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	i_TCGAscape_Amplification_Peaks	i_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_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
C10orf119	79892	broad.mit.edu	36	10	121590454	121590454	+	Missense_Mutation	SNP	C	A	A			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:121590454C>A	uc001ler.2	-	c.1139G>T	c.(1138-1140)AGA>ATA	p.R380I	C10orf119_uc001leq.1_Missense_Mutation_p.R205I|C10orf119_uc001les.1_Missense_Mutation_p.R205I	NM_024834	NP_079110	Q9BTE3	MCMBP_HUMAN	chromosome 10 open reading frame 119	380					cell division|DNA-dependent DNA replication|mitosis|S phase of mitotic cell cycle|sister chromatid cohesion	nucleus	chromatin binding				0		Lung NSC(174;0.109)|all_lung(145;0.142)												0.764706	43.282856	44.371633	13	4	CC		KEEP	---	---	---	---	capture		all cancers(201;0.0044)	Missense_Mutation	SNP	121590454	121590454	1623	10	C	A	A	32	32	C10orf119	A	3	3
CACNB2	783	broad.mit.edu	36	10	18469672	18469672	+	Missense_Mutation	SNP	A	G	G			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:18469672A>G	uc001ipr.2	+	c.1A>G	c.(1-3)ATG>GTG	p.M1V	CACNB2_uc009xjz.1_Missense_Mutation_p.M1V|CACNB2_uc001ips.2_Missense_Mutation_p.M1V|CACNB2_uc001ipt.2_Missense_Mutation_p.M1V|CACNB2_uc001ipu.2_5'Flank|CACNB2_uc001ipv.2_5'Flank|CACNB2_uc009xka.1_5'Flank	NM_201596	NP_963890	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2	1					axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)	2					Magnesium Sulfate(DB00653)|Verapamil(DB00661)					328				0.857143	20.953332	21.712359	6	1	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18469672	18469672	2669	10	A	G	G	4	4	CACNB2	G	4	4
PDGFD	80310	broad.mit.edu	36	11	103285670	103285670	+	Nonsense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:103285670G>A	uc001phq.1	-	c.1075C>T	c.(1075-1077)CGA>TGA	p.R359*	PDGFD_uc001php.1_Nonsense_Mutation_p.R353*	NM_025208	NP_079484	Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D isoform 1	359					positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			large_intestine(1)	1		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)												0.492754	205.95518	205.962086	68	70	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)	Nonsense_Mutation	SNP	103285670	103285670	12081	11	G	A	A	40	40	PDGFD	A	5	1
NLRX1	79671	broad.mit.edu	36	11	118559285	118559285	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118559285G>A	uc001pvu.1	+	c.2855G>A	c.(2854-2856)CGC>CAC	p.R952H	NLRX1_uc001pvv.1_Intron|NLRX1_uc001pvw.1_Missense_Mutation_p.R952H|NLRX1_uc001pvx.1_Missense_Mutation_p.R952H|PDZD3_uc001pvy.1_5'Flank|PDZD3_uc001pvz.1_5'Flank|PDZD3_uc001pwa.1_5'Flank|PDZD3_uc001pwb.1_5'Flank	NM_024618	NP_078894	Q86UT6	NLRX1_HUMAN	NLR family member X1 isoform 1	952	Required for the repression of MAVS- induced interferon signaling.				innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production	mitochondrial outer membrane	ATP binding			ovary(1)	1	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)												0.45098	65.8168	65.923748	23	28	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)	Missense_Mutation	SNP	118559285	118559285	10888	11	G	A	A	38	38	NLRX1	A	1	1
