5'Flank|MUC4_uc003fuz.2_Missense_Mutation_p.A694D|MUC4_uc003fva.2_Missense_Mutation_p.A576D|MUC4_uc003fvb.2_Missense_Mutation_p.A612D|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Missense_Mutation_p.A612D|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Missense_Mutation_p.A576D|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Missense_Mutation_p.A660D|MUC4_uc011bti.1_Missense_Mutation_p.A660D|MUC4_uc011btj.1_Missense_Mutation_p.A837D|MUC4_uc011btk.1_Missense_Mutation_p.A576D|MUC4_uc011btl.1_Missense_Mutation_p.A605D|MUC4_uc011btm.1_Missense_Mutation_p.A785D|MUC4_uc011btn.1_Missense_Mutation_p.A576D|MUC4_uc003fvo.2_Missense_Mutation_p.A860D|MUC4_uc003fvp.2_Missense_Mutation_p.A809D	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	1853					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGGAGGGCAGGCCTCGCAGCC	0.677													16	178	---	---	---	---	PASS
SLC2A9	56606	broad.mit.edu	37	4	9828095	9828095	+	Silent	SNP	T	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr4:9828095T>G	uc003gmc.2	-	12	1610	c.1549A>C	c.(1549-1551)AGG>CGG	p.R517R	SLC2A9_uc003gmd.2_Silent_p.R488R	NM_020041	NP_064425	Q9NRM0	GTR9_HUMAN	solute carrier family 2, member 9 protein	517	Cytoplasmic (Potential).				glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3						GCTTTGTTCCTTTTGGAAAAT	0.428													6	316	---	---	---	---	PASS
ANKRD17	26057	broad.mit.edu	37	4	74043162	74043162	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr4:74043162C>A	uc003hgp.2	-	2	599	c.482G>T	c.(481-483)GGT>GTT	p.G161V	ANKRD17_uc003hgo.2_Missense_Mutation_p.G48V|ANKRD17_uc003hgq.2_Missense_Mutation_p.G161V|ANKRD17_uc003hgr.2_Missense_Mutation_p.G161V	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	161					interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GAGGTCTGCACCATCAGCAGT	0.413													8	231	---	---	---	---	PASS
BMP2K	55589	broad.mit.edu	37	4	79747250	79747250	+	Silent	SNP	C	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr4:79747250C>A	uc003hlk.2	+	2	404	c.238C>A	c.(238-240)CGA>AGA	p.R80R	BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_Silent_p.R80R	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a	80	Protein kinase.					nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1						TGCATTGAAGCGAATGTATGT	0.363													4	238	---	---	---	---	PASS
MMRN1	22915	broad.mit.edu	37	4	90872798	90872798	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr4:90872798G>C	uc003hst.2	+	7	3232	c.3161G>C	c.(3160-3162)GGC>GCC	p.G1054A	MMRN1_uc010iku.2_Missense_Mutation_p.G357A|MMRN1_uc011cds.1_Missense_Mutation_p.G796A	NM_007351	NP_031377	Q13201	MMRN1_HUMAN	multimerin 1	1054	EGF-like.				cell adhesion|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen				ovary(4)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		CAAAATGGGGGCACGTGCATA	0.423													31	81	---	---	---	---	PASS
CMYA5	202333	broad.mit.edu	37	5	79026181	79026181	+	Silent	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr5:79026181C>T	uc003kgc.2	+	2	1665	c.1593C>T	c.(1591-1593)ATC>ATT	p.I531I		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	531	Glu-rich.					perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AAGAAGAGATCGTAGAACTTG	0.418													83	156	---	---	---	---	PASS
VCAN	1462	broad.mit.edu	37	5	82808055	82808055	+	Silent	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr5:82808055C>T	uc003kii.3	+	6	1238	c.882C>T	c.(880-882)TGC>TGT	p.C294C	VCAN_uc003kij.3_Silent_p.C294C|VCAN_uc010jau.2_Silent_p.C294C|VCAN_uc003kik.3_Silent_p.C294C|VCAN_uc003kih.3_Silent_p.C294C	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	294	Link 2.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)		TTGACCAGTGCGATTACGGGT	0.602													9	81	---	---	---	---	PASS
PCDHA10	56139	broad.mit.edu	37	5	140237390	140237390	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr5:140237390C>T	uc003lhx.2	+	1	1757	c.1757C>T	c.(1756-1758)GCG>GTG	p.A586V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc011dad.1_Missense_Mutation_p.A586V	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	586	Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)|breast(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCGGTGGTTGCGGGTCACGTG	0.657													13	28	---	---	---	---	PASS
