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
ESPNP	284729	broad.mit.edu	37	1	17034110	17034110	+	Missense_Mutation	SNP	C	T	T	rs55767123		TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr1:17034110C>T	uc001azn.1	-	3	494	c.380G>A	c.(379-381)GGC>GAC	p.G127D	ESPNP_uc010ocj.1_Missense_Mutation_p.G57D	NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						GATCTCCCCGCCGTGCAGCAG	0.612													3	10	---	---	---	---	PASS
TRIM33	51592	broad.mit.edu	37	1	115005788	115005788	+	Silent	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr1:115005788G>A	uc001eew.2	-	4	945	c.861C>T	c.(859-861)TTC>TTT	p.F287F	TRIM33_uc010ows.1_5'UTR|TRIM33_uc001eex.2_Silent_p.F287F	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform	287	B box-type 2.				negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATGTTTCACAGAAAAGTTTCA	0.353			T	RET	papillary thyroid								5	74	---	---	---	---	PASS
ITGA10	8515	broad.mit.edu	37	1	145530284	145530284	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr1:145530284G>T	uc001eoa.2	+	6	575	c.499G>T	c.(499-501)GAT>TAT	p.D167Y	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Missense_Mutation_p.D36Y|ITGA10_uc009wiw.2_Missense_Mutation_p.D24Y|ITGA10_uc010oyw.1_Missense_Mutation_p.D112Y	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	167	VWFA.|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)					AACATACATGGATGTTGTCAT	0.498													7	205	---	---	---	---	PASS
ARHGAP30	257106	broad.mit.edu	37	1	161021490	161021490	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr1:161021490A>C	uc001fxl.2	-	10	1380	c.1034T>G	c.(1033-1035)GTG>GGG	p.V345G	ARHGAP30_uc001fxk.2_Missense_Mutation_p.V345G|ARHGAP30_uc001fxm.2_Missense_Mutation_p.V191G|ARHGAP30_uc009wtx.2_Missense_Mutation_p.V18G|ARHGAP30_uc001fxn.1_Missense_Mutation_p.V191G	NM_001025598	NP_001020769	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30 isoform 1	345					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|upper_aerodigestive_tract(1)	3	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GCTGGGCCCCACCAGCCCCTC	0.582													10	29	---	---	---	---	PASS
PRG4	10216	broad.mit.edu	37	1	186276508	186276508	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr1:186276508T>G	uc001gru.3	+	7	1708	c.1657T>G	c.(1657-1659)TCA>GCA	p.S553A	PRG4_uc001grt.3_Missense_Mutation_p.S512A|PRG4_uc009wyl.2_Missense_Mutation_p.S460A|PRG4_uc009wym.2_Missense_Mutation_p.S419A|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	553	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|27.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						CAAGGAGCCTTCACCCACCAC	0.642													4	64	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179426189	179426189	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr2:179426189T>G	uc010zfg.1	-	275	77190	c.76966A>C	c.(76966-76968)ATG>CTG	p.M25656L	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.M19351L|TTN_uc010zfi.1_Missense_Mutation_p.M19284L|TTN_uc010zfj.1_Missense_Mutation_p.M19159L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	26583							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACTCATACATCAGTCCTTCA	0.398													74	149	---	---	---	---	PASS
KLHL18	23276	broad.mit.edu	37	3	47361170	47361170	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr3:47361170C>T	uc003crd.2	+	2	283	c.157C>T	c.(157-159)CGG>TGG	p.R53W	KLHL18_uc003crc.2_Missense_Mutation_p.R53W|KLHL18_uc011bav.1_Intron	NM_025010	NP_079286	O94889	KLH18_HUMAN	kelch-like 18	53											0		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		CAGTGCCCACCGGATTGTCTT	0.418													60	170	---	---	---	---	PASS
