Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	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	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
ELOVL3	83401	broad.mit.edu	37	10	103988910	103988910	+	Missense_Mutation	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:103988910G>C	uc001kut.2	+	c.714G>C	c.(712-714)TGG>TGC	p.W238C		NM_152310	NP_689523	Q9HB03	ELOV3_HUMAN	elongation of very long chain fatty acids like	238	Helical; (Potential).				fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|fatty acid elongation, saturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding			ovary(2)	2		Colorectal(252;0.207)		Epithelial(162;4.47e-08)|all cancers(201;7.96e-07)										0.606061	69.788823	70.154352	20	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103988910	103988910	5267	10	G	C	C	C	572	44	ELOVL3	3	3
DMBT1	1755	broad.mit.edu	37	10	124335998	124335998	+	Missense_Mutation	SNP	T	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:124335998T>G	uc001lgk.1	+	c.367T>G	c.(367-369)TGG>GGG	p.W123G	DMBT1_uc001lgl.1_Missense_Mutation_p.W123G|DMBT1_uc001lgm.1_Missense_Mutation_p.W123G|DMBT1_uc009xzz.1_Missense_Mutation_p.W123G|DMBT1_uc010qtx.1_Missense_Mutation_p.W123G|DMBT1_uc009yaa.1_5'UTR	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	123	SRCR 1.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				Ovarian(182;93 2026 18125 22222 38972)								0.282723	135.91798	143.992163	54	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124335998	124335998	4757	10	T	G	G	G	715	55	DMBT1	4	4
PARD3	56288	broad.mit.edu	37	10	34663923	34663923	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:34663923C>A	uc010qej.1	-	c.1547G>T	c.(1546-1548)GGA>GTA	p.G516V	PARD3_uc010qek.1_Missense_Mutation_p.G516V|PARD3_uc010qel.1_Missense_Mutation_p.G516V|PARD3_uc010qem.1_Missense_Mutation_p.G516V|PARD3_uc010qen.1_Missense_Mutation_p.G516V|PARD3_uc010qeo.1_Missense_Mutation_p.G516V|PARD3_uc010qep.1_Missense_Mutation_p.G472V|PARD3_uc010qeq.1_Missense_Mutation_p.G472V|PARD3_uc001ixo.1_Missense_Mutation_p.G246V|PARD3_uc001ixp.1_Missense_Mutation_p.G381V|PARD3_uc001ixq.1_Missense_Mutation_p.G516V|PARD3_uc001ixr.1_Missense_Mutation_p.G516V|PARD3_uc001ixt.1_Missense_Mutation_p.G337V|PARD3_uc001ixu.1_Missense_Mutation_p.G472V|PARD3_uc001ixs.1_Missense_Mutation_p.G169V	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog	516	PDZ 2.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)												0.295775	47.041488	49.641222	21	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34663923	34663923	11860	10	C	A	A	A	390	30	PARD3	2	2
BMS1	9790	broad.mit.edu	37	10	43291968	43291968	+	Missense_Mutation	SNP	C	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:43291968C>G	uc001jaj.2	+	c.1276C>G	c.(1276-1278)CGA>GGA	p.R426G		NM_014753	NP_055568	Q14692	BMS1_HUMAN	BMS1-like, ribosome assembly protein	426					ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)	2														0.380952	45.040482	45.577679	16	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43291968	43291968	1497	10	C	G	G	G	399	31	BMS1	3	3
SEC24C	9632	broad.mit.edu	37	10	75520491	75520491	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:75520491G>T	uc001juw.2	+	c.871G>T	c.(871-873)GGC>TGC	p.G291C	SEC24C_uc010qkn.1_Non-coding_Transcript|SEC24C_uc009xrj.1_Missense_Mutation_p.G149C|SEC24C_uc001jux.2_Missense_Mutation_p.G291C|SEC24C_uc010qko.1_Missense_Mutation_p.G149C|SEC24C_uc010qkp.1_Intron|SEC24C_uc010qkq.1_Intron	NM_004922	NP_004913	P53992	SC24C_HUMAN	SEC24-related protein C	291					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|zinc ion binding			central_nervous_system(1)	1	Prostate(51;0.0112)													0.608696	84.195118	84.673693	28	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75520491	75520491	14482	10	G	T	T	T	559	43	SEC24C	2	2
ITIH5	80760	broad.mit.edu	37	10	7657947	7657947	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:7657947G>T	uc001ijq.2	-	c.937C>A	c.(937-939)CAG>AAG	p.Q313K	ITIH5_uc001ijp.2_Missense_Mutation_p.Q99K|ITIH5_uc001ijr.1_Missense_Mutation_p.Q313K	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	313	VWFA.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4														0.333333	37.966475	38.923663	13	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7657947	7657947	8211	10	G	T	T	T	598	46	ITIH5	2	2
DYNC2H1	79659	broad.mit.edu	37	11	103060406	103060406	+	Missense_Mutation	SNP	C	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:103060406C>G	uc001phn.1	+	c.7298C>G	c.(7297-7299)CCA>CGA	p.P2433R	DYNC2H1_uc001pho.2_Missense_Mutation_p.P2433R|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2433	AAA 3 (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)										0.232558	21.531343	24.346488	10	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103060406	103060406	5032	11	C	G	G	G	273	21	DYNC2H1	3	3
GUCY1A2	2977	broad.mit.edu	37	11	106558443	106558443	+	Silent	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:106558443C>A	uc009yxn.1	-	c.2124G>T	c.(2122-2124)CGG>CGT	p.R708R	GUCY1A2_uc001pjg.1_Silent_p.R677R|GUCY1A2_uc010rvo.1_Silent_p.R698R	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	677					intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|pancreas(2)|ovary(1)	6		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)						248				0.189189	43.132549	53.14982	21	90	KEEP	---	---	---	---	capture		Silent	SNP	106558443	106558443	7173	11	C	A	A	A	223	18	GUCY1A2	2	2
MUC2	4583	broad.mit.edu	37	11	1104063	1104063	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1104063G>T	uc001lsx.1	+	c.15340G>T	c.(15340-15342)GCC>TCC	p.A5114S		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	5114	CTCK.					inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)									0.263158	9.843508	10.828376	5	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1104063	1104063	10369	11	G	T	T	T	546	42	MUC2	2	2
COPB1	1315	broad.mit.edu	37	11	14512211	14512211	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:14512211A>G	uc001mli.2	-	c.506T>C	c.(505-507)CTT>CCT	p.L169P	COPB1_uc001mlg.2_Missense_Mutation_p.L169P|COPB1_uc001mlh.2_Missense_Mutation_p.L169P	NM_016451	NP_057535	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	169					COPI coating of Golgi vesicle|interspecies interaction between organisms|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(1)|central_nervous_system(1)	2														0.294118	14.567741	15.212953	5	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14512211	14512211	3866	11	A	G	G	G	39	3	COPB1	4	4
PDE3B	5140	broad.mit.edu	37	11	14666084	14666084	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:14666084C>A	uc001mln.2	+	c.463C>A	c.(463-465)CTG>ATG	p.L155M	PDE3B_uc001mlm.2_Missense_Mutation_p.L155M|PDE3B_uc010rcr.1_Missense_Mutation_p.L155M|PSMA1_uc001mll.2_5'Flank	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B	155	Helical; (Potential).				cAMP catabolic process|insulin receptor signaling pathway|negative regulation of cAMP-mediated signaling|negative regulation of cell adhesion mediated by integrin|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0														0.5	17.149966	17.149966	6	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14666084	14666084	12059	11	C	A	A	A	363	28	PDE3B	2	2
C11orf49	79096	broad.mit.edu	37	11	47179382	47179382	+	Silent	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:47179382T>A	uc001ndr.2	+	c.666T>A	c.(664-666)CTT>CTA	p.L222L	C11orf49_uc001nds.2_Silent_p.L222L|C11orf49_uc001ndp.2_Silent_p.L222L|C11orf49_uc001ndq.2_Silent_p.L222L|C11orf49_uc010rgx.1_Silent_p.L125L|C11orf49_uc010rgy.1_Silent_p.L213L|C11orf49_uc010rgz.1_Silent_p.L138L	NM_001003677	NP_001003677	Q9H6J7	CK049_HUMAN	hypothetical protein LOC79096 isoform 2	222											0														0.206349	58.341914	68.467306	26	100	KEEP	---	---	---	---	capture		Silent	SNP	47179382	47179382	1684	11	T	A	A	A	808	63	C11orf49	3	3
OR4A15	81328	broad.mit.edu	37	11	55135509	55135509	+	Silent	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55135509G>A	uc010rif.1	+	c.150G>A	c.(148-150)GAG>GAA	p.E50E		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	50	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.415094	65.355778	65.707388	22	31	KEEP	---	---	---	---	capture		Silent	SNP	55135509	55135509	11446	11	G	A	A	A	451	35	OR4A15	2	2
OR5D14	219436	broad.mit.edu	37	11	55563785	55563785	+	Missense_Mutation	SNP	A	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55563785A>T	uc010rim.1	+	c.754A>T	c.(754-756)ATC>TTC	p.I252F		NM_001004735	NP_001004735	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D,	252	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3		all_epithelial(135;0.196)												0.15	16.96883	23.988376	9	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55563785	55563785	11565	11	A	T	T	T	104	8	OR5D14	3	3
GLYATL1	92292	broad.mit.edu	37	11	58711090	58711090	+	Silent	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:58711090G>A	uc001nnh.1	+	c.99G>A	c.(97-99)CTG>CTA	p.L33L	GLYATL1_uc001nnf.2_5'UTR|GLYATL1_uc001nni.1_5'UTR|GLYATL1_uc001nnj.1_5'UTR	NM_080661	NP_542392	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	Error:Variant_position_missing_in_Q969I3_after_alignment						mitochondrion	glycine N-acyltransferase activity			ovary(1)	1					Glycine(DB00145)									0.5	40.847177	40.847177	14	14	KEEP	---	---	---	---	capture		Silent	SNP	58711090	58711090	6748	11	G	A	A	A	587	46	GLYATL1	2	2
MYO7A	4647	broad.mit.edu	37	11	76924924	76924924	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:76924924C>T	uc001oyb.2	+	c.6458C>T	c.(6457-6459)CCC>CTC	p.P2153L	MYO7A_uc001oyc.2_Missense_Mutation_p.P2113L|MYO7A_uc001oye.2_Non-coding_Transcript	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1	2153	FERM 2.				actin filament-based movement|equilibrioception|eye photoreceptor cell development|lysosome organization|response to stimulus|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4														0.326087	91.729901	94.192487	30	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76924924	76924924	10477	11	C	T	T	T	286	22	MYO7A	2	2
ANO4	121601	broad.mit.edu	37	12	101514344	101514344	+	Missense_Mutation	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:101514344T>A	uc010svm.1	+	c.2617T>A	c.(2617-2619)TAC>AAC	p.Y873N	ANO4_uc001thw.2_Missense_Mutation_p.Y838N|ANO4_uc001thx.2_Missense_Mutation_p.Y873N|ANO4_uc001thy.2_Missense_Mutation_p.Y393N	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4	873	Cytoplasmic (Potential).					chloride channel complex	chloride channel activity			ovary(4)	4														0.358974	42.239358	42.922282	14	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101514344	101514344	707	12	T	A	A	A	689	53	ANO4	3	3
SBNO1	55206	broad.mit.edu	37	12	123801854	123801854	+	Missense_Mutation	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:123801854G>C	uc010tap.1	-	c.2849C>G	c.(2848-2850)GCA>GGA	p.A950G	SBNO1_uc010tao.1_Missense_Mutation_p.A949G|SBNO1_uc010taq.1_Intron|SBNO1_uc001ues.1_5'Flank	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	950							ATP binding|DNA binding|hydrolase activity			breast(5)|ovary(1)|kidney(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)										0.222222	21.380309	23.936795	8	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123801854	123801854	14343	12	G	C	C	C	598	46	SBNO1	3	3
ZC3H10	84872	broad.mit.edu	37	12	56514815	56514815	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:56514815C>T	uc001sjp.1	+	c.469C>T	c.(469-471)CGT>TGT	p.R157C		NM_032786	NP_116175	Q96K80	ZC3HA_HUMAN	zinc finger CCCH-type containing 10	157	C3H1-type 3.						nucleic acid binding|zinc ion binding				0			OV - Ovarian serous cystadenocarcinoma(18;0.12)											0.195652	22.65131	26.620608	9	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56514815	56514815	18147	12	C	T	T	T	299	23	ZC3H10	1	1
TMEM5	10329	broad.mit.edu	37	12	64202478	64202478	+	Missense_Mutation	SNP	A	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:64202478A>T	uc001srq.1	+	c.938A>T	c.(937-939)GAA>GTA	p.E313V	TMEM5_uc001srr.1_Missense_Mutation_p.E210V|TMEM5_uc001srs.1_Missense_Mutation_p.E53V	NM_014254	NP_055069	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5	313	Extracellular (Potential).					integral to plasma membrane					0		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)										0.241935	35.893687	39.659972	15	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64202478	64202478	16713	12	A	T	T	T	117	9	TMEM5	3	3
RAB3IP	117177	broad.mit.edu	37	12	70149292	70149292	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70149292C>T	uc001svp.2	+	c.152C>T	c.(151-153)ACC>ATC	p.T51I	RAB3IP_uc001svl.1_Missense_Mutation_p.T35I|RAB3IP_uc001svm.2_Missense_Mutation_p.T35I|RAB3IP_uc001svn.2_Missense_Mutation_p.T35I|RAB3IP_uc001svo.2_Non-coding_Transcript|RAB3IP_uc001svq.2_Missense_Mutation_p.T51I|RAB3IP_uc001svr.2_Non-coding_Transcript|RAB3IP_uc001svs.2_Non-coding_Transcript	NM_175623	NP_783322	Q96QF0	RAB3I_HUMAN	RAB3A interacting protein isoform alpha 2	51					cilium assembly|Golgi to plasma membrane transport|protein localization to organelle|protein transport	centrosome|cytosol|microtubule basal body|nucleus	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)											0.237288	31.813774	35.541922	14	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70149292	70149292	13397	12	C	T	T	T	234	18	RAB3IP	2	2
TM9SF2	9375	broad.mit.edu	37	13	100190023	100190023	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:100190023A>G	uc001voj.1	+	c.622A>G	c.(622-624)ATC>GTC	p.I208V	TM9SF2_uc010afz.1_Intron	NM_004800	NP_004791	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2 precursor	208	Lumenal (Potential).				transport	endosome membrane|integral to plasma membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)													0.457143	45.992112	46.048407	16	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100190023	100190023	16508	13	A	G	G	G	104	8	TM9SF2	4	4
F7	2155	broad.mit.edu	37	13	113773001	113773001	+	Silent	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:113773001C>A	uc001vsv.2	+	c.1080C>A	c.(1078-1080)CTC>CTA	p.L360L	F7_uc001vsw.2_Silent_p.L338L|F7_uc010tjt.1_Silent_p.L291L	NM_000131	NP_000122	P08709	FA7_HUMAN	coagulation factor VII isoform a precursor	360	Peptidase S1.				anti-apoptosis|blood coagulation, extrinsic pathway|peptidyl-glutamic acid carboxylation|positive regulation of leukocyte chemotaxis|positive regulation of platelet-derived growth factor receptor signaling pathway|positive regulation of positive chemotaxis|positive regulation of protein kinase B signaling cascade|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|Golgi lumen|plasma membrane	calcium ion binding|glycoprotein binding|serine-type endopeptidase activity				0	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)									0.416667	27.651857	27.795307	10	14	KEEP	---	---	---	---	capture		Silent	SNP	113773001	113773001	5543	13	C	A	A	A	366	29	F7	2	2