ITK	3702	broad.mit.edu	37	5	156670752	156670752	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr5:156670752C>T	uc003lwo.1	+	12	1262	c.1180C>T	c.(1180-1182)CGG>TGG	p.R394W		NM_005546	NP_005537	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	394	Protein kinase.				cellular defense response|intracellular signal transduction|T cell receptor signaling pathway	cytosol|plasma membrane	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(12)|ovary(8)|skin(4)|stomach(1)|central_nervous_system(1)	26	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CAAAACCATTCGGGAAGGGGC	0.498			T	SYK	peripheral T-cell lymphoma								65	126	---	---	---	---	PASS
RIOK1	83732	broad.mit.edu	37	6	7405482	7405482	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr6:7405482A>G	uc003mxn.2	+	12	1271	c.1097A>G	c.(1096-1098)GAT>GGT	p.D366G	RIOK1_uc003mxo.2_Missense_Mutation_p.D125G	NM_031480	NP_113668	Q9BRS2	RIOK1_HUMAN	RIO kinase 1 isoform 1	366	Protein kinase.						ATP binding|protein serine/threonine kinase activity			ovary(2)|stomach(1)|skin(1)	4	Ovarian(93;0.0418)					CTTCTGACAGATTTCTTTATG	0.363													32	79	---	---	---	---	PASS
HLA-DQB2	3120	broad.mit.edu	37	6	32726626	32726626	+	Splice_Site	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr6:32726626C>T	uc003oby.3	-	3	729	c.646_splice	c.e3+1	p.R216_splice	HLA-DQB2_uc003obz.2_Splice_Site_p.R216_splice	NR_003937		Q5SR06	Q5SR06_HUMAN	SubName: Full=Major histocompatibility complex, class II, DQ beta 2; SubName: Full=Putative uncharacterized protein ENSP00000372579;						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	integral to membrane|MHC class II protein complex					0						TTTCCCCTTACGCCACTCCAC	0.562													23	66	---	---	---	---	PASS
TRAF3IP2	10758	broad.mit.edu	37	6	111912533	111912533	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr6:111912533G>T	uc011ebc.1	-	3	1372	c.757C>A	c.(757-759)CCC>ACC	p.P253T	TRAF3IP2_uc003pvg.2_Missense_Mutation_p.P253T|TRAF3IP2_uc003pvf.2_Missense_Mutation_p.P253T|TRAF3IP2_uc010kdw.2_Missense_Mutation_p.P253T|TRAF3IP2_uc010kdx.2_Missense_Mutation_p.P253T	NM_147686	NP_679211	O43734	CIKS_HUMAN	TRAF3 interacting protein 2 isoform 2	262					intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular				ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		GAAAGATTGGGAGGCAGCATC	0.537													31	48	---	---	---	---	PASS
NPC1L1	29881	broad.mit.edu	37	7	44561339	44561339	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr7:44561339A>C	uc003tlb.2	-	12	2981	c.2925T>G	c.(2923-2925)AAT>AAG	p.N975K	NPC1L1_uc003tlc.2_Missense_Mutation_p.N975K|NPC1L1_uc011kbw.1_Missense_Mutation_p.N929K|NPC1L1_uc003tla.2_5'Flank	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 isoform 1	975	Cytoplasmic (Potential).				cholesterol biosynthetic process|intestinal cholesterol absorption|lipoprotein metabolic process	apical plasma membrane|cytoplasmic vesicle membrane|integral to membrane	hedgehog receptor activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5					Ezetimibe(DB00973)	ACTTGTCCTTATTGGGGCCAG	0.577													3	110	---	---	---	---	PASS
SLC25A13	10165	broad.mit.edu	37	7	95750981	95750981	+	Silent	SNP	A	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr7:95750981A>G	uc003uof.3	-	17	2018	c.1827T>C	c.(1825-1827)ATT>ATC	p.I609I	SLC25A13_uc003uog.3_Silent_p.I610I|SLC25A13_uc011kik.1_Silent_p.I501I	NM_014251	NP_055066	Q9UJS0	CMC2_HUMAN	solute carrier family 25, member 13 isoform 2	609					ATP biosynthetic process|gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to plasma membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity			central_nervous_system(3)|skin(1)	4	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	CTCCAAAATCAATGTAGAACC	0.413													79	244	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100684772	100684772	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr7:100684772A>G	uc003uxp.1	+	3	10128	c.10075A>G	c.(10075-10077)ACC>GCC	p.T3359A	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	3359	Extracellular (Potential).|54.|59 X approximate tandem repeats.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					TGAGGCTAGCACCCTTTCCAC	0.488													123	436	---	---	---	---	PASS