DNAH1	25981	broad.mit.edu	37	3	52366398	52366398	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr3:52366398G>A	uc011bef.1	+	8	1535	c.1274G>A	c.(1273-1275)CGC>CAC	p.R425H	DNAH1_uc003ddt.1_Missense_Mutation_p.R425H	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	425	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCTCGGATGCGCAAAGGCCCC	0.582													5	98	---	---	---	---	PASS
TMPRSS7	344805	broad.mit.edu	37	3	111795794	111795794	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr3:111795794C>T	uc010hqb.2	+	14	1819	c.1649C>T	c.(1648-1650)CCG>CTG	p.P550L	TMPRSS7_uc011bhr.1_Missense_Mutation_p.P405L	NM_001042575	NP_001036040	Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	676	Extracellular (Potential).|Peptidase S1.				proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2						TTTGTCTCCCCGGTGAGAAGA	0.453													121	215	---	---	---	---	PASS
ZIC1	7545	broad.mit.edu	37	3	147128521	147128521	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr3:147128521C>A	uc003ewe.2	+	1	1341	c.622C>A	c.(622-624)CAC>AAC	p.H208N		NM_003412	NP_003403	Q15915	ZIC1_HUMAN	zinc finger protein of the cerebellum 1	208					behavior|brain development|cell differentiation|inner ear morphogenesis|pattern specification process|positive regulation of protein import into nucleus|positive regulation of transcription, DNA-dependent|regulation of smoothened signaling pathway	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						GGCCGCGCATCACGGCGCCGG	0.642													15	64	---	---	---	---	PASS
P2RY1	5028	broad.mit.edu	37	3	152554551	152554551	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr3:152554551C>T	uc003ezq.2	+	1	1816	c.980C>T	c.(979-981)GCG>GTG	p.A327V		NM_002563	NP_002554	P47900	P2RY1_HUMAN	purinergic receptor P2Y1	327	Helical; Name=7; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|platelet activation	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TATTTCTTGGCGGGAGATACT	0.463													5	129	---	---	---	---	PASS
SOD3	6649	broad.mit.edu	37	4	24801303	24801303	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr4:24801303G>A	uc003gqz.2	+	2	365	c.160G>A	c.(160-162)GAC>AAC	p.D54N	SOD3_uc003gqy.1_RNA	NM_003102	NP_003093	P08294	SODE_HUMAN	superoxide dismutase 3, extracellular precursor	54					removal of superoxide radicals	extracellular space|nucleus|soluble fraction	copper ion binding|heparin binding|protein binding|superoxide dismutase activity|zinc ion binding				0		Breast(46;0.0503)				GCAGCGGCGGGACGACGACGG	0.716													14	8	---	---	---	---	PASS
ANKRD56	345079	broad.mit.edu	37	4	77818329	77818329	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr4:77818329G>A	uc003hki.2	-	1	674	c.674C>T	c.(673-675)CCG>CTG	p.P225L		NM_001029870	NP_001025041	A6NEL2	ANR56_HUMAN	ankyrin repeat domain 56	225	Ala-rich.										0						AGCCCGTGCCGGCTTCTCCTC	0.706													4	9	---	---	---	---	PASS
SLCO6A1	133482	broad.mit.edu	37	5	101834316	101834316	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr5:101834316G>A	uc003knn.2	-	1	405	c.233C>T	c.(232-234)CCG>CTG	p.P78L	SLCO6A1_uc003kno.2_Missense_Mutation_p.P78L|SLCO6A1_uc003knp.2_Missense_Mutation_p.P78L|SLCO6A1_uc003knq.2_Missense_Mutation_p.P78L	NM_173488	NP_775759	Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family,	78	Cytoplasmic (Potential).			KPG -> NRE (in Ref. 1; AAP33048).		integral to membrane|plasma membrane	transporter activity			ovary(3)|skin(3)|central_nervous_system(1)	7		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		CACTTCTCCCGGCTTCTTGGA	0.488													55	242	---	---	---	---	PASS
