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
LRRC47	57470	broad.mit.edu	37	1	3697704	3697704	+	Missense_Mutation	SNP	G	C	C			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr1:3697704G>C	uc001akx.1	-	7	1728	c.1700C>G	c.(1699-1701)CCG>CGG	p.P567R		NM_020710	NP_065761	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	567					translation		phenylalanine-tRNA ligase activity|RNA binding			large_intestine(1)|ovary(1)	2	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		GGCCTTGGACGGGTACACCAC	0.652													17	69	---	---	---	---	PASS
SPAG17	200162	broad.mit.edu	37	1	118554950	118554950	+	Missense_Mutation	SNP	C	G	G			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr1:118554950C>G	uc001ehk.2	-	30	4401	c.4333G>C	c.(4333-4335)GAT>CAT	p.D1445H		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1445						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CGAGTACCATCTTTCCTTTCA	0.393													14	50	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144856817	144856817	+	Missense_Mutation	SNP	T	C	C	rs3844239	by1000genomes	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr1:144856817T>C	uc001elw.3	-	40	6959	c.6668A>G	c.(6667-6669)GAG>GGG	p.E2223G	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.E2117G|PDE4DIP_uc001elv.3_Missense_Mutation_p.E1230G	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	2223					cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGTGATTACCTCTGTGCCTTG	0.478			T	PDGFRB	MPD								3	44	---	---	---	---	PASS
CD1B	910	broad.mit.edu	37	1	158299693	158299693	+	Nonsense_Mutation	SNP	G	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr1:158299693G>A	uc001frx.2	-	3	664	c.556C>T	c.(556-558)CGA>TGA	p.R186*	CD1B_uc001frw.2_Nonsense_Mutation_p.R79*	NM_001764	NP_001755	P29016	CD1B_HUMAN	CD1B antigen precursor	186	Extracellular (Potential).|Ig-like.				antigen processing and presentation|immune response	endosome membrane|integral to membrane|lysosomal membrane|plasma membrane	protein binding			ovary(2)	2	all_hematologic(112;0.0378)					AAGAGATATCGGGGGCAGGTT	0.463													25	135	---	---	---	---	PASS
PRRX1	5396	broad.mit.edu	37	1	170688957	170688957	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr1:170688957G>A	uc001ghf.2	+	2	379	c.332G>A	c.(331-333)CGT>CAT	p.R111H	PRRX1_uc001ghe.2_Missense_Mutation_p.R111H	NM_022716	NP_073207	P54821	PRRX1_HUMAN	paired mesoderm homeobox 1 isoform pmx-1b	111	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GCTTTGGAGCGTGTCTTTGAG	0.512													20	61	---	---	---	---	PASS
PLXNA2	5362	broad.mit.edu	37	1	208272307	208272307	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr1:208272307G>A	uc001hgz.2	-	6	2373	c.1615C>T	c.(1615-1617)CGC>TGC	p.R539C		NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	539	Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TTGTCCCTGCGGGAGCACCTG	0.562													6	21	---	---	---	---	PASS
TRIB2	28951	broad.mit.edu	37	2	12863619	12863619	+	Silent	SNP	C	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr2:12863619C>T	uc002rbv.3	+	2	1940	c.504C>T	c.(502-504)GAC>GAT	p.D168D	TRIB2_uc010yjp.1_Silent_p.D32D	NM_021643	NP_067675	Q92519	TRIB2_HUMAN	tribbles homolog 2	168	Protein kinase.				negative regulation of fat cell differentiation|negative regulation of interleukin-10 biosynthetic process|negative regulation of protein kinase activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity	cytoplasm|cytoskeleton|nucleus	ATP binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity			stomach(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ACTGCCATGACGGGGGGCTGG	0.577													15	76	---	---	---	---	PASS