KIAA0564	23078	broad.mit.edu	37	13	42440148	42440148	+	Missense_Mutation	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:42440148T>C	uc001uyj.2	-	c.1237A>G	c.(1237-1239)AGT>GGT	p.S413G	KIAA0564_uc001uyk.2_Missense_Mutation_p.S413G	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a	413						extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)	5		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)										0.8	190.015793	195.450449	52	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42440148	42440148	8492	13	T	C	C	C	728	56	KIAA0564	4	4
MARK3	4140	broad.mit.edu	37	14	103931921	103931921	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:103931921A>G	uc001ymz.3	+	c.568A>G	c.(568-570)ATG>GTG	p.M190V	MARK3_uc001ymx.3_Missense_Mutation_p.M190V|MARK3_uc001ymw.3_Missense_Mutation_p.M190V|MARK3_uc001yna.3_Missense_Mutation_p.M190V|MARK3_uc001ymy.3_Intron|MARK3_uc010awp.2_Missense_Mutation_p.M213V|MARK3_uc010tyb.1_Missense_Mutation_p.M1V	NM_001128918	NP_001122390	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	213	Protein kinase.				protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)	2		Melanoma(154;0.155)	Epithelial(46;0.241)							260				0.362637	105.717502	107.198347	33	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103931921	103931921	9697	14	A	G	G	G	208	16	MARK3	4	4
AHNAK2	113146	broad.mit.edu	37	14	105410751	105410751	+	Silent	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105410751C>A	uc010axc.1	-	c.11037G>T	c.(11035-11037)GGG>GGT	p.G3679G	AHNAK2_uc001ypx.2_Silent_p.G3579G	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3679						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)											0.335	166.614678	171.457169	67	133	KEEP	---	---	---	---	capture		Silent	SNP	105410751	105410751	418	14	C	A	A	A	275	22	AHNAK2	2	2
FSCB	84075	broad.mit.edu	37	14	44975731	44975732	+	Nonsense_Mutation	DNP	CC	AG	AG			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:44975731_44975732CC>AG	uc001wvn.2	-	c.459_460GG>CT	c.(457-462)AAGGAA>AACTAA	p.153_154KE>N*		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	153_154						cilium				breast(3)|ovary(2)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(112;0.128)						151				0.263158	124.755989	134.404085	50	140	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	44975731	44975732	6316	14	CC	AG	AG	AG	390	30	FSCB	5	2
OTX2	5015	broad.mit.edu	37	14	57268456	57268456	+	Silent	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:57268456C>T	uc001xcq.2	-	c.891G>A	c.(889-891)TTG>TTA	p.L297L	OTX2_uc001xcp.2_Silent_p.L289L|OTX2_uc010aou.2_Silent_p.L289L	NM_021728	NP_068374	P32243	OTX2_HUMAN	orthodenticle homeobox 2 isoform a	289					axon guidance|forebrain development|midbrain development|regulation of fibroblast growth factor receptor signaling pathway|regulation of smoothened signaling pathway|regulation of transcription, DNA-dependent	growth cone|nucleus	eukaryotic initiation factor 4E binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)													0.386667	82.651622	83.497762	29	46	KEEP	---	---	---	---	capture		Silent	SNP	57268456	57268456	11734	14	C	T	T	T	220	17	OTX2	2	2
PLEKHG3	26030	broad.mit.edu	37	14	65208725	65208725	+	Silent	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:65208725G>A	uc001xhp.2	+	c.2853G>A	c.(2851-2853)AAG>AAA	p.K951K	PLEKHG3_uc001xhn.1_Silent_p.K774K|PLEKHG3_uc001xho.1_Silent_p.K830K|PLEKHG3_uc010aqh.1_Silent_p.K372K|PLEKHG3_uc001xhq.1_Silent_p.K335K	NM_015549	NP_056364	A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G,	830					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)										0.122222	15.461906	28.042551	11	79	KEEP	---	---	---	---	capture		Silent	SNP	65208725	65208725	12496	14	G	A	A	A	451	35	PLEKHG3	2	2
COQ6	51004	broad.mit.edu	37	14	74428033	74428033	+	Nonsense_Mutation	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:74428033T>A	uc001xph.2	+	c.1049T>A	c.(1048-1050)TTG>TAG	p.L350*	ENTPD5_uc001xpi.2_Intron|COQ6_uc001xpe.2_Nonsense_Mutation_p.L275*|COQ6_uc001xpf.2_Nonsense_Mutation_p.L275*|COQ6_uc010tuk.1_Nonsense_Mutation_p.L325*|COQ6_uc001xpg.2_Nonsense_Mutation_p.L350*	NM_182476	NP_872282	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 homolog isoform a	350					oxidation-reduction process|ubiquinone biosynthetic process	mitochondrion	flavin adenine dinucleotide binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen				0				BRCA - Breast invasive adenocarcinoma(234;0.00337)										0.390244	46.190094	46.622853	16	25	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	74428033	74428033	3887	14	T	A	A	A	819	63	COQ6	5	3
NRXN3	9369	broad.mit.edu	37	14	79423666	79423666	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:79423666A>G	uc001xun.2	+	c.1238A>G	c.(1237-1239)AAA>AGA	p.K413R	NRXN3_uc001xum.1_Non-coding_Transcript|NRXN3_uc010asv.1_Missense_Mutation_p.K538R	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	786	Laminin G-like 4.|Extracellular (Potential).				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)										0.333333	85.570801	87.637857	28	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79423666	79423666	11072	14	A	G	G	G	13	1	NRXN3	4	4
ACAN	176	broad.mit.edu	37	15	89386810	89386810	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:89386810G>A	uc010upo.1	+	c.982G>A	c.(982-984)GTC>ATC	p.V328I	ACAN_uc002bmx.2_Missense_Mutation_p.V328I|ACAN_uc010upp.1_Missense_Mutation_p.V328I|ACAN_uc002bna.2_Non-coding_Transcript	NM_013227	NP_037359			aggrecan isoform 2 precursor											ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)											0.551724	47.577109	47.642415	16	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89386810	89386810	118	15	G	A	A	A	520	40	ACAN	1	1
CACNA1H	8912	broad.mit.edu	37	16	1270924	1270924	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1270924G>A	uc002cks.2	+	c.6992G>A	c.(6991-6993)TGT>TAT	p.C2331Y	CACNA1H_uc002ckt.2_Missense_Mutation_p.C2325Y|CACNA1H_uc002cku.2_Missense_Mutation_p.C1026Y|CACNA1H_uc010brj.2_Missense_Mutation_p.C1042Y|CACNA1H_uc002ckv.2_Missense_Mutation_p.C1020Y	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	2331	Cytoplasmic (Potential).				axon guidance|muscle contraction|muscle organ development|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)									0.2	17.450649	21.220781	9	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1270924	1270924	2661	16	G	A	A	A	624	48	CACNA1H	2	2
MAPK8IP3	23162	broad.mit.edu	37	16	1810016	1810016	+	Missense_Mutation	SNP	A	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1810016A>C	uc010uvl.1	+	c.1304A>C	c.(1303-1305)AAA>ACA	p.K435T	MAPK8IP3_uc002cmk.2_Missense_Mutation_p.K434T|MAPK8IP3_uc002cml.2_Missense_Mutation_p.K428T	NM_015133	NP_055948	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting	434					vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding			central_nervous_system(1)	1														0.170732	13.299268	17.503895	7	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1810016	1810016	9669	16	A	C	C	C	39	3	MAPK8IP3	4	4
SRCAP	10847	broad.mit.edu	37	16	30732065	30732065	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30732065C>T	uc002dze.1	+	c.3019C>T	c.(3019-3021)CGG>TGG	p.R1007W	SRCAP_uc002dzf.2_Non-coding_Transcript|SRCAP_uc002dzg.1_Missense_Mutation_p.R864W|SRCAP_uc010bzz.1_Missense_Mutation_p.R577W	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1007	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)	3			Colorectal(24;0.198)											0.21875	48.86116	55.833803	21	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30732065	30732065	15649	16	C	T	T	T	295	23	SRCAP	1	1
PHKG2	5261	broad.mit.edu	37	16	30767768	30767768	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30767768G>T	uc002dzi.1	+	c.740G>T	c.(739-741)CGC>CTC	p.R247L	PHKG2_uc002dzj.1_Missense_Mutation_p.R141L|PHKG2_uc002dzk.1_Missense_Mutation_p.R243L	NM_000294	NP_000285	P15735	PHKG2_HUMAN	phosphorylase kinase, gamma 2 (testis)	243	Protein kinase.				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process|protein phosphorylation	cytosol	ATP binding|calmodulin binding|phosphorylase kinase activity			ovary(1)	1			Colorectal(24;0.198)							76				0.324324	32.723745	33.718573	12	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30767768	30767768	12271	16	G	T	T	T	494	38	PHKG2	1	1
MMP2	4313	broad.mit.edu	37	16	55523613	55523613	+	Missense_Mutation	SNP	T	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:55523613T>G	uc002ehz.3	+	c.1057T>G	c.(1057-1059)TTC>GTC	p.F353V	MMP2_uc010vhd.1_Missense_Mutation_p.F277V|MMP2_uc010ccc.2_Missense_Mutation_p.F303V	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	353	Fibronectin type-II 3.|Collagen-binding.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			ovary(3)|large_intestine(3)|lung(1)|central_nervous_system(1)|kidney(1)	9		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)					275				0.204082	43.755081	51.72077	20	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55523613	55523613	10048	16	T	G	G	G	728	56	MMP2	4	4
MMP2	4313	broad.mit.edu	37	16	55523626	55523626	+	Missense_Mutation	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:55523626G>C	uc002ehz.3	+	c.1070G>C	c.(1069-1071)GGC>GCC	p.G357A	MMP2_uc010vhd.1_Missense_Mutation_p.G281A|MMP2_uc010ccc.2_Missense_Mutation_p.G307A	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	357	Fibronectin type-II 3.|Collagen-binding.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			ovary(3)|large_intestine(3)|lung(1)|central_nervous_system(1)|kidney(1)	9		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)					275				0.204545	38.320802	45.560985	18	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55523626	55523626	10048	16	G	C	C	C	546	42	MMP2	3	3
BBS2	583	broad.mit.edu	37	16	56553688	56553688	+	Silent	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:56553688C>A	uc002ejd.2	-	c.87G>T	c.(85-87)CCG>CCT	p.P29P	BBS2_uc010ccg.2_Silent_p.P29P	NM_031885	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2 protein	29					adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1														0.555556	16.485545	16.512091	5	4	KEEP	---	---	---	---	capture		Silent	SNP	56553688	56553688	1359	16	C	A	A	A	236	19	BBS2	1	1
RAB11FIP3	9727	broad.mit.edu	37	16	570480	570480	+	Nonsense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:570480C>T	uc002chf.2	+	c.2038C>T	c.(2038-2040)CAG>TAG	p.Q680*	RAB11FIP3_uc010uuf.1_Nonsense_Mutation_p.Q384*|RAB11FIP3_uc010uug.1_Nonsense_Mutation_p.Q415*	NM_014700	NP_055515	O75154	RFIP3_HUMAN	rab11-family interacting protein 3 isoform 1	680	Potential.				cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)				Melanoma(160;2366 2595 4474 8099)								0.220588	31.098739	35.988666	15	53	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	570480	570480	13354	16	C	T	T	T	325	25	RAB11FIP3	5	2
CDH16	1014	broad.mit.edu	37	16	66949248	66949248	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:66949248C>T	uc002eql.2	-	c.458G>A	c.(457-459)CGG>CAG	p.R153Q	CDH16_uc010cdy.2_Missense_Mutation_p.R153Q|CDH16_uc002eqm.2_Intron	NM_004062	NP_004053	O75309	CAD16_HUMAN	cadherin 16 precursor	153	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)										0.615385	51.502475	51.80616	16	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66949248	66949248	3230	16	C	T	T	T	299	23	CDH16	1	1
JPH3	57338	broad.mit.edu	37	16	87678370	87678370	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:87678370C>T	uc002fkd.2	+	c.889C>T	c.(889-891)CGC>TGC	p.R297C	JPH3_uc010vou.1_Non-coding_Transcript	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	297	Cytoplasmic (Potential).|MORN 7.				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)										0.666667	106.601362	107.90173	34	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87678370	87678370	8266	16	C	T	T	T	247	19	JPH3	1	1
CBFA2T3	863	broad.mit.edu	37	16	88945809	88945809	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:88945809C>T	uc002fmm.1	-	c.1531G>A	c.(1531-1533)GAC>AAC	p.D511N	CBFA2T3_uc002fml.1_Missense_Mutation_p.D425N|CBFA2T3_uc002fmk.1_Missense_Mutation_p.D10N	NM_005187	NP_005178	O75081	MTG16_HUMAN	myeloid translocation gene on chromosome 16	511	Potential.				cell proliferation|granulocyte differentiation|regulation of transcription, DNA-dependent	Golgi membrane|nucleolus|nucleoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(80;0.0275)						305				0.142857	14.714518	23.316389	10	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88945809	88945809	2817	16	C	T	T	T	390	30	CBFA2T3	2	2
PHF12	57649	broad.mit.edu	37	17	27240044	27240044	+	Silent	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:27240044T>A	uc002hdg.1	-	c.1545A>T	c.(1543-1545)CCA>CCT	p.P515P	PHF12_uc010wbb.1_Silent_p.P497P|PHF12_uc002hdi.1_Silent_p.P511P|PHF12_uc002hdj.1_Silent_p.P515P|PHF12_uc010crw.1_Silent_p.P218P|PHF12_uc002hdh.1_Silent_p.P298P	NM_001033561	NP_001028733	Q96QT6	PHF12_HUMAN	PHD finger protein 12 isoform 1	515	Interaction with SIN3A.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	protein binding|transcription repressor activity|zinc ion binding			ovary(1)	1	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)											0.269231	93.035118	99.31321	35	95	KEEP	---	---	---	---	capture		Silent	SNP	27240044	27240044	12246	17	T	A	A	A	704	55	PHF12	3	3
MYO18A	399687	broad.mit.edu	37	17	27425147	27425147	+	Silent	SNP	A	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:27425147A>T	uc002hdt.1	-	c.3966T>A	c.(3964-3966)GCT>GCA	p.A1322A	MYO18A_uc010wbc.1_Silent_p.A864A|MYO18A_uc002hds.2_Silent_p.A864A|MYO18A_uc010csa.1_Silent_p.A1322A|MYO18A_uc002hdu.1_Silent_p.A1322A|MYO18A_uc010wbd.1_Silent_p.A991A	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a	1322	Potential.				anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			Esophageal Squamous(182;472 2015 7001 15270 22562)								0.259259	187.837437	202.007748	70	200	KEEP	---	---	---	---	capture		Silent	SNP	27425147	27425147	10460	17	A	T	T	T	80	7	MYO18A	3	3
CCL18	6362	broad.mit.edu	37	17	34391745	34391745	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:34391745A>G	uc002hku.2	+	c.43A>G	c.(43-45)ATG>GTG	p.M15V		NM_002988	NP_002979	P55774	CCL18_HUMAN	small inducible cytokine A18 precursor	15					cell-cell signaling|chemotaxis|immune response|inflammatory response|response to biotic stimulus|signal transduction	extracellular space	chemokine activity				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)										0.297872	118.898763	124.046446	42	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34391745	34391745	3014	17	A	G	G	G	104	8	CCL18	4	4