PCDHGC4	56098	broad.mit.edu	37	5	140865886	140865886	+	Silent	SNP	C	T	T	rs148184642	byFrequency	TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr5:140865886C>T	uc003lky.1	+	1	1146	c.1146C>T	c.(1144-1146)AAC>AAT	p.N382N	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lkv.1_Intron|PCDHGC3_uc003lkw.1_Intron|PCDHGC4_uc011dbb.1_Silent_p.N382N|PCDHGC5_uc011dbc.1_5'Flank|PCDHGC5_uc003lla.1_5'Flank	NM_018928	NP_061751	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4 isoform 1	382	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGGGTCAAACGGAGATGTGA	0.562													6	98	---	---	---	---	PASS
KAAG1	353219	broad.mit.edu	37	6	24357720	24357720	+	Translation_Start_Site	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr6:24357720C>T	uc003ndz.1	+	1	590	c.-147C>T	c.(-149--145)CACGT>CATGT		DCDC2_uc003ndx.2_Missense_Mutation_p.V87M|DCDC2_uc003ndy.2_Missense_Mutation_p.V87M	NM_181337	NP_851854	Q9UBP8	KAAG1_HUMAN	kidney associated antigen 1						immune response						0						CCTCCAGCCACGTAATTGCCC	0.587													40	105	---	---	---	---	PASS
LRRC16A	55604	broad.mit.edu	37	6	25472740	25472740	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr6:25472740G>T	uc011djw.1	+	11	1241	c.865G>T	c.(865-867)GAG>TAG	p.E289*	LRRC16A_uc010jpx.2_Nonsense_Mutation_p.E289*|LRRC16A_uc010jpy.2_Nonsense_Mutation_p.E289*|LRRC16A_uc003nez.1_Nonsense_Mutation_p.E128*	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	289	LRR 2.				actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						CAACCCACTGGAGGATAGAGG	0.423													2	1	---	---	---	---	PASS
KIFC1	3833	broad.mit.edu	37	6	33377450	33377450	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr6:33377450C>T	uc003oef.3	+	11	2455	c.2005C>T	c.(2005-2007)CAG>TAG	p.Q669*	KIFC1_uc011drf.1_Nonsense_Mutation_p.Q661*|PHF1_uc011drh.1_5'Flank|PHF1_uc003oeh.2_5'Flank|PHF1_uc003oei.2_5'Flank|PHF1_uc010jux.2_5'Flank	NM_002263	NP_002254	Q9BW19	KIFC1_HUMAN	kinesin family member C1	669					blood coagulation|cell division|microtubule-based movement|mitotic sister chromatid segregation	early endosome|microtubule|microtubule associated complex|microtubule organizing center|nucleus|spindle	ATP binding|microtubule motor activity				0						TGGTACTGCTCAGGCCAACAG	0.363													39	259	---	---	---	---	PASS
FBXL4	26235	broad.mit.edu	37	6	99323344	99323344	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr6:99323344T>G	uc003ppf.1	-	8	2007	c.1649A>C	c.(1648-1650)GAC>GCC	p.D550A	FBXL4_uc003ppg.1_Missense_Mutation_p.D550A|FBXL4_uc003pph.1_Missense_Mutation_p.D152A|FBXL4_uc010kcp.2_Missense_Mutation_p.D128A	NM_012160	NP_036292	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	550	LRR 7.				ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex				skin(2)	2		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		TTCATCAATGTCTGTGTCACA	0.413													46	121	---	---	---	---	PASS
NEUROD6	63974	broad.mit.edu	37	7	31377922	31377922	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr7:31377922G>A	uc003tch.2	-	2	1314	c.961C>T	c.(961-963)CGC>TGC	p.R321C		NM_022728	NP_073565	Q96NK8	NDF6_HUMAN	neurogenic differentiation 6	321					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)	2						GATTGGCTGCGCAGATGTAAG	0.478													10	145	---	---	---	---	PASS