ALK	238	broad.mit.edu	37	2	29416481	29416481	+	Missense_Mutation	SNP	T	C	C	rs1881420	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr2:29416481T>C	uc002rmy.2	-	29	5379	c.4472A>G	c.(4471-4473)AAG>AGG	p.K1491R	ALK_uc010ymo.1_Missense_Mutation_p.K423R	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1491	Cytoplasmic (Potential).				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	TCCGTGGACCTTGTGCAACTC	0.532			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				6	149	---	---	---	---	PASS
FAM123C	205147	broad.mit.edu	37	2	131520858	131520858	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr2:131520858C>T	uc002trw.2	+	2	1403	c.1213C>T	c.(1213-1215)CCA>TCA	p.P405S	FAM123C_uc010fmv.2_Missense_Mutation_p.P405S|FAM123C_uc010fms.1_Missense_Mutation_p.P405S|FAM123C_uc010fmt.1_Missense_Mutation_p.P405S|FAM123C_uc010fmu.1_Missense_Mutation_p.P405S	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	405										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.13)		AGCTGAGAGCCCAGGCACTCC	0.632													18	55	---	---	---	---	PASS
MLH1	4292	broad.mit.edu	37	3	37053568	37053568	+	Missense_Mutation	SNP	A	G	G	rs1799977	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr3:37053568A>G	uc003cgl.2	+	8	715	c.655A>G	c.(655-657)ATC>GTC	p.I219V	MLH1_uc011aye.1_5'UTR|MLH1_uc011ayb.1_5'UTR|MLH1_uc010hge.2_Missense_Mutation_p.I219V|MLH1_uc003cgn.3_5'UTR|MLH1_uc011ayc.1_Missense_Mutation_p.I121V|MLH1_uc011ayd.1_5'UTR|MLH1_uc003cgo.2_5'UTR|MLH1_uc010hgg.1_5'UTR|MLH1_uc010hgh.1_5'UTR|MLH1_uc010hgi.1_5'UTR|MLH1_uc010hgj.1_5'UTR|MLH1_uc010hgk.2_5'UTR|MLH1_uc010hgl.1_5'Flank	NM_000249	NP_000240	P40692	MLH1_HUMAN	MutL protein homolog 1	219					mismatch repair|somatic hypermutation of immunoglobulin genes	chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|protein binding	p.0?(1)		large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1)	77						TATTCGCTCCATCTTTGGAAA	0.368		1	D|Mis|N|F|S		colorectal|endometrial|ovarian|CNS	colorectal|endometrial|ovarian|CNS		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				3	62	---	---	---	---	PASS
CADM2	253559	broad.mit.edu	37	3	86114827	86114827	+	Missense_Mutation	SNP	T	G	G			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr3:86114827T>G	uc003dqj.2	+	9	1762	c.1136T>G	c.(1135-1137)TTT>TGT	p.F379C	CADM2_uc003dqk.2_Missense_Mutation_p.F348C|CADM2_uc003dql.2_Missense_Mutation_p.F381C	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D	379	Helical; (Potential).				adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		GTAGTTGTATTTGTCACGCTG	0.423													4	48	---	---	---	---	PASS
KALRN	8997	broad.mit.edu	37	3	123988019	123988019	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr3:123988019C>A	uc003ehg.2	+	5	1007	c.880C>A	c.(880-882)CAC>AAC	p.H294N	KALRN_uc010hrv.1_Missense_Mutation_p.H294N|KALRN_uc003ehf.1_Missense_Mutation_p.H294N|KALRN_uc011bjy.1_Missense_Mutation_p.H294N	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	294	Spectrin 1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						CACCCGGCAGCACCTGCACCA	0.607													6	36	---	---	---	---	PASS
PLXND1	23129	broad.mit.edu	37	3	129288693	129288693	+	Silent	SNP	G	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr3:129288693G>T	uc003emx.2	-	20	3958	c.3858C>A	c.(3856-3858)TCC>TCA	p.S1286S	PLXND1_uc011blb.1_5'Flank	NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1 precursor	1286	Helical; (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1						TACCCACCACGGAGAGCAGCA	0.622													3	44	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195515387	195515387	+	Missense_Mutation	SNP	T	C	C	rs13065584	by1000genomes	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr3:195515387T>C	uc011bto.1	-	2	3524	c.3064A>G	c.(3064-3066)ACC>GCC	p.T1022A	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	1023	Repeat.				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)		AGAGGGGTGGTGTGACCTGTG	0.567													4	7	---	---	---	---	PASS