P2RX5	5026	broad.mit.edu	37	17	3592814	3592814	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:3592814C>A	uc002fwh.1	-	c.722G>T	c.(721-723)GGG>GTG	p.G241V	P2RX5_uc002fwd.2_Non-coding_Transcript|P2RX5_uc010vrx.1_Missense_Mutation_p.G182V|P2RX5_uc002fwi.2_Missense_Mutation_p.G242V|P2RX5_uc002fwj.2_Missense_Mutation_p.G217V|P2RX5_uc002fwk.2_Missense_Mutation_p.G241V|P2RX5_uc002fwl.2_Missense_Mutation_p.G218V	NM_002561	NP_002552	Q93086	P2RX5_HUMAN	purinergic receptor P2X5 isoform A	242	Extracellular (Potential).				nervous system development|positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0														0.361111	37.864458	38.475987	13	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3592814	3592814	11756	17	C	A	A	A	286	22	P2RX5	2	2
NR1D1	9572	broad.mit.edu	37	17	38253497	38253497	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38253497G>A	uc002htz.1	-	c.191C>T	c.(190-192)CCG>CTG	p.P64L	NR1D1_uc010cwq.1_Non-coding_Transcript|NR1D1_uc010cwr.1_5'Flank	NM_021724	NP_068370	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	64					cellular response to lipopolysaccharide|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of receptor biosynthetic process|negative regulation of toll-like receptor 4 signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin|nucleoplasm	promoter binding|steroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(1)	1	Colorectal(19;0.000442)													0.375	65.664115	66.431199	21	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38253497	38253497	11020	17	G	A	A	A	507	39	NR1D1	1	1
RARA	5914	broad.mit.edu	37	17	38508718	38508718	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38508718G>T	uc002huk.1	+	c.766G>T	c.(766-768)GAC>TAC	p.D256Y	RARA_uc002hul.3_Missense_Mutation_p.D256Y|RARA_uc010wfe.1_Missense_Mutation_p.D159Y|RARA_uc002hun.1_Missense_Mutation_p.D251Y	NM_000964	NP_000955	P10276	RARA_HUMAN	retinoic acid receptor, alpha isoform 1	256	Ligand-binding.				apoptotic cell clearance|cellular response to estrogen stimulus|cellular response to retinoic acid|estrogen receptor signaling pathway|negative regulation of gene-specific transcription|negative regulation of granulocyte differentiation|negative regulation of interferon-gamma production|negative regulation of tumor necrosis factor production|positive regulation of binding|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene-specific transcription|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-5 production|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	cell surface|cytoplasm|nucleoplasm	chromatin DNA binding|enzyme binding|protein domain specific binding|protein heterodimerization activity|receptor binding|retinoic acid binding|retinoic acid receptor activity|retinoic acid-responsive element binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription activator activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)	2		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)					272				0.209302	19.552893	22.916601	9	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38508718	38508718	13512	17	G	T	T	T	481	37	RARA	1	1
KRT15	3866	broad.mit.edu	37	17	39673396	39673396	+	Missense_Mutation	SNP	T	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39673396T>G	uc002hwy.2	-	c.520A>C	c.(520-522)AAC>CAC	p.N174H	KRT15_uc002hwz.2_Silent_p.T36T|KRT15_uc002hxa.2_Intron|KRT15_uc002hxb.1_Intron	NM_002275	NP_002266	P19012	K1C15_HUMAN	keratin 15	174	Rod.|Coil 1B.				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000286)												0.205357	55.99814	64.990184	23	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39673396	39673396	8767	17	T	G	G	G	819	63	KRT15	4	4
NAGS	162417	broad.mit.edu	37	17	42083115	42083115	+	Silent	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:42083115C>T	uc010czn.2	+	c.537C>T	c.(535-537)GCC>GCT	p.A179A	PYY_uc002ieq.2_5'Flank|NAGS_uc002ies.2_Silent_p.A179A|NAGS_uc002iet.2_5'Flank	NM_153006	NP_694551	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	179					arginine biosynthetic process|urea cycle	mitochondrial matrix	acetyl-CoA:L-glutamate N-acetyltransferase activity				0		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)	L-Glutamic Acid(DB00142)									0.363636	12.097388	12.277198	4	7	KEEP	---	---	---	---	capture		Silent	SNP	42083115	42083115	10541	17	C	T	T	T	275	22	NAGS	2	2
TEX2	55852	broad.mit.edu	37	17	62271159	62271159	+	Missense_Mutation	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:62271159T>A	uc002jed.2	-	c.1936A>T	c.(1936-1938)ATG>TTG	p.M646L	TEX2_uc002jec.2_Missense_Mutation_p.M646L|TEX2_uc002jee.2_Missense_Mutation_p.M646L	NM_018469	NP_060939	Q8IWB9	TEX2_HUMAN	testis expressed sequence 2	646					signal transduction|sphingolipid metabolic process	integral to membrane				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)										0.221429	80.972655	90.954087	31	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62271159	62271159	16308	17	T	A	A	A	637	49	TEX2	3	3
MFSD11	79157	broad.mit.edu	37	17	74734527	74734527	+	Silent	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:74734527G>A	uc002jta.2	+	c.93G>A	c.(91-93)GTG>GTA	p.V31V	SFRS2_uc002jsv.2_5'Flank|SFRS2_uc002jsw.1_5'Flank|SFRS2_uc002jsx.1_5'Flank|SFRS2_uc002jsy.3_5'Flank|SFRS2_uc010wtg.1_5'Flank|MFSD11_uc002jsz.1_Non-coding_Transcript|MIR636_hsa-mir-636|MI0003651_5'Flank|MFSD11_uc002jtb.2_Silent_p.V31V|MFSD11_uc010dha.2_Silent_p.V31V|MFSD11_uc002jtc.2_Silent_p.V31V|MFSD11_uc002jtd.3_Silent_p.V31V|MFSD11_uc010dhb.2_Silent_p.V31V|MFSD11_uc002jte.2_Silent_p.V31V	NM_024311	NP_077287	O43934	MFS11_HUMAN	major facilitator superfamily domain containing	31						integral to membrane				ovary(1)	1														0.309524	39.461244	40.817873	13	29	KEEP	---	---	---	---	capture		Silent	SNP	74734527	74734527	9919	17	G	A	A	A	600	47	MFSD11	2	2
USP36	57602	broad.mit.edu	37	17	76823389	76823389	+	Silent	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:76823389C>A	uc002jvz.1	-	c.627G>T	c.(625-627)GCG>GCT	p.A209A	USP36_uc002jwa.1_Silent_p.A209A|USP36_uc002jwd.1_Silent_p.A209A	NM_025090	NP_079366	Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	209					ubiquitin-dependent protein catabolic process	nucleolus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|kidney(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)											0.28125	25.266998	26.639734	9	23	KEEP	---	---	---	---	capture		Silent	SNP	76823389	76823389	17631	17	C	A	A	A	340	27	USP36	1	1
NPC1	4864	broad.mit.edu	37	18	21136274	21136274	+	Missense_Mutation	SNP	T	C	C	rs77815278	byFrequency;by1000genomes	TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:21136274T>C	uc002kum.3	-	c.1259A>G	c.(1258-1260)TAC>TGC	p.Y420C	NPC1_uc010xaz.1_Missense_Mutation_p.Y221C|NPC1_uc010xba.1_Missense_Mutation_p.Y265C	NM_000271	NP_000262	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1 precursor	420					autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			ovary(2)	2	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)													0.176471	14.252096	17.58759	6	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21136274	21136274	10974	18	T	C	C	C	741	57	NPC1	4	4
KIAA1632	57724	broad.mit.edu	37	18	43479488	43479488	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:43479488C>T	uc002lbm.2	-	c.4690G>A	c.(4690-4692)GAG>AAG	p.E1564K	KIAA1632_uc010xcq.1_Missense_Mutation_p.E118K|KIAA1632_uc010xcr.1_Non-coding_Transcript|KIAA1632_uc010xcs.1_Non-coding_Transcript|KIAA1632_uc002lbn.2_Missense_Mutation_p.E439K	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	1564					autophagy						0														0.25	10.187138	11.601874	6	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43479488	43479488	8558	18	C	T	T	T	377	29	KIAA1632	2	2
CNDP2	55748	broad.mit.edu	37	18	72180861	72180861	+	Silent	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:72180861G>T	uc002llm.1	+	c.810G>T	c.(808-810)ACG>ACT	p.T270T	CNDP2_uc002lln.1_Silent_p.T186T|CNDP2_uc010dqs.2_Intron	NM_018235	NP_060705	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2	270						cytoplasm	carboxypeptidase activity|metal ion binding|metallopeptidase activity|protein binding|tripeptidase activity			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)										0.206897	29.384892	33.989671	12	46	KEEP	---	---	---	---	capture		Silent	SNP	72180861	72180861	3732	18	G	T	T	T	496	39	CNDP2	1	1
CNDP1	84735	broad.mit.edu	37	18	72250894	72250894	+	Silent	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:72250894G>T	uc002llq.2	+	c.1407G>T	c.(1405-1407)CCG>CCT	p.P469P	CNDP1_uc002lls.2_Silent_p.P272P	NM_032649	NP_116038	Q96KN2	CNDP1_HUMAN	carnosinase 1 precursor	469					proteolysis	extracellular region	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity|tripeptidase activity				0		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		Melanoma(32;1029 1042 25286 38395 44237)								0.196429	26.00679	30.804917	11	45	KEEP	---	---	---	---	capture		Silent	SNP	72250894	72250894	3731	18	G	T	T	T	483	38	CNDP1	1	1
SMARCA4	6597	broad.mit.edu	37	19	11118587	11118587	+	Nonsense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11118587G>T	uc010dxo.2	+	c.2011G>T	c.(2011-2013)GAA>TAA	p.E671*	SMARCA4_uc002mqf.3_Nonsense_Mutation_p.E671*|SMARCA4_uc010dxp.2_Nonsense_Mutation_p.E671*|SMARCA4_uc002mqg.1_Nonsense_Mutation_p.E671*|SMARCA4_uc010dxq.2_Nonsense_Mutation_p.E671*|SMARCA4_uc010dxr.2_Nonsense_Mutation_p.E671*|SMARCA4_uc002mqj.3_Nonsense_Mutation_p.E671*|SMARCA4_uc010dxs.2_Nonsense_Mutation_p.E671*	NM_001128849	NP_001122321	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	671	Poly-Glu.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of S phase of mitotic cell cycle|nervous system development|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription activator activity|transcription corepressor activity	p.?(1)		lung(29)|ovary(7)|pancreas(7)|large_intestine(5)|prostate(3)|central_nervous_system(2)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|skin(1)|autonomic_ganglia(1)|kidney(1)	61		all_lung(6;0.0512)|Lung NSC(9;0.0568)								582				0.315789	15.35618	15.922709	6	13	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	11118587	11118587	15268	19	G	T	T	T	533	41	SMARCA4	5	2
ZNF791	163049	broad.mit.edu	37	19	12739912	12739912	+	Silent	SNP	C	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:12739912C>G	uc002mua.2	+	c.1569C>G	c.(1567-1569)CCC>CCG	p.P523P	ZNF791_uc010xml.1_Silent_p.P491P|ZNF791_uc010dyu.1_Silent_p.P414P|ZNF791_uc010xmm.1_Silent_p.P414P	NM_153358	NP_699189	Q3KP31	ZN791_HUMAN	zinc finger protein 791	523					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.5	102.770294	102.770294	33	33	KEEP	---	---	---	---	capture		Silent	SNP	12739912	12739912	18761	19	C	G	G	G	301	24	ZNF791	3	3
ZNF99	7652	broad.mit.edu	37	19	22952001	22952001	+	Silent	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22952001C>T	uc010xrh.1	-	c.192G>A	c.(190-192)CTG>CTA	p.L64L		NM_001080409	NP_001073878	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	64	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)												0.24	48.513652	53.140064	18	57	KEEP	---	---	---	---	capture		Silent	SNP	22952001	22952001	18808	19	C	T	T	T	262	21	ZNF99	2	2
C19orf28	126321	broad.mit.edu	37	19	3551133	3551133	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:3551133C>T	uc002lxw.2	-	c.358G>A	c.(358-360)GCG>ACG	p.A120T	C19orf28_uc002lxx.2_Missense_Mutation_p.A120T|C19orf28_uc002lxy.2_Missense_Mutation_p.A111T|C19orf28_uc002lxz.2_Missense_Mutation_p.A120T	NM_021731	NP_068377	Q6NUT3	CS028_HUMAN	hypothetical protein LOC126321 isoform a	120					transmembrane transport	integral to membrane				breast(1)|pancreas(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00251)|STAD - Stomach adenocarcinoma(1328;0.18)										0.461538	18.14888	18.165591	6	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3551133	3551133	1980	19	C	T	T	T	338	26	C19orf28	2	2
WDR62	284403	broad.mit.edu	37	19	36587934	36587934	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36587934C>T	uc002odd.2	+	c.2473C>T	c.(2473-2475)CGT>TGT	p.R825C	WDR62_uc002odc.2_Missense_Mutation_p.R825C	NM_001083961	NP_001077430	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 1	825	WD 13.				cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)											0.857143	21.560282	22.415197	6	1	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36587934	36587934	17886	19	C	T	T	T	403	31	WDR62	1	1
HKR1	284459	broad.mit.edu	37	19	37838716	37838716	+	Silent	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37838716G>A	uc002ogb.2	+	c.255G>A	c.(253-255)CTG>CTA	p.L85L	HKR1_uc002ofx.2_5'UTR|HKR1_uc002ofy.2_5'UTR|HKR1_uc002ofz.2_Silent_p.L66L|HKR1_uc002oga.2_Silent_p.L66L|HKR1_uc010xto.1_Silent_p.L66L|HKR1_uc002ogc.2_Silent_p.L66L|HKR1_uc010xtp.1_Silent_p.L24L|HKR1_uc002ogd.2_Silent_p.L24L	NM_181786	NP_861451	P10072	HKR1_HUMAN	GLI-Kruppel family member HKR1	85	KRAB.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)											0.583333	42.950568	43.095462	14	10	KEEP	---	---	---	---	capture		Silent	SNP	37838716	37838716	7485	19	G	A	A	A	600	47	HKR1	2	2
ACTN4	81	broad.mit.edu	37	19	39219684	39219684	+	Missense_Mutation	SNP	A	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:39219684A>T	uc002oja.1	+	c.2467A>T	c.(2467-2469)AGC>TGC	p.S823C	ACTN4_uc002ojb.1_Missense_Mutation_p.S145C	NM_004924	NP_004915	O43707	ACTN4_HUMAN	actinin, alpha 4	823	EF-hand 2.|2 (Potential).				platelet activation|platelet degranulation|positive regulation of cellular component movement|positive regulation of sodium:hydrogen antiporter activity|protein transport|regulation of apoptosis	extracellular region|nucleolus|perinuclear region of cytoplasm|platelet alpha granule lumen|protein complex|pseudopodium|ribonucleoprotein complex	actin filament binding|calcium ion binding|integrin binding|nucleoside binding|protein homodimerization activity				0	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			Colon(168;199 1940 10254 46213 46384)								0.596774	118.099515	118.61984	37	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39219684	39219684	208	19	A	T	T	T	195	15	ACTN4	3	3
PSG9	5678	broad.mit.edu	37	19	43762450	43762450	+	Missense_Mutation	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43762450G>C	uc002owd.3	-	c.1147C>G	c.(1147-1149)CAA>GAA	p.Q383E	PSG9_uc002owe.3_Missense_Mutation_p.Q290E|PSG9_uc010xwm.1_Missense_Mutation_p.Q290E|PSG9_uc002owf.3_Missense_Mutation_p.Q197E|PSG9_uc002owg.2_Missense_Mutation_p.Q290E|PSG9_uc002owh.2_Missense_Mutation_p.Q197E	NM_002784	NP_002775	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	383	Ig-like C2-type 3.				female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)												0.154321	40.784691	59.511063	25	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43762450	43762450	13115	19	G	C	C	C	611	47	PSG9	3	3