BBS9	27241	broad.mit.edu	37	7	33573723	33573723	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr7:33573723T>C	uc003tdn.1	+	21	2969	c.2456T>C	c.(2455-2457)TTA>TCA	p.L819S	BBS9_uc003tdo.1_Missense_Mutation_p.L784S|BBS9_uc003tdp.1_Missense_Mutation_p.L814S|BBS9_uc003tdq.1_Missense_Mutation_p.L779S|BBS9_uc010kwn.1_RNA|BBS9_uc003tdr.1_Missense_Mutation_p.L343S|BBS9_uc003tds.1_Missense_Mutation_p.L242S|BBS9_uc003tdt.2_RNA	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	819					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			TGCGATAGATTATCCAAAGGT	0.493									Bardet-Biedl_syndrome				45	86	---	---	---	---	PASS
C7orf23	79161	broad.mit.edu	37	7	86848787	86848787	+	Silent	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr7:86848787G>A	uc003uio.2	-	1	245	c.33C>T	c.(31-33)ACC>ACT	p.T11T		NM_024315	NP_077291	Q9BU79	CG023_HUMAN	chromosome 7 open reading frame 23	11						integral to membrane					0	Esophageal squamous(14;0.0058)|all_lung(186;0.191)|Lung NSC(181;0.192)					CCAGGCCACTGGTGCCGTAGG	0.572										HNSCC(41;0.11)			16	68	---	---	---	---	PASS
DOK2	9046	broad.mit.edu	37	8	21768190	21768190	+	Silent	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr8:21768190C>T	uc003wzy.1	-	4	705	c.612G>A	c.(610-612)CGG>CGA	p.R204R	DOK2_uc003wzx.1_Silent_p.R204R|DOK2_uc003wzz.1_Silent_p.R50R|DOK2_uc010lth.1_Silent_p.R50R	NM_003974	NP_003965	O60496	DOK2_HUMAN	docking protein 2	204	IRS-type PTB.				blood coagulation|leukocyte migration	cytosol	identical protein binding|insulin receptor binding				0				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		TCACCTTGTCCCGCCCAAAGC	0.507													15	23	---	---	---	---	PASS
EPPK1	83481	broad.mit.edu	37	8	144942667	144942667	+	Missense_Mutation	SNP	C	A	A	rs111431754		TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr8:144942667C>A	uc003zaa.1	-	1	4768	c.4755G>T	c.(4753-4755)ATG>ATT	p.M1585I		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	1585	Plectin 26.					cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTGGGATGCTCATCCTCTCCT	0.647													33	26	---	---	---	---	PASS
A1CF	29974	broad.mit.edu	37	10	52595982	52595982	+	Silent	SNP	G	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr10:52595982G>T	uc001jjj.2	-	6	644	c.456C>A	c.(454-456)ATC>ATA	p.I152I	A1CF_uc010qhn.1_Silent_p.I160I|A1CF_uc001jji.2_Silent_p.I152I|A1CF_uc001jjh.2_Silent_p.I160I|A1CF_uc010qho.1_Silent_p.I160I|A1CF_uc009xov.2_Silent_p.I152I	NM_138932	NP_620310	Q9NQ94	A1CF_HUMAN	apobec-1 complementation factor isoform 2	152	RRM 2.				cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1						TCTCCGATAAGATTTCTTCTC	0.463													19	196	---	---	---	---	PASS
KIF18A	81930	broad.mit.edu	37	11	28058051	28058051	+	Silent	SNP	A	G	G			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr11:28058051A>G	uc001msc.2	-	14	2291	c.2109T>C	c.(2107-2109)ATT>ATC	p.I703I		NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A	703					blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			ovary(2)	2						GTGTATATACAATAGGCTGAA	0.383													48	191	---	---	---	---	PASS
CATSPER1	117144	broad.mit.edu	37	11	65793239	65793239	+	Silent	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr11:65793239G>A	uc001ogt.2	-	1	750	c.612C>T	c.(610-612)CAC>CAT	p.H204H		NM_053054	NP_444282	Q8NEC5	CTSR1_HUMAN	sperm-associated cation channel 1	204	His-rich.|Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	protein binding			ovary(2)	2						GGGACTCATCGTGTTGGAGCC	0.617													5	137	---	---	---	---	PASS
CABP4	57010	broad.mit.edu	37	11	67223061	67223061	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr11:67223061G>A	uc001olo.2	+	1	244	c.167G>A	c.(166-168)GGC>GAC	p.G56D	GPR152_uc001olm.2_5'Flank|CABP4_uc001oln.2_Intron	NM_145200	NP_660201	P57796	CABP4_HUMAN	calcium binding protein 4	56					visual perception	cytoplasm|extracellular region|terminal button	calcium ion binding				0			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			AAGCGCACTGGCAGCTCTGGG	0.687													13	9	---	---	---	---	PASS