PAK2	5062	broad.mit.edu	37	3	196509522	196509522	+	Missense_Mutation	SNP	C	G	G	rs67093638	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr3:196509522C>G	uc003fwy.3	+	2	327	c.5C>G	c.(4-6)TCT>TGT	p.S2C		NM_002577	NP_002568	Q13177	PAK2_HUMAN	p21-activated kinase 2	2					axon guidance|cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of apoptosis|regulation of defense response to virus by virus|regulation of growth|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|nucleus|perinuclear region of cytoplasm|plasma membrane	ATP binding|identical protein binding|protein kinase binding|protein serine/threonine kinase activity|protein tyrosine kinase activator activity			ovary(1)|lung(1)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		TGAATCATGTCTGATAACGGA	0.408													4	95	---	---	---	---	PASS
NEIL3	55247	broad.mit.edu	37	4	178274835	178274835	+	Missense_Mutation	SNP	A	C	C	rs13112390	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr4:178274835A>C	uc003iut.2	+	8	1530	c.1413A>C	c.(1411-1413)CAA>CAC	p.Q471H	NEIL3_uc010irs.2_3'UTR	NM_018248	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3	471					base-excision repair|nucleotide-excision repair	nucleus	bubble DNA binding|damaged DNA binding|DNA N-glycosylase activity|DNA-(apurinic or apyrimidinic site) lyase activity|double-stranded DNA binding|single-stranded DNA binding|zinc ion binding			lung(2)|ovary(1)|central_nervous_system(1)	4		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		AAACAGCCCAATACTCATCAC	0.333								BER_DNA_glycosylases					4	63	---	---	---	---	PASS
FAM174A	345757	broad.mit.edu	37	5	99871330	99871330	+	Silent	SNP	C	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr5:99871330C>T	uc003knj.1	+	1	216	c.96C>T	c.(94-96)GTC>GTT	p.V32V	uc003kni.2_5'Flank	NM_198507	NP_940909	Q8TBP5	F174A_HUMAN	family with sequence similarity 174, member A	32	Extracellular (Potential).					integral to membrane					0						CCCTGGCAGTCCTGCTGCAGG	0.672													7	82	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140209661	140209661	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr5:140209661C>T	uc003lho.2	+	1	2012	c.1985C>T	c.(1984-1986)ACG>ATG	p.T662M	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_uc011dab.1_Missense_Mutation_p.T662M	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	662	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGACAGCGACGGCCACGGTT	0.697													23	69	---	---	---	---	PASS
PCDHGB3	56102	broad.mit.edu	37	5	140751900	140751900	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr5:140751900C>T	uc003ljw.1	+	1	1939	c.1939C>T	c.(1939-1941)CGT>TGT	p.R647C	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|PCDHGA6_uc003ljy.1_5'Flank|PCDHGB3_uc011dat.1_Missense_Mutation_p.R647C|PCDHGA6_uc011dau.1_5'Flank	NM_018924	NP_061747	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3 isoform 1	647	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTCACTGTGCGTGATGGAGG	0.652													14	89	---	---	---	---	PASS