GRLF1	2909	broad.mit.edu	37	19	47424388	47424388	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:47424388C>T	uc010ekv.2	+	c.2456C>T	c.(2455-2457)TCT>TTT	p.S819F		NM_004491	NP_004482	Q9NRY4	GRLF1_HUMAN	glucocorticoid receptor DNA binding factor 1	819					axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	DNA binding|Rho GTPase activator activity|transcription corepressor activity|transcription repressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)										0.541667	86.553665	86.626177	26	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47424388	47424388	7074	19	C	T	T	T	416	32	GRLF1	2	2
LMTK3	114783	broad.mit.edu	37	19	49004582	49004582	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49004582C>T	uc002pjk.2	-	c.1046G>A	c.(1045-1047)GGG>GAG	p.G349E		NM_001080434	NP_001073903			lemur tyrosine kinase 3											lung(5)|central_nervous_system(1)	6		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)						193				0.478873	99.318771	99.347551	34	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49004582	49004582	9189	19	C	T	T	T	286	22	LMTK3	2	2
KLK2	3817	broad.mit.edu	37	19	51380187	51380187	+	Missense_Mutation	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51380187G>C	uc002ptv.2	+	c.553G>C	c.(553-555)GCT>CCT	p.A185P	KLK2_uc010eog.2_Missense_Mutation_p.A83P|KLK2_uc010yck.1_Missense_Mutation_p.A185P|KLK2_uc002ptu.2_Missense_Mutation_p.A185P|KLK2_uc002ptt.2_Non-coding_Transcript|KLK2_uc010ycl.1_Missense_Mutation_p.A168P|KLK2_uc010ycm.1_Missense_Mutation_p.A83P|KLK2_uc010eoh.2_Missense_Mutation_p.A83P	NM_005551	NP_005542	P20151	KLK2_HUMAN	kallikrein 2, prostatic isoform 1	185	Peptidase S1.				proteolysis		serine-type endopeptidase activity			ovary(1)|skin(1)	2		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.00871)										0.697248	268.174291	272.011956	76	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51380187	51380187	8718	19	G	C	C	C	598	46	KLK2	3	3
NLRP7	199713	broad.mit.edu	37	19	55452944	55452944	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55452944C>T	uc010esl.2	-	c.220G>A	c.(220-222)GTG>ATG	p.V74M	NLRP7_uc002qig.3_Missense_Mutation_p.V46M|NLRP7_uc002qii.3_Missense_Mutation_p.V46M|NLRP7_uc002qih.3_Missense_Mutation_p.V46M|NLRP7_uc010esk.2_Missense_Mutation_p.V46M	NM_001127255	NP_001120727	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7	46	DAPIN.						ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)										0.218182	25.569235	29.599499	12	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55452944	55452944	10885	19	C	T	T	T	234	18	NLRP7	2	2
PNPLA6	10908	broad.mit.edu	37	19	7622061	7622061	+	Silent	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:7622061G>T	uc010xjq.1	+	c.3318G>T	c.(3316-3318)CTG>CTT	p.L1106L	PNPLA6_uc002mgq.1_Silent_p.L1058L|PNPLA6_uc010xjp.1_Silent_p.L1031L|PNPLA6_uc002mgr.1_Silent_p.L1058L|PNPLA6_uc002mgs.2_Silent_p.L1096L|PNPLA6_uc002mgt.1_Non-coding_Transcript	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase isoform b	1097	Patatin.|Cytoplasmic (Potential).				cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3														0.4	45.388435	45.739153	16	24	KEEP	---	---	---	---	capture		Silent	SNP	7622061	7622061	12596	19	G	T	T	T	613	48	PNPLA6	2	2
KANK3	256949	broad.mit.edu	37	19	8389370	8389370	+	Missense_Mutation	SNP	A	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:8389370A>T	uc010dwa.2	-	c.2345T>A	c.(2344-2346)CTA>CAA	p.L782Q		NM_198471	NP_940873	Q6NY19	KANK3_HUMAN	ankyrin repeat domain 47	782	ANK 5.										0														0.5	19.350095	19.350095	6	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8389370	8389370	8282	19	A	T	T	T	195	15	KANK3	3	3
HAO2	51179	broad.mit.edu	37	1	119929411	119929411	+	Missense_Mutation	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:119929411T>C	uc001ehq.1	+	c.728T>C	c.(727-729)GTT>GCT	p.V243A	HAO2_uc001ehr.1_Missense_Mutation_p.V243A	NM_001005783	NP_001005783	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2	243	FMN hydroxy acid dehydrogenase.				fatty acid alpha-oxidation	peroxisome	(S)-2-hydroxy-acid oxidase activity			ovary(1)	1	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)										0.196078	27.022131	31.410663	10	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119929411	119929411	7234	1	T	C	C	C	780	60	HAO2	4	4
CLK2	1196	broad.mit.edu	37	1	155239366	155239366	+	Missense_Mutation	SNP	C	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155239366C>G	uc001fjy.2	-	c.312G>C	c.(310-312)GAG>GAC	p.E104D	RAG1AP1_uc010pey.1_Intron|CLK2_uc001fjw.2_Missense_Mutation_p.E104D|CLK2_uc001fjx.2_5'UTR|CLK2_uc009wqm.2_Missense_Mutation_p.E104D	NM_003993	NP_003984	P49760	CLK2_HUMAN	CDC-like kinase 2	104					protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)							135				0.201923	96.952538	114.133056	42	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155239366	155239366	3675	1	C	G	G	G	415	32	CLK2	3	3
CCT3	7203	broad.mit.edu	37	1	156290753	156290753	+	Silent	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156290753G>C	uc001fol.1	-	c.486C>G	c.(484-486)ACC>ACG	p.T162T	CCT3_uc001fom.1_Silent_p.T161T|CCT3_uc001fon.1_Silent_p.T124T|CCT3_uc010phj.1_Silent_p.T116T|CCT3_uc010phk.1_Silent_p.T116T|CCT3_uc010phl.1_Silent_p.T116T	NM_005998	NP_005989	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 isoform a	162					'de novo' posttranslational protein folding	cytoskeleton|cytosol|plasma membrane	ATP binding|unfolded protein binding			ovary(1)	1	Hepatocellular(266;0.158)													0.257485	101.570675	110.55467	43	124	KEEP	---	---	---	---	capture		Silent	SNP	156290753	156290753	3081	1	G	C	C	C	600	47	CCT3	3	3
BAT2L2	23215	broad.mit.edu	37	1	171509216	171509216	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:171509216G>A	uc010pmg.1	+	c.2605G>A	c.(2605-2607)GCA>ACA	p.A869T	BAT2L2_uc010pmh.1_5'UTR	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	869							protein C-terminus binding				0														0.277372	93.450558	99.532415	38	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	171509216	171509216	1342	1	G	A	A	A	546	42	BAT2L2	2	2
ASTN1	460	broad.mit.edu	37	1	176903371	176903371	+	Missense_Mutation	SNP	C	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:176903371C>G	uc001glc.2	-	c.2588G>C	c.(2587-2589)GGC>GCC	p.G863A	ASTN1_uc001glb.1_Missense_Mutation_p.G863A|ASTN1_uc001gld.1_Missense_Mutation_p.G863A	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	871					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	11										849				0.346154	56.837493	57.922666	18	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176903371	176903371	1083	1	C	G	G	G	338	26	ASTN1	3	3
IRF6	3664	broad.mit.edu	37	1	209961969	209961969	+	Silent	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:209961969C>A	uc001hhq.1	-	c.1200G>T	c.(1198-1200)CGG>CGT	p.R400R	IRF6_uc010psm.1_Silent_p.R305R|IRF6_uc009xct.1_Silent_p.R400R	NM_006147	NP_006138	O14896	IRF6_HUMAN	interferon regulatory factor 6	400					cell cycle arrest|interferon-gamma-mediated signaling pathway|mammary gland epithelial cell differentiation|negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0351)										0.642857	26.7624	27.010299	9	5	KEEP	---	---	---	---	capture		Silent	SNP	209961969	209961969	8137	1	C	A	A	A	379	30	IRF6	2	2
SIPA1L2	57568	broad.mit.edu	37	1	232534998	232534998	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:232534998G>T	uc001hvg.2	-	c.5044C>A	c.(5044-5046)CTC>ATC	p.L1682I	SIPA1L2_uc001hvf.2_Missense_Mutation_p.L738I	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	1682	Potential.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)												0.25	24.130529	26.403428	10	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	232534998	232534998	14825	1	G	T	T	T	429	33	SIPA1L2	2	2
CNKSR1	10256	broad.mit.edu	37	1	26510616	26510616	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26510616G>A	uc001bln.3	+	c.931G>A	c.(931-933)GCC>ACC	p.A311T	CNKSR1_uc010oex.1_Intron|CNKSR1_uc001blm.3_Missense_Mutation_p.A304T|CNKSR1_uc009vsd.2_Missense_Mutation_p.A46T|CNKSR1_uc009vse.2_Missense_Mutation_p.A46T|CNKSR1_uc001blo.2_Missense_Mutation_p.A46T	NM_006314	NP_006305	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras	311	Pro-rich.				Rho protein signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cell cortex|cell-cell junction	protein binding, bridging			kidney(1)	1		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		NSCLC(180;1396 2109 28270 30756 34275)								0.62069	167.57466	168.696576	54	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26510616	26510616	3744	1	G	A	A	A	546	42	CNKSR1	2	2
PPP1R8	5511	broad.mit.edu	37	1	28167669	28167669	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:28167669G>A	uc001bov.1	+	c.416G>A	c.(415-417)GGA>GAA	p.G139E	PPP1R8_uc001bow.1_5'UTR|PPP1R8_uc001box.1_Intron|PPP1R8_uc009vtc.1_Non-coding_Transcript|PPP1R8_uc009vtd.1_Intron	NM_014110	NP_054829	Q12972	PP1R8_HUMAN	protein phosphatase 1 regulatory inhibitor	139	Interaction with CDC5L, SF3B1 and MELK.				mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|RNA splicing|transcription, DNA-dependent	cytoplasm|nuclear speck|spliceosomal complex	DNA binding|endonuclease activity|protein binding|protein serine/threonine phosphatase inhibitor activity|ribonuclease E activity|RNA binding				0		Colorectal(325;3.46e-05)|all_lung(284;0.000129)|Lung NSC(340;0.000259)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.76e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00248)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)										0.147368	21.598091	32.944188	14	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28167669	28167669	12813	1	G	A	A	A	533	41	PPP1R8	2	2
PHACTR4	65979	broad.mit.edu	37	1	28815703	28815703	+	Silent	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:28815703A>G	uc001bpy.2	+	c.1812A>G	c.(1810-1812)ACA>ACG	p.T604T	PHACTR4_uc001bpv.1_Non-coding_Transcript|PHACTR4_uc001bpw.2_Silent_p.T594T|PHACTR4_uc001bpx.2_Silent_p.T578T|PHACTR4_uc001bpz.2_5'Flank	NM_023923	NP_076412	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4 isoform 2	594	RPEL 2.						actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)										0.464286	41.074307	41.105076	13	15	KEEP	---	---	---	---	capture		Silent	SNP	28815703	28815703	12235	1	A	G	G	G	67	6	PHACTR4	4	4
PHC2	1912	broad.mit.edu	37	1	33832751	33832751	+	Silent	SNP	A	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:33832751A>T	uc009vuh.1	-	c.942T>A	c.(940-942)GTT>GTA	p.V314V	PHC2_uc001bxg.1_Silent_p.V314V|PHC2_uc001bxh.1_Silent_p.V285V|PHC2_uc001bxi.1_Silent_p.V314V	NM_198040	NP_932157	Q8IXK0	PHC2_HUMAN	polyhomeotic-like 2 isoform a	314					multicellular organismal development		DNA binding|identical protein binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)												0.162791	30.176917	44.163417	21	108	KEEP	---	---	---	---	capture		Silent	SNP	33832751	33832751	12240	1	A	T	T	T	106	9	PHC2	3	3
DNAJC6	9829	broad.mit.edu	37	1	65855004	65855004	+	Missense_Mutation	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:65855004T>C	uc001dce.1	+	c.1259T>C	c.(1258-1260)GTA>GCA	p.V420A	DNAJC6_uc001dcc.1_Missense_Mutation_p.V394A|DNAJC6_uc001dcd.1_Missense_Mutation_p.V363A|DNAJC6_uc010opc.1_Missense_Mutation_p.V350A	NM_014787	NP_055602	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	363	C2 tensin-type.				cellular membrane organization|post-Golgi vesicle-mediated transport	cytosol	heat shock protein binding|protein tyrosine phosphatase activity|SH3 domain binding			large_intestine(1)|lung(1)|ovary(1)	3														0.339286	61.162954	62.463658	19	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65855004	65855004	4836	1	T	C	C	C	741	57	DNAJC6	4	4
LRRC7	57554	broad.mit.edu	37	1	70502175	70502175	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:70502175G>A	uc001dep.2	+	c.2042G>A	c.(2041-2043)AGT>AAT	p.S681N	LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.2_De_novo_Start_OutOfFrame	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	681						centrosome|focal adhesion|nucleolus	protein binding			ovary(8)|breast(2)|central_nervous_system(2)|liver(1)	13										783				0.318182	39.246492	40.533774	14	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70502175	70502175	9396	1	G	A	A	A	468	36	LRRC7	2	2
HFM1	164045	broad.mit.edu	37	1	91851286	91851286	+	Silent	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:91851286T>C	uc001doa.3	-	c.600A>G	c.(598-600)AAA>AAG	p.K200K	HFM1_uc010osu.1_Intron|HFM1_uc010osv.1_Intron|HFM1_uc001doc.1_Silent_p.K200K	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	200							ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)										0.468085	70.710472	70.754677	22	25	KEEP	---	---	---	---	capture		Silent	SNP	91851286	91851286	7366	1	T	C	C	C	725	56	HFM1	4	4
NKX2-2	4821	broad.mit.edu	37	20	21494245	21494245	+	Silent	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:21494245G>C	uc002wsi.2	-	c.63C>G	c.(61-63)ACC>ACG	p.T21T		NM_002509	NP_002500	O95096	NKX22_HUMAN	NK2 transcription factor related, locus 2	21					brain development	nucleus	transcription regulator activity			pancreas(1)	1														0.315789	41.975343	43.72977	18	39	KEEP	---	---	---	---	capture		Silent	SNP	21494245	21494245	10852	20	G	C	C	C	600	47	NKX2-2	3	3
ZNF343	79175	broad.mit.edu	37	20	2464228	2464228	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:2464228G>A	uc002wge.1	-	c.1379C>T	c.(1378-1380)TCT>TTT	p.S460F	ZNF343_uc010gao.1_Missense_Mutation_p.S460F|ZNF343_uc002wgd.1_Missense_Mutation_p.S370F	NM_024325	NP_077301	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	460					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1														0.309091	47.451739	49.239662	17	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2464228	2464228	18450	20	G	A	A	A	429	33	ZNF343	2	2
ZNF337	26152	broad.mit.edu	37	20	25667036	25667036	+	Silent	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:25667036G>T	uc002wva.2	-	c.18C>A	c.(16-18)GCC>GCA	p.A6A	ZNF337_uc010ztg.1_Silent_p.A6A|ZNF337_uc002wvb.2_Silent_p.A6A|ZNF337_uc002wvc.2_Silent_p.A6A	NM_015655	NP_056470	Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	6					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.285714	22.387756	23.54187	8	20	KEEP	---	---	---	---	capture		Silent	SNP	25667036	25667036	18445	20	G	T	T	T	600	47	ZNF337	2	2
CHD6	84181	broad.mit.edu	37	20	40126136	40126136	+	Missense_Mutation	SNP	T	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:40126136T>G	uc002xka.1	-	c.980A>C	c.(979-981)TAC>TCC	p.Y327S	CHD6_uc002xkd.2_Missense_Mutation_p.Y305S|CHD6_uc002xkc.2_3'UTR	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	327	Chromo 1.				chromatin assembly or disassembly|chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|lung(2)|central_nervous_system(1)|skin(1)	10		Myeloproliferative disorder(115;0.00425)												0.35	89.788093	91.370678	28	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40126136	40126136	3463	20	T	G	G	G	741	57	CHD6	4	4