ACY3	91703	broad.mit.edu	37	11	67412278	67412278	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr11:67412278G>A	uc001omq.2	-	7	868	c.697C>T	c.(697-699)CGC>TGC	p.R233C		NM_080658	NP_542389	Q96HD9	ACY3_HUMAN	aspartoacylase 3	233					interspecies interaction between organisms	apical plasma membrane|cytoplasm	hydrolase activity, acting on ester bonds|metal ion binding				0					L-Aspartic Acid(DB00128)	GCCTCGGTGCGGGGGAAGTCC	0.562													4	7	---	---	---	---	PASS
TRPC6	7225	broad.mit.edu	37	11	101374961	101374961	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr11:101374961G>A	uc001pgk.3	-	2	1164	c.739C>T	c.(739-741)CGG>TGG	p.R247W	TRPC6_uc009ywy.2_Missense_Mutation_p.R247W|TRPC6_uc009ywz.1_Missense_Mutation_p.R247W	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	247	Cytoplasmic (Potential).|ANK 4.				axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		TCATGAGGCCGTTCAATCCTA	0.478													79	180	---	---	---	---	PASS
ABCC9	10060	broad.mit.edu	37	12	22035727	22035727	+	Silent	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr12:22035727G>A	uc001rfi.1	-	14	2012	c.1992C>T	c.(1990-1992)CCC>CCT	p.P664P	ABCC9_uc001rfh.2_Silent_p.P664P|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	664	Cytoplasmic (Potential).				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	CTGTTTCTGCGGGACGTAGAC	0.383													56	232	---	---	---	---	PASS
KRT81	3887	broad.mit.edu	37	12	52680993	52680993	+	Silent	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr12:52680993C>T	uc001sab.2	-	7	1190	c.1140G>A	c.(1138-1140)CAG>CAA	p.Q380Q	KRT86_uc010snq.1_Intron|KRT86_uc009zmg.2_Intron|KRT81_uc001sac.2_5'UTR	NM_002281	NP_002272	Q14533	KRT81_HUMAN	keratin, hair, basic, 1	380	Rod.|Coil 2.					keratin filament	protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.189)		AGGCCATGTCCTGCTTGGCCT	0.672													5	152	---	---	---	---	PASS
SLITRK5	26050	broad.mit.edu	37	13	88329453	88329453	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr13:88329453C>T	uc001vln.2	+	2	2029	c.1810C>T	c.(1810-1812)CGC>TGC	p.R604C	SLITRK5_uc010tic.1_Missense_Mutation_p.R363C	NM_015567	NP_056382	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5 precursor	604	LRRCT 2.|Extracellular (Potential).					integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5	all_neural(89;0.101)|Medulloblastoma(90;0.163)					GACCGACATGCGCTCCATTAA	0.567													21	208	---	---	---	---	PASS
FUT8	2530	broad.mit.edu	37	14	66208993	66208993	+	Silent	SNP	G	C	C			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr14:66208993G>C	uc001xin.2	+	11	2790	c.1593G>C	c.(1591-1593)GTG>GTC	p.V531V	FUT8_uc001xio.2_Silent_p.V531V|FUT8_uc010tsp.1_Silent_p.V368V|FUT8_uc001xir.3_RNA|FUT8_uc001xip.2_Silent_p.V531V|FUT8_uc001xiq.2_Silent_p.V402V|FUT8_uc001xis.2_Silent_p.V125V	NM_178155	NP_835368	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a	531	SH3.|Lumenal (Potential).				in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		TCATTGGTGTGGCTGGAAATC	0.463													20	181	---	---	---	---	PASS
MIR543	100126335	broad.mit.edu	37	14	101498368	101498368	+	RNA	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr14:101498368C>T	hsa-mir-543|MI0005565	+			c.45C>T			MIR495_hsa-mir-495|MI0003135_5'Flank																	0						TTATTTGTGACGAAACATTCG	0.502													8	120	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106691922	106691922	+	RNA	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr14:106691922C>T	uc010tyt.1	-	754		c.20441G>A								Parts of antibodies, mostly variable regions.												0						TCAGGGACCCCCCAGGCTTGA	0.587													9	185	---	---	---	---	PASS