ATP10B	23120	broad.mit.edu	37	5	160033839	160033839	+	Silent	SNP	C	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr5:160033839C>A	uc003lym.1	-	19	3940	c.3093G>T	c.(3091-3093)ACG>ACT	p.T1031T	ATP10B_uc010jit.1_Silent_p.T348T	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1031	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCTGGAGTGGCGTGGAGCGGC	0.512													27	99	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54805688	54805688	+	Missense_Mutation	SNP	A	C	C	rs239798	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr6:54805688A>C	uc003pck.2	+	5	2035	c.1919A>C	c.(1918-1920)AAA>ACA	p.K640T		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	640										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					TATATATATAAAACCTTGGGT	0.373													3	72	---	---	---	---	PASS
SCML4	256380	broad.mit.edu	37	6	108042009	108042009	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr6:108042009G>A	uc010kdf.2	-	6	1122	c.871C>T	c.(871-873)CGC>TGC	p.R291C	SCML4_uc003prz.3_Missense_Mutation_p.R233C|SCML4_uc011eam.1_Missense_Mutation_p.R291C|SCML4_uc003pry.3_Missense_Mutation_p.R49C|SCML4_uc003psa.3_Missense_Mutation_p.R262C	NM_198081	NP_932347	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4	291	SAM.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		GGGCTAGTGCGGGGACCACCA	0.637													4	87	---	---	---	---	PASS
MIR550-2	693134	broad.mit.edu	37	7	32772646	32772646	+	RNA	SNP	C	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr7:32772646C>A	hsa-mir-550-2|MI0003601	+			c.54C>A			AVL9_uc011kai.1_Intron|LOC441208_uc003tcy.3_Intron																	0						CTGTTGTTGTCAGATAGTGTC	0.493													5	126	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82763829	82763829	+	Missense_Mutation	SNP	C	G	G			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr7:82763829C>G	uc003uhx.2	-	3	3326	c.3037G>C	c.(3037-3039)GAA>CAA	p.E1013Q	PCLO_uc003uhv.2_Missense_Mutation_p.E1013Q	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	959	Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						GGAGCTTGTTCAGCTTTGGGC	0.433													12	33	---	---	---	---	PASS
HTR5A	3361	broad.mit.edu	37	7	154862620	154862620	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr7:154862620C>T	uc003wlu.1	+	1	75	c.11C>T	c.(10-12)CCT>CTT	p.P4L	uc011kvt.1_Intron|uc003wlt.2_Intron	NM_024012	NP_076917	P47898	5HT5A_HUMAN	5-hydroxytryptamine receptor 5A	4	Extracellular (By similarity).					integral to plasma membrane	serotonin receptor activity			ovary(2)|large_intestine(1)	3	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)		ATGGATTTACCTGTGAACCTA	0.612													27	133	---	---	---	---	PASS
GSDMD	79792	broad.mit.edu	37	8	144643541	144643541	+	Silent	SNP	C	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr8:144643541C>T	uc010mfe.2	+	9	1387	c.684C>T	c.(682-684)GAC>GAT	p.D228D	GSDMD_uc003yyf.2_Silent_p.D276D|GSDMD_uc003yyi.2_3'UTR|GSDMD_uc003yyg.2_Silent_p.D228D|GSDMD_uc003yyh.2_Silent_p.D159D	NM_024736	NP_079012	P57764	GSDMD_HUMAN	gasdermin D	228											0						GGCTGCCAGACGTCCTTCTCT	0.637													3	14	---	---	---	---	PASS
GLIS3	169792	broad.mit.edu	37	9	4117830	4117830	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr9:4117830C>T	uc003zhw.1	-	3	1377	c.1183G>A	c.(1183-1185)GCC>ACC	p.A395T	GLIS3_uc003zhx.1_Missense_Mutation_p.A550T|GLIS3_uc003zic.1_Missense_Mutation_p.A550T|GLIS3_uc003zie.1_Missense_Mutation_p.A550T|GLIS3_uc010mhh.1_Missense_Mutation_p.A425T|GLIS3_uc003zid.1_Missense_Mutation_p.A328T|GLIS3_uc010mhi.1_Missense_Mutation_p.A357T|GLIS3_uc003zif.1_Missense_Mutation_p.A328T|GLIS3_uc003zig.1_Missense_Mutation_p.A394T|GLIS3_uc003zih.1_Missense_Mutation_p.A328T|GLIS3_uc003zhy.1_Missense_Mutation_p.A328T|GLIS3_uc003zhz.1_Missense_Mutation_p.A328T|GLIS3_uc003zib.1_Missense_Mutation_p.A394T|GLIS3_uc010mhg.1_Missense_Mutation_p.A328T	NM_152629	NP_689842	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform b	395	C2H2-type 2; atypical.				negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TTATAGCGGGCGTTGAAGGGC	0.567													5	141	---	---	---	---	PASS