LAMA5	3911	broad.mit.edu	37	20	60885352	60885352	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:60885352G>A	uc002ycq.2	-	c.10616C>T	c.(10615-10617)ACA>ATA	p.T3539I		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor	3539	Laminin G-like 5.				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding|receptor activity|structural molecule activity			pancreas(1)	1	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.333333	41.227019	42.325584	15	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60885352	60885352	8932	20	G	A	A	A	624	48	LAMA5	2	2
TMX4	56255	broad.mit.edu	37	20	7963206	7963206	+	Missense_Mutation	SNP	T	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:7963206T>G	uc002wmx.1	-	c.742A>C	c.(742-744)AAA>CAA	p.K248Q		NM_021156	NP_066979	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	248	Glu-rich.				cell redox homeostasis|electron transport chain|transport	integral to membrane					0														0.37931	35.418517	35.788915	11	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7963206	7963206	16810	20	T	G	G	G	832	64	TMX4	4	4
COL6A1	1291	broad.mit.edu	37	21	47404299	47404299	+	Missense_Mutation	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:47404299G>C	uc002zhu.1	+	c.344G>C	c.(343-345)AGC>ACC	p.S115T		NM_001848	NP_001839	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1 precursor	115	VWFA 1.|N-terminal globular domain.				axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			ovary(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)									0.464286	42.08996	42.118787	13	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47404299	47404299	3837	21	G	C	C	C	442	34	COL6A1	3	3
PIWIL3	440822	broad.mit.edu	37	22	25151777	25151777	+	Silent	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:25151777T>C	uc003abd.1	-	c.666A>G	c.(664-666)CTA>CTG	p.L222L	PIWIL3_uc011ajx.1_Silent_p.L113L|PIWIL3_uc011ajy.1_Silent_p.L113L|PIWIL3_uc010gut.1_Silent_p.L222L	NM_001008496	NP_001008496	Q7Z3Z3	PIWL3_HUMAN	piwi-like 3	222					cell differentiation|gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatogenesis	cytoplasm	RNA binding			ovary(3)|central_nervous_system(1)	4														0.189655	23.707217	28.921552	11	47	KEEP	---	---	---	---	capture		Silent	SNP	25151777	25151777	12383	22	T	C	C	C	730	57	PIWIL3	4	4
HPS4	89781	broad.mit.edu	37	22	26875276	26875276	+	Silent	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26875276T>C	uc003acl.2	-	c.87A>G	c.(85-87)GAA>GAG	p.E29E	HPS4_uc003aci.2_Silent_p.E24E|HPS4_uc003acj.2_5'UTR|HPS4_uc003ack.2_5'UTR|HPS4_uc003acn.2_5'UTR|HPS4_uc010gvd.1_Silent_p.E29E|HPS4_uc003aco.1_Silent_p.E24E	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	29					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0														0.264706	26.18515	27.870904	9	25	KEEP	---	---	---	---	capture		Silent	SNP	26875276	26875276	7633	22	T	C	C	C	725	56	HPS4	4	4
ST6GAL2	84620	broad.mit.edu	37	2	107460008	107460008	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:107460008G>T	uc002tdq.2	-	c.426C>A	c.(424-426)AGC>AGA	p.S142R	ST6GAL2_uc002tdr.2_Missense_Mutation_p.S142R|ST6GAL2_uc002tds.3_Missense_Mutation_p.S142R	NM_001142351	NP_001135823	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide	142	Lumenal (Potential).				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(3)	9														0.194118	66.664012	81.54838	33	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107460008	107460008	15740	2	G	T	T	T	542	42	ST6GAL2	2	2
ZEB2	9839	broad.mit.edu	37	2	145156993	145156993	+	Missense_Mutation	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:145156993T>A	uc002tvu.2	-	c.1761A>T	c.(1759-1761)AAA>AAT	p.K587N	ZEB2_uc002tvv.2_Missense_Mutation_p.K581N|ZEB2_uc010zbm.1_Missense_Mutation_p.K558N|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Missense_Mutation_p.K616N	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	587					negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|large_intestine(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.112)		Melanoma(33;1235 1264 5755 16332)								0.372093	93.478984	94.714496	32	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145156993	145156993	18212	2	T	A	A	A	725	56	ZEB2	3	3
RIF1	55183	broad.mit.edu	37	2	152300099	152300099	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:152300099C>T	uc002txm.2	+	c.1862C>T	c.(1861-1863)CCA>CTA	p.P621L	RIF1_uc002txl.2_Missense_Mutation_p.P621L|RIF1_uc010fnv.1_Missense_Mutation_p.P585L|RIF1_uc002txn.2_Missense_Mutation_p.P621L|RIF1_uc002txo.2_Missense_Mutation_p.P621L	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1	621					cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|lung(2)|kidney(1)	12				BRCA - Breast invasive adenocarcinoma(221;0.0429)						950				0.381818	121.86054	123.228287	42	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152300099	152300099	13834	2	C	T	T	T	273	21	RIF1	2	2
SCN1A	6323	broad.mit.edu	37	2	166848264	166848264	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:166848264G>T	uc010zcz.1	-	c.5488C>A	c.(5488-5490)CTG>ATG	p.L1830M		NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1841						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|large_intestine(1)	7					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)									0.402062	110.994764	111.811153	39	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166848264	166848264	14396	2	G	T	T	T	425	33	SCN1A	2	2
TTN	7273	broad.mit.edu	37	2	179585221	179585221	+	Missense_Mutation	SNP	A	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179585221A>T	uc010zfg.1	-	c.19536T>A	c.(19534-19536)GAT>GAA	p.D6512E	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.D3173E	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3467										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)							8722				0.186047	19.012949	22.955358	8	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179585221	179585221	17290	2	A	T	T	T	206	16	TTN	3	3
TTN	7273	broad.mit.edu	37	2	179598223	179598223	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179598223C>A	uc010zfg.1	-	c.12065G>T	c.(12064-12066)CGA>CTA	p.R4022L	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.R683L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	948										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)							8722				0.209302	87.23753	100.669378	36	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179598223	179598223	17290	2	C	A	A	A	403	31	TTN	1	1
CCDC150	284992	broad.mit.edu	37	2	197534559	197534559	+	Missense_Mutation	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:197534559T>C	uc002utp.1	+	c.895T>C	c.(895-897)TCT>CCT	p.S299P	CCDC150_uc010zgq.1_Non-coding_Transcript|CCDC150_uc010zgr.1_Intron|CCDC150_uc010zgs.1_5'UTR	NM_001080539	NP_001074008	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	299	Potential.										0														0.215909	51.695954	58.237524	19	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197534559	197534559	2905	2	T	C	C	C	806	62	CCDC150	4	4
SATB2	23314	broad.mit.edu	37	2	200213524	200213524	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:200213524A>G	uc002uuy.1	-	c.1073T>C	c.(1072-1074)GTG>GCG	p.V358A	SATB2_uc010fsq.1_Missense_Mutation_p.V240A|SATB2_uc002uuz.1_Missense_Mutation_p.V358A|SATB2_uc002uva.1_Missense_Mutation_p.V358A|SATB2_uc002uvb.1_Missense_Mutation_p.V101A	NM_015265	NP_056080	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	358	CUT 1.					cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1						Colon(30;262 767 11040 24421 36230)								0.41573	110.85139	111.42619	37	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	200213524	200213524	14335	2	A	G	G	G	78	6	SATB2	4	4
DYTN	391475	broad.mit.edu	37	2	207569584	207569584	+	Missense_Mutation	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:207569584G>C	uc002vbr.1	-	c.466C>G	c.(466-468)CTA>GTA	p.L156V		NM_001093730	NP_001087199	A2CJ06	DYTN_HUMAN	dystrotelin	156						plasma membrane	zinc ion binding			ovary(1)	1				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)										0.428571	20.848139	20.910406	6	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	207569584	207569584	5047	2	G	C	C	C	464	36	DYTN	3	3
PIKFYVE	200576	broad.mit.edu	37	2	209218638	209218638	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:209218638G>T	uc002vcz.2	+	c.5861G>T	c.(5860-5862)GGC>GTC	p.G1954V		NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	1954	Catalytic.|PIPK.				cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding|zinc ion binding			ovary(5)|kidney(2)|central_nervous_system(1)|pancreas(1)	9										756				0.396552	62.512245	63.054203	23	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	209218638	209218638	12348	2	G	T	T	T	546	42	PIKFYVE	2	2
PID1	55022	broad.mit.edu	37	2	229890361	229890361	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:229890361G>A	uc002vpr.3	-	c.740C>T	c.(739-741)TCC>TTC	p.S247F	PID1_uc002vps.3_Missense_Mutation_p.S245F|PID1_uc002vpt.3_Missense_Mutation_p.S214F|PID1_uc002vpu.3_Missense_Mutation_p.S165F	NM_001100818	NP_001094288	Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1	247	PID.					cytoplasm				breast(3)	3		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)										0.184211	31.034692	38.121698	14	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	229890361	229890361	12306	2	G	A	A	A	533	41	PID1	2	2
UGT1A6	54578	broad.mit.edu	37	2	234602290	234602290	+	Missense_Mutation	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:234602290G>C	uc002vuv.3	+	c.640G>C	c.(640-642)GTT>CTT	p.V214L	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Missense_Mutation_p.V214L	NM_001072	NP_001063	P19224	UD16_HUMAN	UDP glycosyltransferase 1 family, polypeptide A6	214					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity				0		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)										0.166667	42.01353	55.440131	21	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	234602290	234602290	17507	2	G	C	C	C	624	48	UGT1A6	3	3
ADCY3	109	broad.mit.edu	37	2	25044490	25044490	+	Missense_Mutation	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:25044490T>A	uc010ykm.1	-	c.3026A>T	c.(3025-3027)GAG>GTG	p.E1009V	ADCY3_uc002rfr.3_Missense_Mutation_p.E595V|ADCY3_uc002rfs.3_Missense_Mutation_p.E1008V	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3	1008	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)													0.181818	49.247576	64.890047	30	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25044490	25044490	296	2	T	A	A	A	702	54	ADCY3	3	3
THADA	63892	broad.mit.edu	37	2	43779441	43779441	+	Silent	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:43779441T>C	uc002rsw.3	-	c.2712A>G	c.(2710-2712)GTA>GTG	p.V904V	THADA_uc010far.2_Silent_p.V173V|THADA_uc002rsx.3_Silent_p.V904V|THADA_uc002rsy.3_Non-coding_Transcript|THADA_uc010fas.1_Non-coding_Transcript|THADA_uc002rsz.2_Silent_p.V614V|THADA_uc010fat.1_Silent_p.V52V|THADA_uc002rta.2_Silent_p.V614V|THADA_uc002rtb.1_Silent_p.V904V	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	904	Potential.						binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)												0.47619	31.246167	31.25663	10	11	KEEP	---	---	---	---	capture		Silent	SNP	43779441	43779441	16368	2	T	C	C	C	626	49	THADA	4	4
PREPL	9581	broad.mit.edu	37	2	44586775	44586775	+	Missense_Mutation	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:44586775T>A	uc002ruf.2	-	c.80A>T	c.(79-81)CAT>CTT	p.H27L	PREPL_uc002rug.2_Missense_Mutation_p.H27L|PREPL_uc002ruh.2_Missense_Mutation_p.H27L|PREPL_uc010fax.2_Missense_Mutation_p.H27L|PREPL_uc002rui.3_Intron|PREPL_uc002ruj.1_Intron|PREPL_uc002ruk.1_Missense_Mutation_p.H27L|C2orf34_uc002rum.2_5'Flank|C2orf34_uc002rul.2_5'Flank	NM_006036	NP_006027	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like isoform C	27					proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)												0.300971	92.091768	95.732379	31	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44586775	44586775	12918	2	T	A	A	A	663	51	PREPL	3	3
MPHOSPH10	10199	broad.mit.edu	37	2	71377048	71377048	+	Missense_Mutation	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71377048T>C	uc002sht.1	+	c.1949T>C	c.(1948-1950)TTA>TCA	p.L650S		NM_005791	NP_005782	O00566	MPP10_HUMAN	M-phase phosphoprotein 10	650	Potential.				RNA splicing, via transesterification reactions|rRNA processing	chromosome|nucleolus|small nucleolar ribonucleoprotein complex	protein binding			ovary(1)	1														0.215686	30.007894	33.804729	11	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71377048	71377048	10117	2	T	C	C	C	793	61	MPHOSPH10	4	4
LRRTM4	80059	broad.mit.edu	37	2	77745564	77745564	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:77745564C>T	uc002snr.2	-	c.1431G>A	c.(1429-1431)ATG>ATA	p.M477I	LRRTM4_uc002snq.2_Missense_Mutation_p.M477I|LRRTM4_uc002sns.2_Missense_Mutation_p.M477I|LRRTM4_uc002snt.2_Missense_Mutation_p.M478I	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	477	Cytoplasmic (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)										0.185185	9.557279	12.068348	5	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77745564	77745564	9418	2	C	T	T	T	377	29	LRRTM4	2	2
SMYD1	150572	broad.mit.edu	37	2	88407960	88407960	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:88407960G>A	uc002ssr.2	+	c.1216G>A	c.(1216-1218)GCT>ACT	p.A406T	SMYD1_uc002ssq.1_Intron|SMYD1_uc002sss.2_Missense_Mutation_p.A102T	NM_198274	NP_938015	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	406					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3														0.137255	9.73929	16.193183	7	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88407960	88407960	15321	2	G	A	A	A	598	46	SMYD1	2	2
ADPRH	141	broad.mit.edu	37	3	119306535	119306535	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:119306535G>T	uc003ecs.2	+	c.884G>T	c.(883-885)CGA>CTA	p.R295L	ADPRH_uc010hqv.2_Missense_Mutation_p.R295L|ADPRH_uc011bjb.1_Missense_Mutation_p.R188L|ADPRH_uc003ect.2_Missense_Mutation_p.R295L	NM_001125	NP_001116	P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	295					protein de-ADP-ribosylation		ADP-ribosylarginine hydrolase activity|magnesium ion binding			ovary(1)	1		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		GBM(133;579 1804 5989 9967 40052)								0.166667	16.951278	22.632356	9	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119306535	119306535	332	3	G	T	T	T	481	37	ADPRH	1	1