BCL8	606	broad.mit.edu	37	15	20874901	20874901	+	Silent	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr15:20874901G>A	uc010tze.1	-	3	444	c.237C>T	c.(235-237)ACC>ACT	p.T79T	BCL8_uc010tzd.1_RNA	NR_027992				RecName: Full=Putative protein BCL8;												0						TTCTGCATATGGTGGTGTAGA	0.333													3	67	---	---	---	---	PASS
IL21R	50615	broad.mit.edu	37	16	27455956	27455956	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr16:27455956C>T	uc002doq.1	+	6	834	c.601C>T	c.(601-603)CGG>TGG	p.R201W	IL21R_uc002dor.1_Missense_Mutation_p.R201W|IL21R_uc002dos.1_Missense_Mutation_p.R201W	NM_181078	NP_851564	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor precursor	201	Extracellular (Potential).|Fibronectin type-III.				natural killer cell activation	integral to membrane	interleukin-21 receptor activity			ovary(2)|lung(1)|breast(1)	4						GCTGCAGGTGCGGGCAGGGCC	0.597			T	BCL6	NHL								8	239	---	---	---	---	PASS
ATP2C2	9914	broad.mit.edu	37	16	84402275	84402275	+	Silent	SNP	G	C	C	rs62048787	by1000genomes	TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr16:84402275G>C	uc002fhx.2	+	1	143	c.54G>C	c.(52-54)GGG>GGC	p.G18G	ATP2C2_uc010chj.2_Silent_p.G18G	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	18	Cytoplasmic (Potential).				ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						TCTCGGGCGGGGGCCGCCAGT	0.706													4	1	---	---	---	---	PASS
TBC1D29	26083	broad.mit.edu	37	17	28890361	28890361	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr17:28890361G>A	uc002hfh.2	+	5	520	c.371G>A	c.(370-372)CGG>CAG	p.R124Q	TBC1D29_uc002hfi.2_RNA	NM_015594	NP_056409	Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29	124						intracellular	Rab GTPase activator activity				0		Myeloproliferative disorder(56;0.0255)				GCCTTGAGCCGGGGAGACAAG	0.423													5	85	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	76497744	76497744	+	RNA	SNP	T	G	G			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr17:76497744T>G	uc002jvt.1	+	2		c.3203T>G								Homo sapiens cDNA FLJ45552 fis, clone BRTHA2038279.																		AGTGGCAGGGTCTGAAGTCCC	0.627													13	24	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	76497776	76497776	+	RNA	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr17:76497776G>A	uc002jvt.1	+	2		c.3235G>A								Homo sapiens cDNA FLJ45552 fis, clone BRTHA2038279.																		CCCTGAACCCGGTGTCCCCTT	0.632													9	125	---	---	---	---	PASS
SGSH	6448	broad.mit.edu	37	17	78187975	78187975	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr17:78187975A>G	uc002jxz.3	-	5	746	c.659T>C	c.(658-660)GTG>GCG	p.V220A	SGSH_uc002jya.3_Missense_Mutation_p.V17A|SGSH_uc002jxy.2_Missense_Mutation_p.V220A|SGSH_uc010wue.1_Missense_Mutation_p.C232R	NM_000199	NP_000190	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase precursor	220					proteoglycan metabolic process	lysosome	metal ion binding|N-sulfoglucosamine sulfohydrolase activity|sulfuric ester hydrolase activity			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TCCTACCAGCACGTCCAGTGG	0.637													11	21	---	---	---	---	PASS