TNFRSF10A	8797	broad.mit.edu	37	8	23056931	23056931	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr8:23056931C>A	uc003xda.2	-	8	927	c.862G>T	c.(862-864)GGG>TGG	p.G288W		NM_003844	NP_003835	O00220	TR10A_HUMAN	tumor necrosis factor receptor superfamily,	288	Cytoplasmic (Potential).				activation of NF-kappaB-inducing kinase activity|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors		caspase activator activity|death receptor activity|TRAIL binding|transcription factor binding			central_nervous_system(3)|ovary(2)|skin(1)	6		Prostate(55;0.0421)|Breast(100;0.14)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)		GCCCCAGGCCCTCGTAGGAGA	0.602													4	90	---	---	---	---	PASS
EXT1	2131	broad.mit.edu	37	8	118812096	118812096	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr8:118812096G>T	uc003yok.1	-	11	2869	c.2096C>A	c.(2095-2097)GCC>GAC	p.A699D		NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1	699	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			CTGTCGCTGGGCAAAGTGGTC	0.527			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				3	112	---	---	---	---	PASS
DBC1	1620	broad.mit.edu	37	9	121976298	121976298	+	Missense_Mutation	SNP	G	A	A	rs148052034	by1000genomes	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr9:121976298G>A	uc004bkc.2	-	6	1277	c.821C>T	c.(820-822)CCG>CTG	p.P274L	DBC1_uc004bkd.2_Missense_Mutation_p.P274L	NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor	274					cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8						GTTGCACTGCGGAAACTCCTC	0.547													34	113	---	---	---	---	PASS
CACNB2	783	broad.mit.edu	37	10	18828621	18828621	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr10:18828621G>A	uc001ipr.2	+	14	2011	c.1951G>A	c.(1951-1953)GAG>AAG	p.E651K	CACNB2_uc009xjz.1_Missense_Mutation_p.E401K|CACNB2_uc001ips.2_Missense_Mutation_p.E627K|CACNB2_uc001ipt.2_Missense_Mutation_p.E613K|CACNB2_uc001ipu.2_Missense_Mutation_p.E623K|CACNB2_uc001ipv.2_Missense_Mutation_p.E599K|CACNB2_uc009xka.1_Missense_Mutation_p.E585K|CACNB2_uc001ipw.2_Missense_Mutation_p.E558K|CACNB2_uc001ipx.2_Missense_Mutation_p.E596K|CACNB2_uc001ipz.2_Missense_Mutation_p.E573K|CACNB2_uc001ipy.2_Missense_Mutation_p.E597K|CACNB2_uc010qco.1_Missense_Mutation_p.E565K|CACNB2_uc001iqa.2_Missense_Mutation_p.E603K|NSUN6_uc001iqb.2_Intron	NM_201596	NP_963890	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2	651					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)	TGAGGCTGGGGAGTGGAACAG	0.423													9	120	---	---	---	---	PASS
PNLIPRP1	5407	broad.mit.edu	37	10	118357365	118357365	+	Silent	SNP	C	T	T	rs113515929	by1000genomes	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr10:118357365C>T	uc001lco.1	+	7	618	c.600C>T	c.(598-600)TTC>TTT	p.F200F	PNLIPRP1_uc001lcp.2_Silent_p.F200F|PNLIPRP1_uc009xys.1_RNA	NM_006229	NP_006220	P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1 precursor	200					lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)		AAGCAAGTTTCGAGAGTACTC	0.458													43	119	---	---	---	---	PASS
TMEM9B	56674	broad.mit.edu	37	11	8969885	8969885	+	Silent	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr11:8969885C>T	uc001mhe.1	-	5	708	c.579G>A	c.(577-579)CGG>CGA	p.R193R	TMEM9B_uc001mhf.1_Silent_p.R119R|TMEM9B_uc010rbt.1_Silent_p.R119R	NM_020644	NP_065695	Q9NQ34	TMM9B_HUMAN	TMEM9 domain family, member B precursor	193					positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	signal transducer activity				0				Epithelial(150;4.39e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0237)		GGACAACATGCCGGTCAAAGA	0.488													4	235	---	---	---	---	PASS
OR5I1	10798	broad.mit.edu	37	11	55703643	55703643	+	Missense_Mutation	SNP	G	T	T	rs144543203		TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr11:55703643G>T	uc010ris.1	-	1	234	c.234C>A	c.(232-234)GAC>GAA	p.D78E		NM_006637	NP_006628	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I,	78	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						TGGGAACAATGTCTGAGAAAT	0.383													4	104	---	---	---	---	PASS
NPAT	4863	broad.mit.edu	37	11	108031665	108031665	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr11:108031665C>T	uc001pjz.3	-	17	4250	c.4148G>A	c.(4147-4149)CGT>CAT	p.R1383H	NPAT_uc010rvv.1_Missense_Mutation_p.R439H	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	1383					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)		ACTAGAAGGACGAGAGTTTCG	0.333													28	89	---	---	---	---	PASS
OR8D2	283160	broad.mit.edu	37	11	124190086	124190086	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr11:124190086G>T	uc010sah.1	-	1	8	c.8C>A	c.(7-9)ACT>AAT	p.T3N		NM_001002918	NP_001002918	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D,	3	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)|central_nervous_system(1)|pancreas(1)	3		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		ATGGTTTGAAGTAGCCATGTC	0.408													10	111	---	---	---	---	PASS