TMCC1	23023	broad.mit.edu	37	3	129370423	129370423	+	Silent	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:129370423C>A	uc003emz.3	-	c.1863G>T	c.(1861-1863)ACG>ACT	p.T621T	TMCC1_uc003emy.3_Silent_p.T297T|TMCC1_uc011blc.1_Silent_p.T442T|TMCC1_uc010htg.2_Silent_p.T507T	NM_001017395	NP_001017395	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	621						integral to membrane					0														0.294643	95.915069	100.093447	33	79	KEEP	---	---	---	---	capture		Silent	SNP	129370423	129370423	16522	3	C	A	A	A	236	19	TMCC1	1	1
PLCH1	23007	broad.mit.edu	37	3	155200618	155200618	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:155200618C>A	uc011bok.1	-	c.3221G>T	c.(3220-3222)TGC>TTC	p.C1074F	PLCH1_uc011boj.1_3'UTR|PLCH1_uc011bol.1_Missense_Mutation_p.C1036F	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	1074					lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)	1			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)											0.248062	78.778486	86.200949	32	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155200618	155200618	12463	3	C	A	A	A	325	25	PLCH1	2	2
C3orf59	151963	broad.mit.edu	37	3	192635485	192635485	+	Silent	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:192635485G>T	uc011bsp.1	-	c.145C>A	c.(145-147)CGG>AGG	p.R49R		NM_178496	NP_848591	Q8IYB1	M21D2_HUMAN	hypothetical protein LOC151963	49											0	all_cancers(143;1.56e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.8e-18)|LUSC - Lung squamous cell carcinoma(58;8.04e-06)|Lung(62;8.62e-06)	GBM - Glioblastoma multiforme(46;3.86e-05)										0.139535	10.772661	16.126206	6	37	KEEP	---	---	---	---	capture		Silent	SNP	192635485	192635485	2330	3	G	T	T	T	493	38	C3orf59	1	1
OSBPL10	114884	broad.mit.edu	37	3	31917965	31917965	+	Missense_Mutation	SNP	A	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:31917965A>C	uc003cev.2	-	c.497T>G	c.(496-498)CTT>CGT	p.L166R	OSBPL10_uc011axf.1_Missense_Mutation_p.L166R	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10	166	PH.				lipid transport		lipid binding				0				STAD - Stomach adenocarcinoma(1;0.00406)										0.230769	23.764588	26.348169	9	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31917965	31917965	11686	3	A	C	C	C	39	3	OSBPL10	4	4
RRP9	9136	broad.mit.edu	37	3	51972152	51972152	+	Missense_Mutation	SNP	A	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:51972152A>T	uc003dbw.1	-	c.239T>A	c.(238-240)CTG>CAG	p.L80Q		NM_004704	NP_004695	O43818	U3IP2_HUMAN	RNA, U3 small nucleolar interacting protein 2	80	Glu-rich.				rRNA processing	nucleolus|small nuclear ribonucleoprotein complex|small nucleolar ribonucleoprotein complex	RNA binding			breast(2)|ovary(1)	3				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)										0.545455	37.600104	37.63951	12	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51972152	51972152	14171	3	A	T	T	T	91	7	RRP9	3	3
INTS12	57117	broad.mit.edu	37	4	106603997	106603997	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:106603997G>A	uc003hxw.2	-	c.1282C>T	c.(1282-1284)CCC>TCC	p.P428S	INTS12_uc010ilr.2_Missense_Mutation_p.P428S	NM_020395	NP_065128	Q96CB8	INT12_HUMAN	integrator complex subunit 12	428	Ser-rich.				snRNA processing	integrator complex	protein binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(123;5.12e-07)										0.370629	154.82354	156.93129	53	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106603997	106603997	8078	4	G	A	A	A	533	41	INTS12	2	2
COL25A1	84570	broad.mit.edu	37	4	109773411	109773411	+	Missense_Mutation	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:109773411T>C	uc003hze.1	-	c.1370A>G	c.(1369-1371)CAA>CGA	p.Q457R	COL25A1_uc003hzg.2_Missense_Mutation_p.Q457R|COL25A1_uc003hzd.2_Non-coding_Transcript|COL25A1_uc003hzf.2_Missense_Mutation_p.Q215R	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1	457	Extracellular (Potential).|Collagen-like 6.					collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)										0.37931	61.625435	62.369946	22	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109773411	109773411	3822	4	T	C	C	C	819	63	COL25A1	4	4
SETD7	80854	broad.mit.edu	37	4	140444545	140444545	+	Missense_Mutation	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:140444545T>A	uc003ihw.2	-	c.607A>T	c.(607-609)ACC>TCC	p.T203S		NM_030648	NP_085151	Q8WTS6	SETD7_HUMAN	SET domain-containing protein 7	203					peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	histone-lysine N-methyltransferase activity|p53 binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.156)													0.206522	46.184849	53.521464	19	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140444545	140444545	14625	4	T	A	A	A	741	57	SETD7	3	3
TLR2	7097	broad.mit.edu	37	4	154626147	154626147	+	Silent	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:154626147C>T	uc003inq.2	+	c.2088C>T	c.(2086-2088)AGC>AGT	p.S696S	TLR2_uc003inr.2_Silent_p.S696S|TLR2_uc003ins.2_Silent_p.S696S	NM_003264	NP_003255	O60603	TLR2_HUMAN	toll-like receptor 2 precursor	696	TIR.|Cytoplasmic (Potential).				cellular response to diacyl bacterial lipopeptide|cellular response to lipoteichoic acid|cellular response to triacyl bacterial lipopeptide|detection of diacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|I-kappaB phosphorylation|induction of apoptosis|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of inflammatory response|positive regulation of interferon-beta production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of tumor necrosis factor production|positive regulation of Wnt receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|integral to plasma membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	Gram-positive bacterial cell surface binding|lipopolysaccharide receptor activity|peptidoglycan binding|protein heterodimerization activity|transmembrane receptor activity|triacyl lipopeptide binding				0	all_hematologic(180;0.093)	Renal(120;0.117)												0.423077	194.305451	195.088402	66	90	KEEP	---	---	---	---	capture		Silent	SNP	154626147	154626147	16481	4	C	T	T	T	337	26	TLR2	2	2
RBM46	166863	broad.mit.edu	37	4	155720435	155720435	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:155720435C>T	uc003ioo.2	+	c.1121C>T	c.(1120-1122)CCT>CTT	p.P374L	RBM46_uc011cim.1_Missense_Mutation_p.P374L|RBM46_uc003iop.1_Missense_Mutation_p.P374L	NM_144979	NP_659416	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	374							nucleotide binding|RNA binding			central_nervous_system(1)	1	all_hematologic(180;0.24)	Renal(120;0.0854)												0.219298	67.959443	76.20081	25	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155720435	155720435	13602	4	C	T	T	T	312	24	RBM46	2	2
FGFBP2	83888	broad.mit.edu	37	4	15964142	15964142	+	Missense_Mutation	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:15964142T>A	uc003gon.2	-	c.611A>T	c.(610-612)GAA>GTA	p.E204V		NM_031950	NP_114156	Q9BYJ0	FGFP2_HUMAN	killer-specific secretory protein of 37 kDa	204						extracellular space	growth factor binding				0														0.463768	84.507532	84.593229	32	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15964142	15964142	6098	4	T	A	A	A	806	62	FGFBP2	3	3
TMEM192	201931	broad.mit.edu	37	4	166009711	166009711	+	Silent	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:166009711G>A	uc003iqz.3	-	c.483C>T	c.(481-483)TTC>TTT	p.F161F		NM_001100389	NP_001093859	Q8IY95	TM192_HUMAN	transmembrane protein 192	161	Lumenal (Potential).					Golgi apparatus|integral to membrane|late endosome|lysosomal membrane|nucleus					0	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0926)										0.666667	27.204662	27.500654	8	4	KEEP	---	---	---	---	capture		Silent	SNP	166009711	166009711	16649	4	G	A	A	A	529	41	TMEM192	2	2
DDX60L	91351	broad.mit.edu	37	4	169344796	169344796	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:169344796C>T	uc003irq.3	-	c.2060G>A	c.(2059-2061)GGC>GAC	p.G687D	DDX60L_uc003irr.1_Missense_Mutation_p.G687D|DDX60L_uc003irs.1_Missense_Mutation_p.G414D	NM_001012967	NP_001012985	Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	687							ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)										0.5	11.800543	11.800543	4	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169344796	169344796	4550	4	C	T	T	T	338	26	DDX60L	2	2
GABRA2	2555	broad.mit.edu	37	4	46252429	46252429	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:46252429C>A	uc003gxc.3	-	c.1252G>T	c.(1252-1254)GAC>TAC	p.D418Y	GABRA2_uc010igc.2_Missense_Mutation_p.D418Y|GABRA2_uc011bzc.1_Missense_Mutation_p.D423Y	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	418	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.25	96.569467	106.11921	42	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46252429	46252429	6412	4	C	A	A	A	377	29	GABRA2	2	2
LPHN3	23284	broad.mit.edu	37	4	62897172	62897172	+	Silent	SNP	A	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:62897172A>T	uc010ihh.2	+	c.3231A>T	c.(3229-3231)ATA>ATT	p.I1077I	LPHN3_uc003hcq.3_Silent_p.I1077I|LPHN3_uc003hct.2_Silent_p.I461I	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	1055	Helical; Name=6; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.240506	49.791822	54.641645	19	60	KEEP	---	---	---	---	capture		Silent	SNP	62897172	62897172	9290	4	A	T	T	T	189	15	LPHN3	3	3
PPEF2	5470	broad.mit.edu	37	4	76794373	76794373	+	Silent	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:76794373C>A	uc003hix.2	-	c.1413G>T	c.(1411-1413)GTG>GTT	p.V471V	PPEF2_uc003hiy.2_Non-coding_Transcript|PPEF2_uc003hiz.1_Silent_p.V471V	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	471	Catalytic.				detection of stimulus involved in sensory perception|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			NSCLC(105;1359 1603 15961 44567 47947)								0.295775	51.841917	54.494855	21	50	KEEP	---	---	---	---	capture		Silent	SNP	76794373	76794373	12738	4	C	A	A	A	366	29	PPEF2	2	2
FRAS1	80144	broad.mit.edu	37	4	79334175	79334175	+	Missense_Mutation	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:79334175T>A	uc003hlb.2	+	c.4361T>A	c.(4360-4362)ATC>AAC	p.I1454N	FRAS1_uc003hkw.2_Missense_Mutation_p.I1454N	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	1453	CSPG 4.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5														0.375	18.04609	18.265545	6	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79334175	79334175	6288	4	T	A	A	A	650	50	FRAS1	3	3
BMP2K	55589	broad.mit.edu	37	4	79793852	79793852	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:79793852C>A	uc003hlk.2	+	c.1693C>A	c.(1693-1695)CTT>ATT	p.L565I	BMP2K_uc003hlj.2_Missense_Mutation_p.L565I|BMP2K_uc003hll.2_Missense_Mutation_p.L29I	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a	565					protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1										318				0.163636	15.237286	21.152425	9	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79793852	79793852	1485	4	C	A	A	A	416	32	BMP2K	2	2
DSPP	1834	broad.mit.edu	37	4	88535135	88535135	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:88535135A>G	uc003hqu.2	+	c.1321A>G	c.(1321-1323)ACA>GCA	p.T441A		NM_014208	NP_055023	Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein preproprotein	441	Asp/Ser-rich.				biomineral tissue development|ossification|skeletal system development	proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent			central_nervous_system(1)	1		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)										0.377778	53.66406	54.253764	17	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88535135	88535135	4966	4	A	G	G	G	182	14	DSPP	4	4
DMXL1	1657	broad.mit.edu	37	5	118502310	118502310	+	Splice_Site_SNP	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:118502310G>T	uc010jcl.1	+	c.4971_splice	c.e22-1	p.R1657_splice	DMXL1_uc003ksd.2_Splice_Site_SNP_p.R1657_splice	NM_005509	NP_005500			Dmx-like 1											ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)										0.195122	16.983171	20.532549	8	33	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	118502310	118502310	4776	5	G	T	T	T	429	33	DMXL1	5	2
ADAMTS19	171019	broad.mit.edu	37	5	128797440	128797440	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:128797440G>T	uc003kvb.1	+	c.719G>T	c.(718-720)GGA>GTA	p.G240V	ADAMTS19_uc003kvc.1_Non-coding_Transcript	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	240					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)	8		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)						425				0.151163	21.123491	31.064101	13	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128797440	128797440	265	5	G	T	T	T	533	41	ADAMTS19	2	2
TIFAB	497189	broad.mit.edu	37	5	134785191	134785191	+	Missense_Mutation	SNP	C	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:134785191C>G	uc003law.3	-	c.439G>C	c.(439-441)GAA>CAA	p.E147Q	C5orf20_uc003lav.2_5'Flank	NM_001099221	NP_001092691	Q6ZNK6	TIFAB_HUMAN	TIFA-related protein TIFAB	147											0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)											0.140351	14.682417	21.782065	8	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134785191	134785191	16423	5	C	G	G	G	403	31	TIFAB	3	3
PCDHA4	56144	broad.mit.edu	37	5	140188847	140188847	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140188847C>T	uc003lhi.2	+	c.2075C>T	c.(2074-2076)GCG>GTG	p.A692V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Missense_Mutation_p.A692V|PCDHA4_uc011daa.1_Missense_Mutation_p.A692V	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	692	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.376623	82.557263	83.585276	29	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140188847	140188847	11946	5	C	T	T	T	351	27	PCDHA4	1	1
PCDHA11	56138	broad.mit.edu	37	5	140249915	140249915	+	Silent	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140249915C>T	uc003lia.2	+	c.1227C>T	c.(1225-1227)GAC>GAT	p.D409D	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Silent_p.D409D	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	409	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.377049	123.942148	125.586683	46	76	KEEP	---	---	---	---	capture		Silent	SNP	140249915	140249915	11941	5	C	T	T	T	220	17	PCDHA11	2	2
PCDHB1	29930	broad.mit.edu	37	5	140432448	140432448	+	Missense_Mutation	SNP	A	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140432448A>C	uc003lik.1	+	c.1393A>C	c.(1393-1395)AAC>CAC	p.N465H		NM_013340	NP_037472	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1 precursor	465	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.455882	102.920449	103.0353	31	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140432448	140432448	11954	5	A	C	C	C	65	5	PCDHB1	4	4