AATK	9625	broad.mit.edu	37	17	79094618	79094618	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr17:79094618T>C	uc010dia.2	-	11	3198	c.3118A>G	c.(3118-3120)AGG>GGG	p.R1040G	AATK_uc010dhz.2_Intron	NM_001080395	NP_001073864	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1040						integral to membrane|mitochondrion|perinuclear region of cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1)	9	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			ACCCCAGGCCTGAGACAGACC	0.716													2	11	---	---	---	---	PASS
ZNF24	7572	broad.mit.edu	37	18	32917272	32917272	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr18:32917272T>C	uc002kyt.2	-	4	1188	c.1031A>G	c.(1030-1032)TAT>TGT	p.Y344C	ZNF24_uc002kys.2_Missense_Mutation_p.Y344C	NM_006965	NP_008896	P17028	ZNF24_HUMAN	zinc finger protein 24	344	C2H2-type 4.				myelination|negative regulation of transcription, DNA-dependent|viral reproduction	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GCTTTGACTATACGATTTCCC	0.358													21	169	---	---	---	---	PASS
GZMM	3004	broad.mit.edu	37	19	548562	548562	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr19:548562T>G	uc002low.1	+	3	278	c.233T>G	c.(232-234)GTG>GGG	p.V78G		NM_005317	NP_005308	P51124	GRAM_HUMAN	granzyme M precursor	78	Peptidase S1.				apoptosis|cytolysis|innate immune response|proteolysis	extracellular region	serine-type endopeptidase activity				0		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGAGGCTGGTGCTGGGGCTC	0.687													11	54	---	---	---	---	PASS
PIP5K1C	23396	broad.mit.edu	37	19	3661952	3661952	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr19:3661952G>T	uc002lyj.1	-	4	324	c.267C>A	c.(265-267)TAC>TAA	p.Y89*	PIP5K1C_uc010xhq.1_Nonsense_Mutation_p.Y89*|PIP5K1C_uc010xhr.1_Nonsense_Mutation_p.Y89*	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	89	PIPK.				axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		GGCCCACGGTGTAGCCGATGC	0.682													5	15	---	---	---	---	PASS
AKAP8L	26993	broad.mit.edu	37	19	15512380	15512380	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr19:15512380C>T	uc002naw.1	-	5	496	c.397G>A	c.(397-399)GTC>ATC	p.V133I	AKAP8L_uc002nax.1_RNA|AKAP8L_uc010xoh.1_Missense_Mutation_p.V72I|AKAP8L_uc002nay.1_Missense_Mutation_p.V133I|AKAP8L_uc002naz.2_5'UTR	NM_014371	NP_055186	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like	133						cytoplasm|nuclear matrix	DEAD/H-box RNA helicase binding|DNA binding|zinc ion binding			ovary(1)	1						TCACTCAGGACGGCCCTCGAG	0.592													5	23	---	---	---	---	PASS
CYP4F2	8529	broad.mit.edu	37	19	16003198	16003198	+	Missense_Mutation	SNP	C	T	T	rs140630977		TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr19:16003198C>T	uc002nbs.1	-	5	496	c.446G>A	c.(445-447)CGG>CAG	p.R149Q	CYP4F2_uc010xot.1_5'UTR|CYP4F2_uc010xou.1_5'UTR	NM_001082	NP_001073	P78329	CP4F2_HUMAN	cytochrome P450, family 4, subfamily F,	149					leukotriene metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding	p.R149Q(1)		ovary(1)|skin(1)	2						CGTCAGCATCCGACGGTGGCG	0.567													27	131	---	---	---	---	PASS
CYP2D6	1565	broad.mit.edu	37	22	42524924	42524924	+	Silent	SNP	A	G	G	rs111606937	by1000genomes	TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr22:42524924A>G	uc003bce.2	-	4	618	c.528T>C	c.(526-528)GGT>GGC	p.G176G	uc003bcd.1_Intron|CYP2D6_uc010gyu.2_5'UTR|CYP2D6_uc003bcf.2_Silent_p.G125G	NM_000106	NP_000097	Q6NWU0	Q6NWU0_HUMAN	cytochrome P450, family 2, subfamily D,	176							electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen			breast(1)|skin(1)	2						TGTCCAAGAGACCGTTGGGGC	0.667													3	13	---	---	---	---	PASS
XIST	7503	broad.mit.edu	37	X	73061256	73061256	+	RNA	SNP	C	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chrX:73061256C>T	uc004ebm.1	-	1		c.11333G>A				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0						TACAGCTGTCCGAGGAGCTAG	0.393													26	21	---	---	---	---	PASS