TUBBP5	643224	broad.mit.edu	37	9	141071110	141071110	+	Silent	SNP	A	G	G			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr9:141071110A>G	uc004com.2	+	4	774	c.513A>G	c.(511-513)CCA>CCG	p.P171P	TUBBP5_uc010ncq.2_3'UTR					RecName: Full=Putative tubulin beta-4q chain;												0						TGCGCTTCCCAGGCCAGCTGA	0.597													4	96	---	---	---	---	PASS
FAM21C	253725	broad.mit.edu	37	10	46254776	46254776	+	Missense_Mutation	SNP	A	C	C	rs144609657	by1000genomes	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr10:46254776A>C	uc001jcu.2	+	17	1661	c.1562A>C	c.(1561-1563)TAC>TCC	p.Y521S	FAM21C_uc001jcs.1_Missense_Mutation_p.Y466S|FAM21C_uc001jct.2_Missense_Mutation_p.Y521S|FAM21C_uc010qfi.1_Missense_Mutation_p.Y497S|FAM21C_uc010qfj.1_Intron|FAM21C_uc010qfk.1_5'UTR	NM_015262	NP_056077	A8K5W5	A8K5W5_HUMAN	hypothetical protein LOC253725	521										ovary(1)	1						ACCTTATCTTACAGCAAAAAT	0.413													4	38	---	---	---	---	PASS
GPRIN2	9721	broad.mit.edu	37	10	47000217	47000217	+	Missense_Mutation	SNP	G	A	A	rs72780221	by1000genomes	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr10:47000217G>A	uc001jec.2	+	3	1472	c.1337G>A	c.(1336-1338)CGC>CAC	p.R446H	GPRIN2_uc010qfq.1_Missense_Mutation_p.R209H	NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth	446											0						TCCCTGCGGCGCCCCAGCTGC	0.716													4	12	---	---	---	---	PASS
NRAP	4892	broad.mit.edu	37	10	115372082	115372082	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr10:115372082C>A	uc001laj.2	-	30	3573	c.3409G>T	c.(3409-3411)GAC>TAC	p.D1137Y	NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Missense_Mutation_p.D1102Y|NRAP_uc001lal.3_Missense_Mutation_p.D1137Y	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	1137	Nebulin 29.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TGTTTGTAGTCCTGATTGCTG	0.542													13	81	---	---	---	---	PASS
MKI67	4288	broad.mit.edu	37	10	129899578	129899578	+	Missense_Mutation	SNP	T	C	C	rs8473	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr10:129899578T>C	uc001lke.2	-	14	9844	c.9649A>G	c.(9649-9651)AAA>GAA	p.K3217E	MKI67_uc001lkf.2_Missense_Mutation_p.K2857E	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	3217					cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGCACAGATTTGCTCTCCAAA	0.443													6	102	---	---	---	---	PASS
KNDC1	85442	broad.mit.edu	37	10	135012126	135012126	+	Missense_Mutation	SNP	G	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr10:135012126G>T	uc001llz.1	+	14	2115	c.2114G>T	c.(2113-2115)GGC>GTC	p.G705V	KNDC1_uc001lma.1_Missense_Mutation_p.G640V|KNDC1_uc001lmb.1_Missense_Mutation_p.G117V	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	705					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		GAGAGGGGCGGCCAGAGGGAG	0.721													3	20	---	---	---	---	PASS
ST5	6764	broad.mit.edu	37	11	8729383	8729383	+	Missense_Mutation	SNP	G	C	C			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr11:8729383G>C	uc001mgt.2	-	12	2557	c.2371C>G	c.(2371-2373)CGG>GGG	p.R791G	ST5_uc009yfr.2_Missense_Mutation_p.R371G|ST5_uc001mgu.2_Missense_Mutation_p.R371G|ST5_uc001mgv.2_Missense_Mutation_p.R791G|ST5_uc010rbq.1_RNA|ST5_uc010rbp.1_Missense_Mutation_p.R304G|ST5_uc009yfs.2_RNA	NM_213618	NP_998783	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1	791	DENN.				positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		TCTGGCAACCGGGGCCCTTTC	0.577													3	20	---	---	---	---	PASS