FBXL7	23194	broad.mit.edu	37	5	15928384	15928384	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:15928384G>T	uc003jfn.1	+	c.513G>T	c.(511-513)AAG>AAT	p.K171N		NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	171	LRR 1.				ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3														0.352941	17.444765	17.769034	6	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15928384	15928384	5961	5	G	T	T	T	451	35	FBXL7	2	2
ATP10B	23120	broad.mit.edu	37	5	160049494	160049494	+	Silent	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:160049494G>T	uc003lym.1	-	c.1719C>A	c.(1717-1719)TCC>TCA	p.S573S	ATP10B_uc010jit.1_5'Flank|ATP10B_uc003lyn.2_Silent_p.S131S	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	573	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)											0.315789	26.85541	28.020422	12	26	KEEP	---	---	---	---	capture		Silent	SNP	160049494	160049494	1136	5	G	T	T	T	548	43	ATP10B	2	2
MYO10	4651	broad.mit.edu	37	5	16694647	16694647	+	Silent	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:16694647C>T	uc003jft.3	-	c.3633G>A	c.(3631-3633)CAG>CAA	p.Q1211Q	MYO10_uc011cnc.1_Silent_p.Q90Q|MYO10_uc011cnd.1_Silent_p.Q568Q|MYO10_uc011cne.1_Silent_p.Q568Q|MYO10_uc010itx.2_Silent_p.Q834Q	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1211					axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3														0.132653	21.839094	34.652998	13	85	KEEP	---	---	---	---	capture		Silent	SNP	16694647	16694647	10457	5	C	T	T	T	311	24	MYO10	2	2
MYO10	4651	broad.mit.edu	37	5	16694657	16694657	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:16694657C>A	uc003jft.3	-	c.3623G>T	c.(3622-3624)CGC>CTC	p.R1208L	MYO10_uc011cnc.1_Missense_Mutation_p.R87L|MYO10_uc011cnd.1_Missense_Mutation_p.R565L|MYO10_uc011cne.1_Missense_Mutation_p.R565L|MYO10_uc010itx.2_Missense_Mutation_p.R831L	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1208					axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3														0.141414	20.519355	32.691597	14	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16694657	16694657	10457	5	C	A	A	A	351	27	MYO10	1	1
FOXI1	2299	broad.mit.edu	37	5	169533408	169533408	+	Missense_Mutation	SNP	C	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:169533408C>G	uc003mai.3	+	c.447C>G	c.(445-447)ATC>ATG	p.I149M	FOXI1_uc003maj.3_Missense_Mutation_p.I149M	NM_012188	NP_036320	Q12951	FOXI1_HUMAN	forkhead box I1 isoform a	149	Fork-head.				epidermal cell fate specification|negative regulation of gene-specific transcription from RNA polymerase II promoter|otic placode formation|pattern specification process|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			breast(3)|central_nervous_system(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.458333	35.903577	35.94142	11	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169533408	169533408	6254	5	C	G	G	G	408	32	FOXI1	3	3
HK3	3101	broad.mit.edu	37	5	176314276	176314276	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176314276C>T	uc003mfa.2	-	c.1663G>A	c.(1663-1665)GTG>ATG	p.V555M	HK3_uc003mez.2_Missense_Mutation_p.V111M	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	555	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|breast(1)	5	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.147059	7.355235	11.423539	5	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176314276	176314276	7483	5	C	T	T	T	221	17	HK3	2	2
NSD1	64324	broad.mit.edu	37	5	176637505	176637505	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176637505C>A	uc003mfr.3	+	c.2105C>A	c.(2104-2106)CCT>CAT	p.P702H	NSD1_uc003mft.3_Missense_Mutation_p.P433H|NSD1_uc003mfs.1_Missense_Mutation_p.P599H|NSD1_uc011dfx.1_Missense_Mutation_p.P350H	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	702					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)						492				0.456522	63.464614	63.540878	21	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176637505	176637505	11074	5	C	A	A	A	312	24	NSD1	2	2
GNB2L1	10399	broad.mit.edu	37	5	180668496	180668496	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:180668496A>G	uc003mni.1	-	c.425T>C	c.(424-426)GTC>GCC	p.V142A	GNB2L1_uc003mnh.1_Missense_Mutation_p.V101A|GNB2L1_uc003mnk.1_Missense_Mutation_p.V64A|GNB2L1_uc003mnj.1_Missense_Mutation_p.V96A|GNB2L1_uc003mnl.1_5'UTR|GNB2L1_uc011dhk.1_Missense_Mutation_p.V142A|GNB2L1_uc010jls.2_Missense_Mutation_p.V101A|GNB2L1_uc011dhl.1_Missense_Mutation_p.V142A	NM_006098	NP_006089	P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein),	142					negative regulation of cell growth|negative regulation of phagocytosis|negative regulation of translation|negative regulation of Wnt receptor signaling pathway|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of gastrulation|positive regulation of GTPase activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein homooligomerization|positive regulation of protein phosphorylation|regulation of cell cycle|regulation of cell division|regulation of establishment of cell polarity|regulation of protein localization	dendrite|midbody|neuronal cell body|nucleus|perinuclear region of cytoplasm|phagocytic cup|small ribosomal subunit	ion channel inhibitor activity|protein kinase C binding|protein phosphatase binding|protein tyrosine kinase inhibitor activity|receptor tyrosine kinase binding|SH2 domain binding				0	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)										0.382353	80.324397	81.152547	26	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	180668496	180668496	6787	5	A	G	G	G	130	10	GNB2L1	4	4
SEMA5A	9037	broad.mit.edu	37	5	9379955	9379955	+	Missense_Mutation	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:9379955T>C	uc003jek.2	-	c.104A>G	c.(103-105)CAT>CGT	p.H35R		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	35	Sema.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2														0.247664	128.925577	141.293105	53	161	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9379955	9379955	14523	5	T	C	C	C	663	51	SEMA5A	4	4
EYA4	2070	broad.mit.edu	37	6	133767772	133767772	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:133767772A>G	uc011ecs.1	+	c.88A>G	c.(88-90)ATG>GTG	p.M30V	EYA4_uc011ecq.1_Missense_Mutation_p.M30V|EYA4_uc011ecr.1_Missense_Mutation_p.M30V|EYA4_uc003qec.3_Missense_Mutation_p.M30V|EYA4_uc003qed.3_Missense_Mutation_p.M30V|EYA4_uc003qee.3_Missense_Mutation_p.M30V	NM_004100	NP_004091	O95677	EYA4_HUMAN	eyes absent 4 isoform a	30					anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		Melanoma(57;398 1237 3528 4702 7415)								0.509804	94.054225	94.058584	26	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133767772	133767772	5525	6	A	G	G	G	208	16	EYA4	4	4
C6orf118	168090	broad.mit.edu	37	6	165715261	165715261	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:165715261C>T	uc003qum.3	-	c.550G>A	c.(550-552)GTG>ATG	p.V184M	C6orf118_uc011egi.1_Non-coding_Transcript	NM_144980	NP_659417	Q5T5N4	CF118_HUMAN	hypothetical protein LOC168090	184											0		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)										0.19697	28.349179	33.986035	13	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165715261	165715261	2425	6	C	T	T	T	234	18	C6orf118	2	2
RPS6KA2	6196	broad.mit.edu	37	6	166944759	166944759	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:166944759G>A	uc003qvd.1	-	c.334C>T	c.(334-336)CTC>TTC	p.L112F	RPS6KA2_uc011ego.1_5'UTR|RPS6KA2_uc010kkl.1_5'UTR|RPS6KA2_uc003qvb.1_Missense_Mutation_p.L87F|RPS6KA2_uc003qvc.1_Missense_Mutation_p.L95F	NM_021135	NP_066958	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	87	Protein kinase 1.				axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|protein phosphorylation|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)						997				0.154639	22.338235	33.45297	15	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166944759	166944759	14131	6	G	A	A	A	442	34	RPS6KA2	2	2
HIST1H3H	8357	broad.mit.edu	37	6	27778233	27778233	+	Missense_Mutation	SNP	G	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:27778233G>C	uc003njm.2	+	c.382G>C	c.(382-384)GCA>CCA	p.A128P	HIST1H2BL_uc003njl.2_5'Flank	NM_003536	NP_003527	P68431	H31_HUMAN	histone cluster 1, H3h	128					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1														0.40625	39.068035	39.314004	13	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27778233	27778233	7447	6	G	C	C	C	494	38	HIST1H3H	3	3
HIST1H2AM	8336	broad.mit.edu	37	6	27860906	27860906	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:27860906C>A	uc003nkb.1	-	c.22G>T	c.(22-24)GGC>TGC	p.G8C	HIST1H3J_uc003nka.2_5'Flank|HIST1H2BO_uc003nkc.1_5'Flank	NM_003514	NP_003505	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	8					nucleosome assembly	nucleosome|nucleus	DNA binding|enzyme binding			ovary(2)	2														0.288462	38.204914	40.290827	15	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27860906	27860906	7424	6	C	A	A	A	286	22	HIST1H2AM	2	2
UBR2	23304	broad.mit.edu	37	6	42604830	42604830	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:42604830C>T	uc011dur.1	+	c.1756C>T	c.(1756-1758)CCA>TCA	p.P586S	UBR2_uc011dus.1_Missense_Mutation_p.P231S|UBR2_uc010jxv.1_Missense_Mutation_p.P90S|UBR2_uc003osh.2_Non-coding_Transcript	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	586						nucleus|plasma membrane	zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)											0.382979	50.628666	51.196185	18	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42604830	42604830	17460	6	C	T	T	T	338	26	UBR2	2	2
TTBK1	84630	broad.mit.edu	37	6	43251531	43251531	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43251531C>T	uc003ouq.1	+	c.3053C>T	c.(3052-3054)CCG>CTG	p.P1018L		NM_032538	NP_115927	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1018					protein phosphorylation	cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)							85				0.160714	17.822896	23.891707	9	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43251531	43251531	17230	6	C	T	T	T	299	23	TTBK1	1	1
DSP	1832	broad.mit.edu	37	6	7572277	7572277	+	Silent	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:7572277C>A	uc003mxp.1	+	c.2106C>A	c.(2104-2106)ATC>ATA	p.I702I	DSP_uc003mxq.1_Silent_p.I702I	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	702	Globular 1.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)	8	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)										0.391304	51.557368	52.026873	18	28	KEEP	---	---	---	---	capture		Silent	SNP	7572277	7572277	4965	6	C	A	A	A	369	29	DSP	2	2
COL12A1	1303	broad.mit.edu	37	6	75836119	75836119	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:75836119C>A	uc003phs.2	-	c.6408G>T	c.(6406-6408)TGG>TGT	p.W2136C	COL12A1_uc003pht.2_Missense_Mutation_p.W972C	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	2136	Fibronectin type-III 17.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)	8														0.265306	30.441913	32.891849	13	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75836119	75836119	3807	6	C	A	A	A	286	22	COL12A1	2	2
FAM3C	10447	broad.mit.edu	37	7	121000097	121000097	+	Missense_Mutation	SNP	T	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:121000097T>A	uc003vjx.2	-	c.467A>T	c.(466-468)AAA>ATA	p.K156I	FAM3C_uc010lkm.2_Missense_Mutation_p.K156I	NM_014888	NP_055703	Q92520	FAM3C_HUMAN	family with sequence similarity 3, member C	156					multicellular organismal development	cytoplasmic membrane-bounded vesicle|extracellular region	cytokine activity				0	all_neural(327;0.117)													0.348837	42.508456	43.377129	15	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121000097	121000097	5779	7	T	A	A	A	728	56	FAM3C	3	3
CALU	813	broad.mit.edu	37	7	128399046	128399046	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:128399046C>A	uc003vns.2	+	c.537C>A	c.(535-537)TTC>TTA	p.F179L	CALU_uc003vnq.2_Missense_Mutation_p.F179L|CALU_uc003vnr.2_Missense_Mutation_p.F179L	NM_001130674	NP_001124146	O43852	CALU_HUMAN	calumenin isoform b precursor	179	EF-hand 3.				platelet activation|platelet degranulation	extracellular region|Golgi apparatus|melanosome|sarcoplasmic reticulum lumen	calcium ion binding|protein binding				0														0.21	46.344076	54.10916	21	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128399046	128399046	2711	7	C	A	A	A	389	30	CALU	2	2
DGKI	9162	broad.mit.edu	37	7	137363363	137363363	+	Missense_Mutation	SNP	C	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:137363363C>G	uc003vtt.2	-	c.546G>C	c.(544-546)GAG>GAC	p.E182D	DGKI_uc003vtu.2_5'UTR	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	182	Phorbol-ester/DAG-type 1.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2														0.233871	71.388478	79.373726	29	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137363363	137363363	4650	7	C	G	G	G	415	32	DGKI	3	3
TMEM176B	28959	broad.mit.edu	37	7	150491059	150491059	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150491059G>A	uc003wht.3	-	c.305C>T	c.(304-306)GCG>GTG	p.A102V	TMEM176B_uc003whu.3_Missense_Mutation_p.A102V|TMEM176B_uc003whv.3_Intron|TMEM176B_uc003whw.3_Missense_Mutation_p.A102V	NM_001101313	NP_001094783	Q3YBM2	T176B_HUMAN	transmembrane protein 176B isoform a	102	Helical; (Potential).				cell differentiation|organ morphogenesis	integral to membrane|nuclear membrane				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.1875	30.19534	39.00846	18	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150491059	150491059	16627	7	G	A	A	A	494	38	TMEM176B	1	1
DNAH11	8701	broad.mit.edu	37	7	21901534	21901534	+	Missense_Mutation	SNP	C	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:21901534C>G	uc003svc.2	+	c.11287C>G	c.(11287-11289)CGC>GGC	p.R3763G		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3763					microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														0.275	29.581924	31.427494	11	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21901534	21901534	4781	7	C	G	G	G	247	19	DNAH11	3	3
TYW1	55253	broad.mit.edu	37	7	66479459	66479459	+	Missense_Mutation	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:66479459G>T	uc003tvn.2	+	c.481G>T	c.(481-483)GAT>TAT	p.D161Y	TYW1_uc010lai.2_Non-coding_Transcript	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	161	Flavodoxin-like.				oxidation-reduction process|tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0		Lung NSC(55;0.0846)|all_lung(88;0.183)								1				0.297297	88.143551	92.214873	33	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66479459	66479459	17375	7	G	T	T	T	585	45	TYW1	2	2
SAMD9	54809	broad.mit.edu	37	7	92735313	92735313	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:92735313C>A	uc003umf.2	-	c.98G>T	c.(97-99)AGG>ATG	p.R33M	SAMD9_uc003umg.2_Missense_Mutation_p.R33M	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	33	SAM.					cytoplasm				ovary(3)|breast(1)|central_nervous_system(1)	5	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)											0.28972	82.596719	86.828831	31	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92735313	92735313	14306	7	C	A	A	A	312	24	SAMD9	2	2