ROBO4	54538	broad.mit.edu	37	11	124756546	124756546	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr11:124756546C>T	uc001qbg.2	-	16	2748	c.2608G>A	c.(2608-2610)GAG>AAG	p.E870K	ROBO4_uc010sas.1_Missense_Mutation_p.E725K|ROBO4_uc001qbh.2_3'UTR|ROBO4_uc001qbi.2_Missense_Mutation_p.E428K	NM_019055	NP_061928	Q8WZ75	ROBO4_HUMAN	roundabout homolog 4, magic roundabout	870					angiogenesis|cell differentiation	integral to membrane	receptor activity			ovary(1)|skin(1)	2	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		AAGGAGCCCTCGCTGGGGGTG	0.667													14	33	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	92920	92920	+	Missense_Mutation	SNP	C	G	G	rs145563795	by1000genomes	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr12:92920C>G	uc010sdi.1	-	1	99	c.71G>C	c.(70-72)AGT>ACT	p.S24T	uc010sdj.1_RNA					SubName: Full=DEAD/H box polypeptide 11 like 11;																		ACTCACAAGACTGTGATCCAA	0.622													4	13	---	---	---	---	PASS
ATP2B1	490	broad.mit.edu	37	12	90020309	90020309	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr12:90020309T>C	uc001tbh.2	-	7	1232	c.1051A>G	c.(1051-1053)AAA>GAA	p.K351E	ATP2B1_uc001tbg.2_Missense_Mutation_p.K351E|ATP2B1_uc001tbf.2_Missense_Mutation_p.K21E	NM_001682	NP_001673	P20020	AT2B1_HUMAN	plasma membrane calcium ATPase 1 isoform 1b	351	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						AAATTTGCTTTCTTTTTATCT	0.373													21	190	---	---	---	---	PASS
GNPTAB	79158	broad.mit.edu	37	12	102158763	102158763	+	Silent	SNP	T	C	C	rs10778148	byFrequency	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr12:102158763T>C	uc001tit.2	-	13	2111	c.1932A>G	c.(1930-1932)ACA>ACG	p.T644T		NM_024312	NP_077288	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase	644					cell differentiation	Golgi membrane|integral to membrane|nucleus	metal ion binding|transcription factor binding|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity			ovary(1)|skin(1)	2						CCTTCTGGGCTGTAGAATTCA	0.403													6	350	---	---	---	---	PASS
UBC	7316	broad.mit.edu	37	12	125396377	125396377	+	Silent	SNP	A	G	G	rs16918544	byFrequency	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr12:125396377A>G	uc001ugs.3	-	2	2389	c.1941T>C	c.(1939-1941)GAT>GAC	p.D647D	UBC_uc001ugr.2_RNA|UBC_uc001ugu.1_Silent_p.D571D|UBC_uc001ugt.2_Silent_p.D495D|UBC_uc001ugv.2_Silent_p.D115D	NM_021009	NP_066289	P0CG48	UBC_HUMAN	ubiquitin C	647	Ubiquitin-like 9.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		ACCTCTGCTGATCAGGAGGGA	0.527													7	484	---	---	---	---	PASS
PDS5B	23047	broad.mit.edu	37	13	33252986	33252986	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr13:33252986A>G	uc010abf.2	+	10	1135	c.977A>G	c.(976-978)CAT>CGT	p.H326R	PDS5B_uc001uuo.2_Missense_Mutation_p.H326R|PDS5B_uc010abg.2_RNA|PDS5B_uc010teb.1_Missense_Mutation_p.H28R	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog	326				H -> N (in Ref. 8; AAH39256).	cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		AATGATATCCATGTACCAATC	0.333													17	84	---	---	---	---	PASS
CHD8	57680	broad.mit.edu	37	14	21871248	21871248	+	Silent	SNP	A	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr14:21871248A>G	uc001was.1	-	18	2899	c.2805T>C	c.(2803-2805)CTT>CTC	p.L935L	CHD8_uc001war.1_Silent_p.L831L|CHD8_uc001wav.1_Silent_p.L377L	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1214	Helicase C-terminal.				ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		GATTAATACCAAGTCCACCAG	0.483													3	89	---	---	---	---	PASS
MIR329-2	574409	broad.mit.edu	37	14	101493478	101493478	+	RNA	SNP	T	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr14:101493478T>A	hsa-mir-329-2|MI0001726	+			c.42T>A			MIR494_hsa-mir-494|MI0003134_5'Flank|uc010txm.1_5'Flank|hsa-mir-1193|MI0014205_5'Flank																	0						TGTTTCTTTATTGAGGACGAA	0.478													5	276	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	29084045	29084045	+	RNA	SNP	T	G	G	rs75345913	by1000genomes	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr15:29084045T>G	uc001zcj.2	+	3		c.396T>G								Homo sapiens, Similar to hect domain and RLD 2, clone IMAGE:4581928, mRNA.																		TTATTCGTATTTTTTGGTAAC	0.229													3	11	---	---	---	---	PASS