RNF214	257160	broad.mit.edu	37	11	117152314	117152314	+	Splice_Site	SNP	A	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr11:117152314A>T	uc001pqt.2	+	10	1282	c.1237_splice	c.e10-2	p.D413_splice	RNF214_uc001pqu.2_Splice_Site_p.D413_splice|RNF214_uc010rxf.1_Splice_Site_p.D258_splice	NM_207343	NP_997226	Q8ND24	RN214_HUMAN	ring finger protein 214								zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		TTTTTTTTTTAGGACCAATTT	0.428													5	132	---	---	---	---	PASS
PRB1	5542	broad.mit.edu	37	12	11506211	11506211	+	Missense_Mutation	SNP	A	C	C	rs76504934	by1000genomes	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr12:11506211A>C	uc001qzw.1	-	4	863	c.826T>G	c.(826-828)TCT>GCT	p.S276A	PRB1_uc001qzu.1_Missense_Mutation_p.S143A|PRB1_uc001qzv.1_Missense_Mutation_p.S123A	NM_005039	NP_005030	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1 isoform 1	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						extracellular region					0			OV - Ovarian serous cystadenocarcinoma(49;0.185)			CCTGGAGGAGATCGGGCACTT	0.607													7	114	---	---	---	---	PASS
ITGA7	3679	broad.mit.edu	37	12	56082025	56082025	+	Silent	SNP	G	C	C	rs17117883	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr12:56082025G>C	uc001shh.2	-	23	3250	c.3030C>G	c.(3028-3030)TCC>TCG	p.S1010S	ITGA7_uc001shg.2_Silent_p.S1006S|ITGA7_uc010sps.1_Silent_p.S913S|ITGA7_uc001shf.2_5'Flank|ITGA7_uc009znw.2_Silent_p.S253S|ITGA7_uc009znx.2_Silent_p.S887S	NM_001144996	NP_001138468	Q13683	ITA7_HUMAN	integrin alpha 7 isoform 1 precursor	1050	Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development|regulation of cell shape	integrin complex	receptor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5						TCTTTATGGAGGACTTCACTG	0.542													4	85	---	---	---	---	PASS
C14orf21	161424	broad.mit.edu	37	14	24769334	24769334	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr14:24769334C>A	uc001wol.1	+	1	237	c.174C>A	c.(172-174)AGC>AGA	p.S58R	C14orf21_uc001wom.1_5'Flank|DHRS1_uc001woj.1_5'Flank|DHRS1_uc001wok.2_5'Flank	NM_174913	NP_777573	Q86U38	CN021_HUMAN	hypothetical protein LOC161424	58							RNA binding			breast(2)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(265;0.0185)		CGCACCTGAGCCCGGAAGCTC	0.662													7	96	---	---	---	---	PASS
KIAA0284	283638	broad.mit.edu	37	14	105361169	105361169	+	Silent	SNP	A	C	C			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr14:105361169A>C	uc010axb.2	+	19	4763	c.4539A>C	c.(4537-4539)TCA>TCC	p.S1513S	INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Silent_p.S1443S|KIAA0284_uc001yps.2_Silent_p.S1454S|KIAA0284_uc001ypt.2_Silent_p.S181S	NM_001112726	NP_001106197	Q9Y4F5	K0284_HUMAN	hypothetical protein LOC283638 isoform 1	1548						cytoplasm|microtubule				breast(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.178)		GCCCACCCTCACCCGCCTCAG	0.711													7	19	---	---	---	---	PASS
CLK3	1198	broad.mit.edu	37	15	74917313	74917313	+	Missense_Mutation	SNP	A	G	G			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr15:74917313A>G	uc010uln.1	+	6	1509	c.1048A>G	c.(1048-1050)ATC>GTC	p.I350V	CLK3_uc002ayg.3_Missense_Mutation_p.I202V|CLK3_uc002ayh.3_5'UTR|CLK3_uc002ayj.3_Missense_Mutation_p.I179V|CLK3_uc002ayk.3_Missense_Mutation_p.I129V|CLK3_uc002ayl.3_Missense_Mutation_p.I35V	NM_001130028	NP_001123500	P49761	CLK3_HUMAN	CDC-like kinase 3 isoform a	350	Protein kinase.					acrosomal vesicle|nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)	2						CCGGCTAGAAATCAACGTGCT	0.542													7	42	---	---	---	---	PASS
RASGRF1	5923	broad.mit.edu	37	15	79382656	79382656	+	Missense_Mutation	SNP	G	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr15:79382656G>A	uc002beq.2	-	1	560	c.185C>T	c.(184-186)CCC>CTC	p.P62L	RASGRF1_uc002bep.2_Missense_Mutation_p.P62L|RASGRF1_uc002ber.3_Missense_Mutation_p.P62L	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	62	PH 1.				activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6						AAGCCCCGAGGGCCGCGAGCT	0.642													16	47	---	---	---	---	PASS