CHRNA10	57053	broad.mit.edu	36	11	3647040	3647040	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:3647040G>A	uc001lyf.1	-	c.324C>T	c.(322-324)AGC>AGT	p.S108S		NM_020402	NP_065135	Q9GZZ6	ACH10_HUMAN	cholinergic receptor, nicotinic, alpha 10	108	Extracellular (Potential).				regulation of cell proliferation|synaptic transmission, cholinergic	cell junction|postsynaptic membrane	calcium channel activity|receptor activity|receptor binding			ovary(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0164)|all_neural(188;0.0577)			Chloroprocaine(DB01161)|Methadone(DB00333)|Nicotine(DB00184)|Pentolinium(DB01090)|Procaine(DB00721)|Trimethaphan(DB01116)	Melanoma(153;17 1869 2949 7120 36888)								0.44186	49.402947	49.531609	19	24	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.0344)|LUSC - Lung squamous cell carcinoma(625;0.192)	Silent	SNP	3647040	3647040	3516	11	G	A	A	46	46	CHRNA10	A	2	2
PYGM	5837	broad.mit.edu	36	11	64270825	64270825	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:64270825C>T	uc001oax.2	-	c.2411G>A	c.(2410-2412)CGG>CAG	p.R804Q	RASGRP2_uc009ypu.1_5'Flank|RASGRP2_uc009ypv.1_5'Flank|RASGRP2_uc009ypw.1_5'Flank|RASGRP2_uc001oaw.1_5'Flank|PYGM_uc001oay.2_Missense_Mutation_p.R716Q	NM_005609	NP_005600	P11217	PYGM_HUMAN	glycogen phosphorylase	804					glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)									0.46	70.183609	70.244272	23	27	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64270825	64270825	13320	11	C	T	T	23	23	PYGM	T	1	1
RIN1	9610	broad.mit.edu	36	11	65859839	65859839	+	Missense_Mutation	SNP	A	G	G			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65859839A>G	uc001ohn.1	-	c.352T>C	c.(352-354)TCC>CCC	p.S118P	RIN1_uc009yrd.1_5'UTR	NM_004292	NP_004283	Q13671	RIN1_HUMAN	ras inhibitor RIN1	118	SH2.				endocytosis|signal transduction	cytoplasm|cytoskeleton|plasma membrane	GTPase activator activity|protein binding			lung(1)	1														0.384615	6.631632	6.827511	5	8	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65859839	65859839	13848	11	A	G	G	11	11	RIN1	G	4	4
ANO2	57101	broad.mit.edu	36	12	5542803	5542803	+	Missense_Mutation	SNP	C	G	G			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5542803C>G	uc001qnm.1	-	c.2923G>C	c.(2923-2925)GCA>CCA	p.A975P		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	979	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7														0.428571	6.514155	6.546933	3	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5542803	5542803	705	12	C	G	G	26	26	ANO2	G	3	3
KLRG1	10219	broad.mit.edu	36	12	9033539	9033539	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:9033539C>T	uc001qvh.2	+	c.41C>T	c.(40-42)ACG>ATG	p.T14M	KLRG1_uc001qvg.1_Missense_Mutation_p.T14M	NM_005810	NP_005801	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G,	14	Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|cellular defense response|inflammatory response|regulation of immune response	integral to membrane	receptor activity|sugar binding			central_nervous_system(1)	1														0.382979	53.639385	54.203581	18	29	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9033539	9033539	8735	12	C	T	T	19	19	KLRG1	T	1	1
AHNAK2	113146	broad.mit.edu	36	14	104482703	104482703	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104482703G>A	uc010axc.1	-	c.10130C>T	c.(10129-10131)CCG>CTG	p.P3377L	AHNAK2_uc001ypx.2_Missense_Mutation_p.P3277L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3377						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)												0.49359	234.134668	234.14065	77	79	GG		KEEP	---	---	---	---	capture	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		Missense_Mutation	SNP	104482703	104482703	418	14	G	A	A	39	39	AHNAK2	A	1	1