GANC	2595	broad.mit.edu	37	15	42602622	42602622	+	Silent	SNP	G	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr15:42602622G>A	uc001zpi.2	+	9	1178	c.864G>A	c.(862-864)TCG>TCA	p.S288S	GANC_uc001zph.2_Silent_p.S288S|GANC_uc001zpj.1_Silent_p.S27S	NM_198141	NP_937784	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	288					carbohydrate metabolic process		carbohydrate binding|maltose alpha-glucosidase activity			central_nervous_system(2)	2		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)		TGAATGCCTCGGAAACACTGG	0.418													36	70	---	---	---	---	PASS
C15orf51	196968	broad.mit.edu	37	15	100333090	100333090	+	RNA	SNP	T	C	C	rs115410867	by1000genomes	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr15:100333090T>C	uc010urx.1	-	5		c.1102A>G			C15orf51_uc010ury.1_RNA	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0						GCCATTCTTTTGCTGGGCTTG	0.478													5	196	---	---	---	---	PASS
CACNG3	10368	broad.mit.edu	37	16	24373178	24373178	+	Silent	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr16:24373178C>T	uc002dmf.2	+	4	2142	c.942C>T	c.(940-942)CCC>CCT	p.P314P		NM_006539	NP_006530	O60359	CCG3_HUMAN	voltage-dependent calcium channel gamma-3	314					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0				GBM - Glioblastoma multiforme(48;0.0809)		GCACCACGCCCGTCTGAACTG	0.552													27	72	---	---	---	---	PASS
ZKSCAN2	342357	broad.mit.edu	37	16	25251248	25251248	+	Silent	SNP	G	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr16:25251248G>T	uc002dod.3	-	7	3200	c.2793C>A	c.(2791-2793)ACC>ACA	p.T931T	ZKSCAN2_uc010vcl.1_Silent_p.T727T	NM_001012981	NP_001012999	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	931	C2H2-type 6.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|breast(1)	4				GBM - Glioblastoma multiforme(48;0.0378)		CCCGATGTTTGGTAAGAACAG	0.463													4	195	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													3	11	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268158	70268158	+	RNA	SNP	A	C	C			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr16:70268158A>C	uc010cfp.1	-	3		c.257T>G								Homo sapiens cDNA, FLJ98908.																		TTCTTCATTAAAACAGCTACT	0.333													3	10	---	---	---	---	PASS
OSGIN1	29948	broad.mit.edu	37	16	83998851	83998851	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr16:83998851T>C	uc002fha.2	+	7	1305	c.922T>C	c.(922-924)TTC>CTC	p.F308L	OSGIN1_uc002fhb.2_Missense_Mutation_p.F225L|OSGIN1_uc002fhc.2_Missense_Mutation_p.F225L	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	308					cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						GGTGAGCGGCTTCCTGACCAG	0.692													21	69	---	---	---	---	PASS
VPS53	55275	broad.mit.edu	37	17	465950	465950	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr17:465950T>C	uc002frn.2	-	14	1496	c.1349A>G	c.(1348-1350)GAT>GGT	p.D450G	VPS53_uc002frk.2_5'UTR|VPS53_uc010cjo.1_Missense_Mutation_p.D450G|VPS53_uc002frl.2_RNA|VPS53_uc002frm.2_Missense_Mutation_p.D421G|VPS53_uc002fro.2_Missense_Mutation_p.D252G|VPS53_uc010cjp.1_Missense_Mutation_p.D173G	NM_018289	NP_060759	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 2	450					protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		GGCTTTGAAATCAGCCACAAA	0.478													9	53	---	---	---	---	PASS
FXR2	9513	broad.mit.edu	37	17	7495581	7495581	+	Silent	SNP	T	C	C			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr17:7495581T>C	uc002gia.1	-	16	2144	c.1917A>G	c.(1915-1917)TCA>TCG	p.S639S	MPDU1_uc010vuc.1_Intron|SOX15_uc002ghy.1_5'Flank|SOX15_uc002ghz.1_5'Flank	NM_004860	NP_004851	P51116	FXR2_HUMAN	fragile X mental retardation syndrome related	639						cytosolic large ribosomal subunit	protein binding|RNA binding				0				READ - Rectum adenocarcinoma(115;0.17)		CCTTCTGTCCTGAAAGAGAGT	0.507													3	144	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577094	7577094	+	Missense_Mutation	SNP	G	A	A	rs28934574		TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr17:7577094G>A	uc002gim.2	-	8	1038	c.844C>T	c.(844-846)CGG>TGG	p.R282W	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.R282W|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R150W|TP53_uc010cng.1_Missense_Mutation_p.R150W|TP53_uc002gii.1_Missense_Mutation_p.R150W|TP53_uc010cnh.1_Missense_Mutation_p.R282W|TP53_uc010cni.1_Missense_Mutation_p.R282W|TP53_uc002gij.2_Missense_Mutation_p.R282W	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	282	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|DR -> EW (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; 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.R282W(367)|p.R282G(27)|p.R282Q(20)|p.R282P(14)|p.R282R(8)|p.0?