CSMD3	114788	broad.mit.edu	37	8	113331070	113331070	+	Nonsense_Mutation	SNP	A	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113331070A>T	uc003ynu.2	-	c.7356T>A	c.(7354-7356)TGT>TGA	p.C2452*	CSMD3_uc003yns.2_Nonsense_Mutation_p.C1654*|CSMD3_uc003ynt.2_Nonsense_Mutation_p.C2412*|CSMD3_uc011lhx.1_Nonsense_Mutation_p.C2348*|CSMD3_uc003ynw.1_Nonsense_Mutation_p.C163*	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2452	Extracellular (Potential).|Sushi 13.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.4	30.045934	30.264261	10	15	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	113331070	113331070	4087	8	A	T	T	T	128	10	CSMD3	5	3
FER1L6	654463	broad.mit.edu	37	8	125107213	125107213	+	Silent	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:125107213T>C	uc003yqw.2	+	c.4629T>C	c.(4627-4629)TGT>TGC	p.C1543C		NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1543	Cytoplasmic (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|skin(1)	7	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)											0.52381	106.156032	106.186321	33	30	KEEP	---	---	---	---	capture		Silent	SNP	125107213	125107213	6052	8	T	C	C	C	738	57	FER1L6	4	4
ZNF16	7564	broad.mit.edu	37	8	146156498	146156498	+	Missense_Mutation	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:146156498T>C	uc003zet.2	-	c.1675A>G	c.(1675-1677)ACC>GCC	p.T559A	ZNF16_uc003zeu.2_Missense_Mutation_p.T559A	NM_001029976	NP_001025147	P17020	ZNF16_HUMAN	zinc finger protein 16	559	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)										0.584906	111.437047	111.771688	31	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146156498	146156498	18329	8	T	C	C	C	780	60	ZNF16	4	4
NEFL	4747	broad.mit.edu	37	8	24813515	24813515	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:24813515C>T	uc003xee.2	-	c.515G>A	c.(514-516)CGC>CAC	p.R172H		NM_006158	NP_006149	P07196	NFL_HUMAN	neurofilament, light polypeptide 68kDa	172	Rod.|Coil 1B.				anterograde axon cargo transport|axon transport of mitochondrion|neurofilament bundle assembly|retrograde axon cargo transport|synaptic transmission	cytosol|neurofilament	identical protein binding|protein C-terminus binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)										0.3	7.122691	7.479244	3	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24813515	24813515	10714	8	C	T	T	T	351	27	NEFL	1	1
KCNU1	157855	broad.mit.edu	37	8	36788569	36788569	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:36788569G>A	uc010lvw.2	+	c.2837G>A	c.(2836-2838)GGT>GAT	p.G946D	KCNU1_uc003xjw.2_Non-coding_Transcript	NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	946	Cytoplasmic (Potential).					voltage-gated potassium channel complex	binding|catalytic activity|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)										0.470588	75.196192	75.234537	24	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36788569	36788569	8398	8	G	A	A	A	572	44	KCNU1	2	2
OR13C3	138803	broad.mit.edu	37	9	107298956	107298956	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107298956G>A	uc004bcb.1	-	c.139C>T	c.(139-141)CTT>TTT	p.L47F		NM_001001961	NP_001001961	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C,	47	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1						GBM(86;1248 1274 14222 15028 46219)								0.432432	48.504185	48.649028	16	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107298956	107298956	11341	9	G	A	A	A	429	33	OR13C3	2	2
OR13C5	138799	broad.mit.edu	37	9	107360999	107360999	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107360999C>A	uc011lvp.1	-	c.696G>T	c.(694-696)GAG>GAT	p.E232D		NM_001004482	NP_001004482	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C,	232	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)	3														0.16129	19.009027	25.777621	10	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107360999	107360999	11343	9	C	A	A	A	311	24	OR13C5	2	2
COL27A1	85301	broad.mit.edu	37	9	117027203	117027203	+	Splice_Site_SNP	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:117027203G>T	uc011lxl.1	+	c.3250_splice	c.e30-1	p.G1084_splice	COL27A1_uc004bii.2_Splice_Site_SNP	NM_032888	NP_116277			collagen, type XXVII, alpha 1 precursor						cell adhesion		extracellular matrix structural constituent			ovary(3)	3														0.203125	25.346929	30.584089	13	51	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	117027203	117027203	3823	9	G	T	T	T	455	35	COL27A1	5	2
RAPGEF1	2889	broad.mit.edu	37	9	134459980	134459980	+	Silent	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:134459980G>A	uc004cbb.2	-	c.2733C>T	c.(2731-2733)GTC>GTT	p.V911V	RAPGEF1_uc004cbc.2_Silent_p.V893V	NM_198679	NP_941372	Q13905	RPGF1_HUMAN	guanine nucleotide-releasing factor 2 isoform b	893	Ras-GEF.				activation of MAPKK activity|nerve growth factor receptor signaling pathway|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome	guanyl-nucleotide exchange factor activity|SH3 domain binding			ovary(2)|lung(1)|skin(1)	4		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)										0.525	66.884604	66.907224	21	19	KEEP	---	---	---	---	capture		Silent	SNP	134459980	134459980	13503	9	G	A	A	A	522	41	RAPGEF1	2	2
CDC37L1	55664	broad.mit.edu	37	9	4697785	4697785	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:4697785A>G	uc003zio.2	+	c.653A>G	c.(652-654)CAT>CGT	p.H218R		NM_017913	NP_060383	Q7L3B6	CD37L_HUMAN	cell division cycle 37 homolog (S.	218	Self-association and interaction with Hsp90.					cytoplasm					0	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)										0.269231	16.212588	17.46293	7	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4697785	4697785	3197	9	A	G	G	G	104	8	CDC37L1	4	4
RLN2	6019	broad.mit.edu	37	9	5300119	5300119	+	Silent	SNP	T	C	C			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:5300119T>C	uc003zja.1	-	c.537A>G	c.(535-537)AGA>AGG	p.R179R	RLN2_uc003ziz.1_3'UTR	NM_134441	NP_604390	P04090	REL2_HUMAN	relaxin 2 isoform 1 preproprotein	179					female pregnancy	extracellular region	hormone activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.0987)										0.304348	62.259294	64.610185	21	48	KEEP	---	---	---	---	capture		Silent	SNP	5300119	5300119	13869	9	T	C	C	C	647	50	RLN2	4	4
C9orf41	138199	broad.mit.edu	37	9	77599827	77599827	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:77599827A>G	uc004ajq.2	-	c.1124T>C	c.(1123-1125)GTA>GCA	p.V375A	C9orf41_uc011lsi.1_Non-coding_Transcript	NM_152420	NP_689633	Q8N4J0	CI041_HUMAN	hypothetical protein LOC138199	375										ovary(1)	1														0.25	26.6594	28.70346	9	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77599827	77599827	2597	9	A	G	G	G	182	14	C9orf41	4	4
SLITRK2	84631	broad.mit.edu	37	X	144904667	144904667	+	Missense_Mutation	SNP	G	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:144904667G>A	uc004fcd.2	+	c.724G>A	c.(724-726)GTC>ATC	p.V242I	SLITRK2_uc010nsp.2_Missense_Mutation_p.V242I|SLITRK2_uc010nso.2_Missense_Mutation_p.V242I|SLITRK2_uc011mwq.1_Missense_Mutation_p.V242I|SLITRK2_uc011mwr.1_Missense_Mutation_p.V242I|SLITRK2_uc011mws.1_Missense_Mutation_p.V242I|SLITRK2_uc004fcg.2_Missense_Mutation_p.V242I|SLITRK2_uc011mwt.1_Missense_Mutation_p.V242I	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2 precursor	242	Extracellular (Potential).|LRRCT 1.					integral to membrane				ovary(4)|pancreas(1)	5	Acute lymphoblastic leukemia(192;6.56e-05)													0.709302	193.710322	197.107261	61	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	144904667	144904667	15241	23	G	A	A	A	624	48	SLITRK2	2	2
KLHL15	80311	broad.mit.edu	37	X	24006107	24006107	+	Silent	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:24006107C>A	uc004dba.3	-	c.1746G>T	c.(1744-1746)CTG>CTT	p.L582L		NM_030624	NP_085127	Q96M94	KLH15_HUMAN	kelch-like 15	582	Kelch 5.									ovary(1)|breast(1)	2														0.343284	61.754047	63.231462	23	44	KEEP	---	---	---	---	capture		Silent	SNP	24006107	24006107	8683	23	C	A	A	A	262	21	KLHL15	2	2
ACRC	93953	broad.mit.edu	37	X	70824260	70824260	+	Missense_Mutation	SNP	A	G	G			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70824260A>G	uc004eae.2	+	c.1133A>G	c.(1132-1134)AAT>AGT	p.N378S	BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	378						nucleus				ovary(3)	3	Renal(35;0.156)													0.625	17.877102	17.986873	5	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70824260	70824260	172	23	A	G	G	G	52	4	ACRC	4	4
BRWD3	254065	broad.mit.edu	37	X	80001218	80001218	+	Silent	SNP	G	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:80001218G>T	uc004edt.2	-	c.441C>A	c.(439-441)ACC>ACA	p.T147T	BRWD3_uc004edo.2_5'UTR|BRWD3_uc004edp.2_5'UTR|BRWD3_uc004edq.2_5'UTR|BRWD3_uc010nmj.1_Intron|BRWD3_uc004edr.2_5'UTR|BRWD3_uc004eds.2_5'UTR|BRWD3_uc004edu.2_5'UTR|BRWD3_uc004edv.2_5'UTR|BRWD3_uc004edw.2_5'UTR|BRWD3_uc004edx.2_5'UTR|BRWD3_uc004edy.2_5'UTR|BRWD3_uc004edz.2_5'UTR|BRWD3_uc004eea.2_5'UTR|BRWD3_uc004eeb.2_Intron	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	147										ovary(4)	4														0.307692	10.694736	11.123548	4	9	KEEP	---	---	---	---	capture		Silent	SNP	80001218	80001218	1557	23	G	T	T	T	444	35	BRWD3	2	2
HDX	139324	broad.mit.edu	37	X	83724072	83724072	+	Missense_Mutation	SNP	C	A	A			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:83724072C>A	uc004eek.1	-	c.659G>T	c.(658-660)TGT>TTT	p.C220F	HDX_uc011mqv.1_Missense_Mutation_p.C220F|HDX_uc004eel.1_Missense_Mutation_p.C162F	NM_144657	NP_653258	Q7Z353	HDX_HUMAN	highly divergent homeobox	220					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						Pancreas(53;231 1169 36156 43751 51139)								0.709677	223.051577	226.704357	66	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83724072	83724072	7309	23	C	A	A	A	221	17	HDX	2	2
ZNF711	7552	broad.mit.edu	37	X	84525150	84525150	+	Missense_Mutation	SNP	C	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:84525150C>T	uc004eeq.2	+	c.1244C>T	c.(1243-1245)ACA>ATA	p.T415I	ZNF711_uc004eeo.2_Missense_Mutation_p.T369I|ZNF711_uc004eep.2_Missense_Mutation_p.T369I|ZNF711_uc011mqy.1_5'UTR	NM_021998	NP_068838	Q9Y462	ZN711_HUMAN	zinc finger protein 711	369					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|transcription regulator activity|zinc ion binding			ovary(3)	3														0.571429	24.500898	24.562989	8	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84525150	84525150	18712	23	C	T	T	T	221	17	ZNF711	2	2
C10orf140	387640	broad.mit.edu	37	10	21805466	21805467	+	In_Frame_Ins	INS	-	CCTCCT	CCTCCT	rs117797501	by1000genomes	TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:21805466_21805467insCCTCCT	uc009xkd.2	-	c.1285_1286insAGGAGG	c.(1285-1287)GGG>GAGGAGGGG	p.428_429insEE		NM_207371	NP_997254	Q1XH10	DLN1_HUMAN	hypothetical protein LOC387640	347_348	Ser-rich.|Glu-rich.					nucleus	nucleotide binding			ovary(1)	1														0.33			2	4		---	---	---	---	capture_indel		In_Frame_Ins	INS	21805466	21805467	1632	10	-	CCTCCT	CCTCCT	CCTCCT	286	22	C10orf140	5	5
PIAS1	8554	broad.mit.edu	37	15	68378698	68378698	+	Frame_Shift_Del	DEL	G	-	-			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:68378698_68378698delG	uc002aqz.2	+	c.79_79delG	c.(79-81)GGGfs	p.G27fs	PIAS1_uc010ujx.1_Frame_Shift_Del_p.G27fs	NM_016166	NP_057250	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	27	SAP.				androgen receptor signaling pathway|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|positive regulation of protein sumoylation|positive regulation of transcription, DNA-dependent|regulation of interferon-gamma-mediated signaling pathway|transcription, DNA-dependent	nuclear speck	androgen receptor binding|DNA binding|enzyme binding|SUMO ligase activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)	1														0.61			11	7		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	68378698	68378698	12299	15	G	-	-	-	507	39	PIAS1	5	5
PLAC4	191585	broad.mit.edu	37	21	42551432	42551432	+	Frame_Shift_Del	DEL	T	-	-	rs5844069		TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:42551432_42551432delT	uc002yyz.2	-	c.124_124delA	c.(124-126)AGAfs	p.R42fs	BACE2_uc002yyw.2_Intron|BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_182832	NP_878252	Q8WY50	PLAC4_HUMAN	placenta-specific 4	42											0		Prostate(19;2.29e-06)												0.36			4	7		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	42551432	42551432	12440	21	T	-	-	-	713	55	PLAC4	5	5
MN1	4330	broad.mit.edu	37	22	28194933	28194934	+	In_Frame_Ins	INS	-	TGC	TGC	rs45480998	byFrequency	TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:28194933_28194934insTGC	uc003adj.2	-	c.1598_1599insGCA	c.(1597-1599)CAA>CAGCAA	p.533_533Q>QQ		NM_002430	NP_002421	Q10571	MN1_HUMAN	meningioma  1	533	Poly-Gln.						binding			central_nervous_system(3)|large_intestine(1)|ovary(1)	5									p.QQQQQQ540del(MEG01-Tumor)|p.Q550del(NCIH1373-Tumor)|p.Q550del(NCIH23-Tumor)	140				0.33			3	6		---	---	---	---	capture_indel		In_Frame_Ins	INS	28194933	28194934	10064	22	-	TGC	TGC	TGC	777	60	MN1	5	5
TAF1B	9014	broad.mit.edu	37	2	9989571	9989571	+	Frame_Shift_Del	DEL	A	-	-			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:9989571_9989571delA	uc002qzz.2	+	c.187_187delA	c.(187-189)AAAfs	p.K63fs	TAF1B_uc010exc.2_Frame_Shift_Del_p.K63fs|TAF1B_uc002qzy.3_Frame_Shift_Del_p.K63fs|TAF1B_uc010yja.1_5'UTR|TAF1B_uc010exd.2_5'UTR	NM_005680	NP_005671	Q53T94	TAF1B_HUMAN	TBP-associated factor 1B	63					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)													0.40			6	9		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	9989571	9989571	16041	2	A	-	-	-	169	13	TAF1B	5	5
MON1A	84315	broad.mit.edu	37	3	49947983	49947984	+	Frame_Shift_Del	DEL	GC	-	-			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49947983_49947984delGC	uc003cxz.2	-	c.1238_1239delGC	c.(1237-1239)CGCfs	p.R413fs	MON1A_uc003cya.2_Frame_Shift_Del_p.R251fs|MON1A_uc003cyb.2_Frame_Shift_Del_p.R251fs	NM_032355	NP_115731	Q86VX9	MON1A_HUMAN	MON1 homolog A isoform a	316							protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)										0.50			10	10		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	49947983	49947984	10089	3	GC	-	-	-	587	46	MON1A	5	5
F8	2157	broad.mit.edu	37	X	154157685	154157686	+	Frame_Shift_Ins	INS	-	T	T			TCGA-80-5611-01	TCGA-80-5611-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:154157685_154157686insT	uc004fmt.2	-	c.4379_4380insA	c.(4378-4380)AATfs	p.N1460fs		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	1460	B.		N -> K (in HEMA).		acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|oxidation-reduction process|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)					359				0.58			42	31		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	154157685	154157686	5544	23	-	T	T	T	206	16	F8	5	5