KIAA0556	23247	broad.mit.edu	37	16	27585275	27585275	+	Nonsense_Mutation	SNP	G	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr16:27585275G>T	uc002dow.2	+	2	85	c.61G>T	c.(61-63)GAG>TAG	p.E21*		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	21										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						AGAGAAAAAGGAGGTAAATGT	0.488													11	29	---	---	---	---	PASS
ZNF689	115509	broad.mit.edu	37	16	30620889	30620889	+	Silent	SNP	A	C	C			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr16:30620889A>C	uc002dyx.2	-	2	596	c.276T>G	c.(274-276)GCT>GCG	p.A92A	ZNF689_uc010bzy.2_5'UTR	NM_138447	NP_612456	Q96CS4	ZN689_HUMAN	zinc finger protein HIT-39	92	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			Colorectal(24;0.198)			GCGGATCTAGAGCAGCCGGTT	0.547													20	64	---	---	---	---	PASS
KIAA1609	57707	broad.mit.edu	37	16	84522897	84522897	+	Missense_Mutation	SNP	G	C	C	rs436278	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr16:84522897G>C	uc002fib.2	-	4	623	c.516C>G	c.(514-516)GAC>GAG	p.D172E	KIAA1609_uc010vod.1_Missense_Mutation_p.D145E|KIAA1609_uc002fic.2_RNA	NM_020947	NP_065998	Q6P9B6	K1609_HUMAN	hypothetical protein LOC57707	172							protein binding			ovary(2)	2						GCAGCTTCATGTCAGAGAGCA	0.448													3	65	---	---	---	---	PASS
KRTAP3-3	85293	broad.mit.edu	37	17	39150167	39150167	+	Silent	SNP	G	A	A	rs12452295	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr17:39150167G>A	uc002hvr.1	-	1	219	c.183C>T	c.(181-183)TGC>TGT	p.C61C		NM_033185	NP_149441	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	61						keratin filament	structural molecule activity				0		Breast(137;0.00043)				AGGTGGGCACGCAGGGCTGAG	0.632													5	114	---	---	---	---	PASS
EPX	8288	broad.mit.edu	37	17	56274420	56274420	+	Missense_Mutation	SNP	T	C	C	rs149610649	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr17:56274420T>C	uc002ivq.2	+	7	1008	c.922T>C	c.(922-924)TTT>CTT	p.F308L		NM_000502	NP_000493	P11678	PERE_HUMAN	eosinophil peroxidase preproprotein	308		Calcium; via carbonyl oxygen (By similarity).			hydrogen peroxide catabolic process		heme binding|peroxidase activity|protein binding			ovary(2)	2						GCTCACCTCCTTTGTGGACGC	0.597													5	146	---	---	---	---	PASS
SETBP1	26040	broad.mit.edu	37	18	42532845	42532845	+	Silent	SNP	C	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr18:42532845C>A	uc010dni.2	+	4	3836	c.3540C>A	c.(3538-3540)GGC>GGA	p.G1180G		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	1180						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AAGCCACAGGCTTCTCCAGCC	0.522									Schinzel-Giedion_syndrome				9	102	---	---	---	---	PASS
THEG	51298	broad.mit.edu	37	19	375680	375680	+	Silent	SNP	C	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr19:375680C>T	uc002lol.2	-	1	330	c.291G>A	c.(289-291)GAG>GAA	p.E97E	THEG_uc002lom.2_Silent_p.E97E	NM_016585	NP_057669	Q9P2T0	THEG_HUMAN	Theg homolog isoform 1	97					cell differentiation|chaperone-mediated protein complex assembly|multicellular organismal development|spermatogenesis	nucleus	protein binding			ovary(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-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)		CAGGAATGTCCTCTTCCAAGT	0.657													36	169	---	---	---	---	PASS
ZNF257	113835	broad.mit.edu	37	19	22271354	22271354	+	Missense_Mutation	SNP	C	T	T	rs17853619		TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr19:22271354C>T	uc010ecx.2	+	4	971	c.802C>T	c.(802-804)CGG>TGG	p.R268W	ZNF257_uc010ecy.2_Missense_Mutation_p.R236W	NM_033468	NP_258429	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	268	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGCCTTTAACCGGTCTTCACA	0.388													3	33	---	---	---	---	PASS