(7)|p.R282L(3)|p.D281fs*63(2)|p.?(2)|p.R282fs*24(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.R280fs*62(1)|p.R282_E287delRRTEEE(1)|p.G279fs*59(1)|p.S269fs*21(1)|p.C275_R283delCACPGRDRR(1)|p.D281_R282insXX(1)|p.L265_K305del41(1)|p.R282H(1)|p.R283_T284>T(1)|p.V272_K292del21(1)|p.R282fs*63(1)|p.C275fs*20(1)|p.D281_R282delDR(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)		TCTGTGCGCCGGTCTCTCCCA	0.557		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)			24	38	---	---	---	---	PASS
FLJ36000	284124	broad.mit.edu	37	17	21904125	21904125	+	RNA	SNP	G	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr17:21904125G>A	uc002gza.2	+	1		c.64G>A				NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						ggagtcgcaaggggccgagca	0.000													3	63	---	---	---	---	PASS
KRT40	125115	broad.mit.edu	37	17	39135205	39135205	+	Silent	SNP	A	G	G	rs8064910	by1000genomes	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr17:39135205A>G	uc010cxh.1	-	8	1208	c.1047T>C	c.(1045-1047)TGT>TGC	p.C349C	KRT40_uc002hvq.1_RNA	NM_182497	NP_872303	Q6A162	K1C40_HUMAN	type I hair keratin KA36	349	Rod.|Coil 2.			C -> R (in Ref. 1; CAH10353).		intermediate filament	structural molecule activity				0		Breast(137;0.00043)				TATCGATCAGACACTGAATTT	0.527													4	222	---	---	---	---	PASS
STAT5B	6777	broad.mit.edu	37	17	40362212	40362212	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr17:40362212G>A	uc002hzh.2	-	15	2052	c.1883C>T	c.(1882-1884)ACC>ATC	p.T628I		NM_012448	NP_036580	P51692	STA5B_HUMAN	signal transducer and activator of transcription	628	SH2.				2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|skin(1)	6		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)	CCAAGCAATGGTGATGCCGCC	0.428													3	86	---	---	---	---	PASS
GGA3	23163	broad.mit.edu	37	17	73235138	73235138	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr17:73235138C>T	uc002jni.1	-	15	1816	c.1807G>A	c.(1807-1809)GAT>AAT	p.D603N	GGA3_uc002jnj.1_Missense_Mutation_p.D570N|GGA3_uc010wrw.1_Missense_Mutation_p.D481N|GGA3_uc002jnk.1_Missense_Mutation_p.D531N|GGA3_uc010wrx.1_Missense_Mutation_p.D481N|GGA3_uc010wry.1_Missense_Mutation_p.D531N	NM_138619	NP_619525	Q9NZ52	GGA3_HUMAN	ADP-ribosylation factor binding protein 3	603	GAE.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|breast(1)	2			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			CCGTTTTTATCGTAGGCTGTC	0.592											OREG0024729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	27	---	---	---	---	PASS
TRIM65	201292	broad.mit.edu	37	17	73887232	73887232	+	Silent	SNP	C	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr17:73887232C>T	uc002jpx.2	-	6	1218	c.1182G>A	c.(1180-1182)TCG>TCA	p.S394S		NM_173547	NP_775818	Q6PJ69	TRI65_HUMAN	tripartite motif-containing 65	394	B30.2/SPRY.					intracellular	zinc ion binding				0			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCAGTGTCACCGAGTGGTCTG	0.692													4	88	---	---	---	---	PASS
GIPC3	126326	broad.mit.edu	37	19	3589510	3589510	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr19:3589510C>A	uc002lyd.3	+	4	689	c.662C>A	c.(661-663)ACC>AAC	p.T221N		NM_133261	NP_573568	Q8TF64	GIPC3_HUMAN	GIPC PDZ domain containing family, member 3	221										breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGAGGGAGACCCTGCGGCTT	0.393													10	81	---	---	---	---	PASS
SAFB2	9667	broad.mit.edu	37	19	5598870	5598870	+	Silent	SNP	G	A	A	rs149716077		TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr19:5598870G>A	uc002mcd.2	-	13	1928	c.1716C>T	c.(1714-1716)GTC>GTT	p.V572V		NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	572					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		TATCCATCACGACCGTCCGCT	0.507													30	75	---	---	---	---	PASS