KLHL4	56062	broad.mit.edu	37	X	86888856	86888856	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chrX:86888856G>A	uc004efb.2	+	8	1839	c.1657G>A	c.(1657-1659)GTA>ATA	p.V553I	KLHL4_uc004efa.2_Missense_Mutation_p.V553I	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1	553	Kelch 3.					cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						GTGGAATTACGTAGCCAGTAT	0.433													5	41	---	---	---	---	PASS
ETV3	2117	broad.mit.edu	37	1	157104016	157104017	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr1:157104016_157104017insT	uc001fqr.2	-	4	576_577	c.287_288insA	c.(286-288)TACfs	p.Y96fs	ETV3_uc001fqt.2_Frame_Shift_Ins_p.Y96fs	NM_001145312	NP_001138784	P41162	ETV3_HUMAN	ets variant gene 3 isoform 1	96	ETS.						sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(266;0.158)	Prostate(1639;0.174)				TGTTGTAATAGTATCTGTAAAA	0.371													39	46	---	---	---	---	
DHFR	1719	broad.mit.edu	37	5	79945228	79945232	+	Frame_Shift_Del	DEL	TAAAT	-	-			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr5:79945228_79945232delTAAAT	uc003kgy.1	-	3	710_714	c.218_222delATTTA	c.(217-222)AATTTAfs	p.N73fs	DHFR_uc011ctl.1_Frame_Shift_Del_p.N153fs|DHFR_uc011ctm.1_Frame_Shift_Del_p.N21fs|DHFR_uc010jap.1_RNA|DHFR_uc003kgx.1_Frame_Shift_Del_p.N222fs	NM_000791	NP_000782	P00374	DYR_HUMAN	dihydrofolate reductase	73_74	DHFR.				folic acid metabolic process|glycine biosynthetic process|nucleotide biosynthetic process|one-carbon metabolic process|regulation of transcription involved in G1/S phase of mitotic cell cycle|response to methotrexate|tetrahydrofolate metabolic process	cytosol	dihydrofolate reductase activity|drug binding|folate reductase activity|NADP binding				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.69e-46)|Epithelial(54;7.49e-41)|all cancers(79;1.54e-35)	Dapsone(DB00250)|Dimethyl sulfoxide(DB01093)|Lamotrigine(DB00555)|Methotrexate(DB00563)|NADH(DB00157)|Pemetrexed(DB00642)|Proguanil(DB01131)|Pyrimethamine(DB00205)|Trimethoprim(DB00440)|Trimetrexate(DB01157)	TGCTGAGAACTAAATTAATTCTACC	0.332													74	23	---	---	---	---	
NOL8	55035	broad.mit.edu	37	9	95069196	95069199	+	Frame_Shift_Del	DEL	TGTT	-	-			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr9:95069196_95069199delTGTT	uc004arv.2	-	11	3131_3134	c.2794_2797delAACA	c.(2794-2799)AACAGAfs	p.N932fs	NOL8_uc010mqw.2_RNA|NOL8_uc004arw.2_Frame_Shift_Del_p.N164fs|NOL8_uc011ltw.1_Frame_Shift_Del_p.N864fs	NM_017948	NP_060418	Q76FK4	NOL8_HUMAN	nucleolar protein 8	932_933					DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding			ovary(1)	1						ACTGATCCTCTGTTTGTAGAATTG	0.338													281	7	---	---	---	---	
NLRP1	22861	broad.mit.edu	37	17	5462267	5462268	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CH-5751-01A-11D-1576-08	TCGA-CH-5751-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	072e5acd-3329-42b8-9aec-d6166ac61e35	0e96e352-8a8f-4960-ad33-d64018480ff1	g.chr17:5462267_5462268insT	uc002gci.2	-	4	2303_2304	c.1748_1749insA	c.(1747-1749)AAGfs	p.K583fs	NLRP1_uc002gcg.1_Frame_Shift_Ins_p.K583fs|NLRP1_uc002gck.2_Frame_Shift_Ins_p.K583fs|NLRP1_uc002gcj.2_Frame_Shift_Ins_p.K583fs|NLRP1_uc002gcl.2_Frame_Shift_Ins_p.K583fs|NLRP1_uc002gch.3_Frame_Shift_Ins_p.K583fs|NLRP1_uc010clh.2_Frame_Shift_Ins_p.K583fs	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1	583	NACHT.				defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)				TGAAAAGGGTCTTTTTTTGCCA	0.535													101	7	---	---	---	---	