NRIP1	8204	broad.mit.edu	37	21	16340289	16340289	+	Silent	SNP	C	T	T	rs2229741	byFrequency	TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr21:16340289C>T	uc002yjx.2	-	4	823	c.225G>A	c.(223-225)GGG>GGA	p.G75G		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	75					androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		GCATGCCAGACCCCTGATATG	0.443													3	38	---	---	---	---	PASS
USP16	10600	broad.mit.edu	37	21	30411465	30411465	+	Missense_Mutation	SNP	A	G	G			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr21:30411465A>G	uc002ymy.2	+	8	1053	c.851A>G	c.(850-852)CAG>CGG	p.Q284R	USP16_uc002ymx.2_Missense_Mutation_p.Q283R|USP16_uc002ymw.2_Missense_Mutation_p.Q284R|USP16_uc011acm.1_Missense_Mutation_p.Q269R|USP16_uc011acn.1_Intron|USP16_uc011aco.1_5'UTR	NM_006447	NP_006438	Q9Y5T5	UBP16_HUMAN	ubiquitin specific protease 16 isoform a	284					cell division|histone deubiquitination|mitosis|positive regulation of transcription, DNA-dependent|protein homotetramerization|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|histone binding|transcription coactivator activity|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(2)|breast(1)|pancreas(1)	4						CTCTTTTCTCAGGTCTGTAAA	0.373													5	56	---	---	---	---	PASS
CCT8L2	150160	broad.mit.edu	37	22	17073169	17073169	+	Missense_Mutation	SNP	C	A	A			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr22:17073169C>A	uc002zlp.1	-	1	532	c.272G>T	c.(271-273)CGG>CTG	p.R91L		NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1	91					cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				TCCTGCTTCCCGGAGGAGCCA	0.602													3	47	---	---	---	---	PASS
CECR1	51816	broad.mit.edu	37	22	17688129	17688129	+	Missense_Mutation	SNP	A	C	C	rs77918321		TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr22:17688129A>C	uc002zmk.1	-	2	586	c.374T>G	c.(373-375)GTG>GGG	p.V125G	CECR1_uc010gqu.1_Missense_Mutation_p.V125G|CECR1_uc011agi.1_Missense_Mutation_p.V83G|CECR1_uc011agj.1_Missense_Mutation_p.V83G	NM_017424	NP_059120	Q9NZK5	CECR1_HUMAN	cat eye syndrome critical region protein 1	125					adenosine catabolic process|hypoxanthine salvage|inosine biosynthetic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				GACATTCCTCACCAGCCAGTC	0.537													7	66	---	---	---	---	PASS
MN1	4330	broad.mit.edu	37	22	28194936	28194936	+	Silent	SNP	C	T	T	rs45597040		TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chr22:28194936C>T	uc003adj.2	-	1	2551	c.1596G>A	c.(1594-1596)CAG>CAA	p.Q532Q		NM_002430	NP_002421	Q10571	MN1_HUMAN	meningioma  1	532	Poly-Gln.						binding			central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	10						gctgctgttgctgctgctgct	0.388			T	ETV6	AML|meningioma								3	12	---	---	---	---	PASS
ARHGAP36	158763	broad.mit.edu	37	X	130220378	130220378	+	Missense_Mutation	SNP	C	T	T			TCGA-G9-6384-01A-11D-1786-08	TCGA-G9-6384-10A-01D-1786-08									Somatic	Phase_I	Capture				Illumina GAIIx	667ba573-9cd4-4916-8b54-d529c24cd63e	4b005f8d-1af2-4aff-87b6-de830251409b	g.chrX:130220378C>T	uc004evz.2	+	10	1702	c.1357C>T	c.(1357-1359)CGC>TGC	p.R453C	ARHGAP36_uc004ewa.2_Missense_Mutation_p.R441C|ARHGAP36_uc004ewb.2_Missense_Mutation_p.R422C|ARHGAP36_uc004ewc.2_Missense_Mutation_p.R317C	NM_144967	NP_659404	Q6ZRI8	RHG36_HUMAN	hypothetical protein LOC158763 precursor	453					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3						TTTTATCAGACGCAGGAACTT	0.473													22	30	---	---	---	---	PASS