CLEC4M	10332	broad.mit.edu	37	19	7830869	7830869	+	Missense_Mutation	SNP	G	A	A	rs28413926	byFrequency	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr19:7830869G>A	uc002mih.2	+	5	609	c.491G>A	c.(490-492)CGG>CAG	p.R164Q	CLEC4M_uc010xjv.1_Missense_Mutation_p.R159Q|CLEC4M_uc002mhy.2_Missense_Mutation_p.R131Q|CLEC4M_uc010xjw.1_Missense_Mutation_p.G166E|CLEC4M_uc010dvt.2_Intron|CLEC4M_uc010dvs.2_Missense_Mutation_p.R163Q|CLEC4M_uc010xjx.1_Missense_Mutation_p.R136Q|CLEC4M_uc002mhz.2_Intron|CLEC4M_uc002mic.2_Missense_Mutation_p.R159Q|CLEC4M_uc002mia.2_Intron	NM_001144910	NP_001138382	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M isoform	164	Extracellular (Probable).|7 X approximate tandem repeats.|3.				cell-cell recognition|endocytosis|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to plasma membrane	ICAM-3 receptor activity|mannose binding|metal ion binding|peptide antigen binding|virion binding			pancreas(1)	1						GAGCTGACCCGGCTGAAGGCT	0.582													8	143	---	---	---	---	PASS
OR7G3	390883	broad.mit.edu	37	19	9237435	9237435	+	Silent	SNP	A	G	G	rs10407484	byFrequency	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr19:9237435A>G	uc010xkl.1	-	1	192	c.192T>C	c.(190-192)TCT>TCC	p.S64S		NM_001001958	NP_001001958	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G,	64	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						AGGACAGGATAGAGAGGAGGA	0.552													3	189	---	---	---	---	PASS
NCAN	1463	broad.mit.edu	37	19	19338359	19338359	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr19:19338359C>G	uc002nlz.2	+	8	2029	c.1930C>G	c.(1930-1932)CTA>GTA	p.L644V	NCAN_uc010ecc.1_Missense_Mutation_p.L208V	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	644					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			AGAGTGGATGCTACCACACCC	0.637													7	76	---	---	---	---	PASS
ZNF181	339318	broad.mit.edu	37	19	35232275	35232275	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr19:35232275T>C	uc002nvu.3	+	4	1452	c.989T>C	c.(988-990)TTT>TCT	p.F330S	ZNF181_uc010xsa.1_Missense_Mutation_p.F329S|ZNF181_uc010xsb.1_Missense_Mutation_p.F329S|ZNF181_uc010xsc.1_Missense_Mutation_p.F265S	NM_001029997	NP_001025168	Q2M3W8	ZN181_HUMAN	zinc finger protein 181 isoform 1	330	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			GGAAAGTCTTTTAGTCGTGTG	0.398													3	168	---	---	---	---	PASS
ZNF181	339318	broad.mit.edu	37	19	35232279	35232279	+	Missense_Mutation	SNP	T	G	G	rs150124360		TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr19:35232279T>G	uc002nvu.3	+	4	1456	c.993T>G	c.(991-993)AGT>AGG	p.S331R	ZNF181_uc010xsa.1_Missense_Mutation_p.S330R|ZNF181_uc010xsb.1_Missense_Mutation_p.S330R|ZNF181_uc010xsc.1_Missense_Mutation_p.S266R	NM_001029997	NP_001025168	Q2M3W8	ZN181_HUMAN	zinc finger protein 181 isoform 1	331	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			AGTCTTTTAGTCGTGTGTCCC	0.403													3	169	---	---	---	---	PASS
ZNF285	26974	broad.mit.edu	37	19	44891217	44891217	+	Missense_Mutation	SNP	T	C	C	rs144198432	by1000genomes	TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr19:44891217T>C	uc002ozd.3	-	4	1277	c.1190A>G	c.(1189-1191)GAG>GGG	p.E397G	ZFP112_uc010xwz.1_Intron|ZNF285_uc010xxa.1_Missense_Mutation_p.E404G	NM_152354	NP_689567	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	397					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(2)	4						GTAGGGCTTCTCTCCAGTGTG	0.483													5	123	---	---	---	---	PASS
TRAPPC6A	79090	broad.mit.edu	37	19	45668125	45668125	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr19:45668125G>A	uc002paw.2	-	3	275	c.256C>T	c.(256-258)CGC>TGC	p.R86C	TRAPPC6A_uc002pav.2_Missense_Mutation_p.R100C			O75865	TPC6A_HUMAN	SubName: Full=TRAPPC6Adelta29-42; SubName: Full=Trafficking protein particle complex 6A, isoform CRA_a;	86					vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00872)|GBM - Glioblastoma multiforme(486;0.233)		TGATTGGTGCGCAGGCTGTCC	0.647													4	158	---	---	---	---	PASS
SEMG2	6407	broad.mit.edu	37	20	43851631	43851631	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr20:43851631C>A	uc010ggz.2	+	2	1415	c.1358C>A	c.(1357-1359)CCT>CAT	p.P453H	SEMG2_uc002xnk.2_Missense_Mutation_p.P453H|SEMG2_uc002xnl.2_Intron	NM_003008	NP_002999	Q02383	SEMG2_HUMAN	semenogelin II precursor	453	Repeat-rich region.|4 X 60 AA tandem repeats, type I.				sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(1)	1		Myeloproliferative disorder(115;0.0122)				GTAACAATTCCTAGTCAAGAT	0.393													5	127	---	---	---	---	PASS
ZNFX1	57169	broad.mit.edu	37	20	47864642	47864642	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr20:47864642A>G	uc002xui.2	-	14	5166	c.4919T>C	c.(4918-4920)CTA>CCA	p.L1640P		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1640							metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			AATCTCTTCTAGCCGCTGTTT	0.507													42	82	---	---	---	---	PASS
SHOX	6473	broad.mit.edu	37	X	601572	601572	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chrX:601572G>A	uc004cph.1	+	4	1194	c.503G>A	c.(502-504)CGG>CAG	p.R168Q	SHOX_uc004cpi.2_Missense_Mutation_p.R168Q	NM_000451	NP_000442	O15266	SHOX_HUMAN	short stature homeobox isoform SHOXa	168	Homeobox.		R -> W (in LMD).		skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TTCCAGAACCGGAGAGCCAAG	0.592													45	137	---	---	---	---	PASS
ZBED1	9189	broad.mit.edu	37	X	2407936	2407936	+	Silent	SNP	G	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chrX:2407936G>A	uc004cqg.2	-	2	1026	c.825C>T	c.(823-825)ATC>ATT	p.I275I	DHRSX_uc004cqf.3_Intron|ZBED1_uc004cqh.1_Silent_p.I275I	NM_004729	NP_004720	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	275						nuclear chromosome	DNA binding|metal ion binding|protein dimerization activity|transposase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACGCCTTCACGATGTCCTTGC	0.627													72	189	---	---	---	---	PASS
CCDC22	28952	broad.mit.edu	37	X	49099406	49099406	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chrX:49099406C>A	uc004dnd.1	+	4	572	c.416C>A	c.(415-417)GCA>GAA	p.A139E	CCDC22_uc011mna.1_Missense_Mutation_p.A139E|CCDC22_uc004dnc.1_RNA	NM_014008	NP_054727	O60826	CCD22_HUMAN	coiled-coil domain containing 22	139										central_nervous_system(1)	1						GACCAGCTGGCACTGCCTTGG	0.587													4	5	---	---	---	---	PASS
MID2	11043	broad.mit.edu	37	X	107159358	107159358	+	Silent	SNP	A	G	G			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chrX:107159358A>G	uc004enl.2	+	6	1773	c.1200A>G	c.(1198-1200)ACA>ACG	p.T400T	MID2_uc004enk.2_Silent_p.T400T	NM_012216	NP_036348	Q9UJV3	TRIM1_HUMAN	midline 2 isoform 1	400	Fibronectin type-III.					centrosome|microtubule	ligase activity|zinc ion binding			ovary(1)	1						ATTATTTAACAGGTGTGAAAA	0.254													3	196	---	---	---	---	PASS
SPANXN1	494118	broad.mit.edu	37	X	144337274	144337274	+	Silent	SNP	G	T	T			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chrX:144337274G>T	uc004fcb.2	+	2	159	c.159G>T	c.(157-159)GCG>GCT	p.A53A		NM_001009614	NP_001009614	Q5VSR9	SPXN1_HUMAN	SPANX-N1 protein	53											0	Acute lymphoblastic leukemia(192;6.56e-05)					CAGTATTAGCGTTTTGCTACA	0.433													3	123	---	---	---	---	PASS
IRF2	3660	broad.mit.edu	37	4	185340707	185340707	+	Frame_Shift_Del	DEL	G	-	-			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr4:185340707delG	uc003iwf.3	-	3	303	c.103delC	c.(103-105)CAGfs	p.Q35fs		NM_002199	NP_002190	P14316	IRF2_HUMAN	interferon regulatory factor 2	35	IRF tryptophan pentad repeat.				blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	focal adhesion|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		CAGGGGATCTGAAAAATCTTC	0.423													73	24	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180699084	180699085	+	RNA	INS	-	A	A			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr5:180699084_180699085insA	uc003mnq.2	+	3		c.448_449insA								Homo sapiens cDNA clone IMAGE:3910094, partial cds.																		GGCTTTCCATCAGAAAAAAAAA	0.411													4	2	---	---	---	---	
USP31	57478	broad.mit.edu	37	16	23080918	23080918	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr16:23080918delT	uc002dll.2	-	16	2508	c.2508delA	c.(2506-2508)CCAfs	p.P836fs	USP31_uc002dlk.2_Frame_Shift_Del_p.P108fs|USP31_uc010vca.1_Frame_Shift_Del_p.P139fs|USP31_uc010bxm.2_Frame_Shift_Del_p.P124fs	NM_020718	NP_065769	Q70CQ4	UBP31_HUMAN	ubiquitin specific peptidase 31	836	Ser-rich.				ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(3)|lung(3)|breast(2)|pancreas(1)|skin(1)	10				GBM - Glioblastoma multiforme(48;0.0187)		TTCTCACAAATGGTCGAGTTG	0.438													49	12	---	---	---	---	
ADNP	23394	broad.mit.edu	37	20	49508203	49508204	+	Frame_Shift_Ins	INS	-	T	T	rs6096163		TCGA-EJ-5514-01A-01D-1576-08	TCGA-EJ-5514-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	f28f091d-5cd5-447f-b956-3ef7eb305fe2	7b498228-7d17-4b2e-b815-123ebfe1f366	g.chr20:49508203_49508204insT	uc002xvt.1	-	5	3392_3393	c.3047_3048insA	c.(3046-3048)AAGfs	p.K1016fs	ADNP_uc002xvu.1_Frame_Shift_Ins_p.K1016fs	NM_015339	NP_056154	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector	1016						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						GCATGGTAGCCTTTTTTTTGGC	0.460													316	8	---	---	---	---	