ACIN1	22985	broad.mit.edu	36	14	22634337	22634337	+	De_novo_Start_InFrame	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:22634337G>A	uc001wit.2	-	c.-1C>T	c.(-3-1)AACGA>AATGA		ACIN1_uc010akg.1_De_novo_Start_InFrame|C14orf119_uc001wiu.1_5'Flank|C14orf119_uc010akh.1_5'Flank	NM_014977	NP_055792			apoptotic chromatin condensation inducer 1						apoptotic chromosome condensation|erythrocyte differentiation|positive regulation of monocyte differentiation	cytosol	ATPase activity|enzyme binding|nucleic acid binding|nucleotide binding			ovary(2)|large_intestine(1)	3	all_cancers(95;1.36e-05)													0.403846	59.763956	60.184392	21	31	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.00816)	De_novo_Start_InFrame	SNP	22634337	22634337	143	14	G	A	A	40	40	ACIN1	A	5	1
KCNH5	27133	broad.mit.edu	36	14	62537840	62537840	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:62537840G>A	uc001xfx.1	-	c.395C>T	c.(394-396)ACG>ATG	p.T132M	KCNH5_uc001xfy.1_Missense_Mutation_p.T132M|KCNH5_uc001xfz.1_Missense_Mutation_p.T74M|KCNH5_uc001xga.2_Missense_Mutation_p.T74M	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	132	PAC.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|central_nervous_system(1)	5														0.363636	9.996299	10.176482	4	7	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)	Missense_Mutation	SNP	62537840	62537840	8340	14	G	A	A	40	40	KCNH5	A	1	1
LTBP2	4053	broad.mit.edu	36	14	74041271	74041271	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:74041271C>T	uc001xqa.1	-	c.4416G>A	c.(4414-4416)GTG>GTA	p.V1472V		NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding	1472					protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)	1														0.386364	48.370279	48.86613	17	27	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)	Silent	SNP	74041271	74041271	9450	14	C	T	T	21	21	LTBP2	T	2	2
KIAA1409	57578	broad.mit.edu	36	14	93139437	93139437	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:93139437G>A	uc001ybv.1	+	c.3143G>A	c.(3142-3144)CGT>CAT	p.R1048H	KIAA1409_uc001ybs.1_Missense_Mutation_p.R1048H	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	1225						integral to membrane				ovary(10)|large_intestine(3)	13		all_cancers(154;0.0354)|all_epithelial(191;0.216)								1186				0.5	62.043581	62.043581	21	21	GG		KEEP	---	---	---	---	capture		Epithelial(152;0.188)	Missense_Mutation	SNP	93139437	93139437	8539	14	G	A	A	40	40	KIAA1409	A	1	1
SERPINA12	145264	broad.mit.edu	36	14	94023450	94023450	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:94023450G>A	uc001ydj.1	-	c.1188C>T	c.(1186-1188)AGC>AGT	p.S396S		NM_173850	NP_776249	Q8IW75	SPA12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	396					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4									p.S396S(SKUT1-Tumor)	148				0.574713	157.556988	157.979958	50	37	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(157;0.235)	Silent	SNP	94023450	94023450	14577	14	G	A	A	38	38	SERPINA12	A	1	1
SHC4	399694	broad.mit.edu	36	15	47004433	47004433	+	Missense_Mutation	SNP	C	A	A			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:47004433C>A	uc001zxb.1	-	c.591G>T	c.(589-591)ATG>ATT	p.M197I		NM_203349	NP_976224	Q6S5L8	SHC4_HUMAN	rai-like protein	197	PID.				intracellular signal transduction	cell junction|postsynaptic membrane				ovary(3)|pancreas(2)	5		all_lung(180;0.00466)												0.76	65.237156	66.779074	19	6	CC		KEEP	---	---	---	---	capture		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)	Missense_Mutation	SNP	47004433	47004433	14765	15	C	A	A	21	21	SHC4	A	3	3
MYO5C	55930	broad.mit.edu	36	15	50324855	50324855	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:50324855G>A	uc010bff.1	-	c.2166C>T	c.(2164-2166)CAC>CAT	p.H722H		NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC	722	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(1)	13														0.878788	94.194953	98.833117	29	4	GG		KEEP	---	---	---	---	capture		all cancers(107;0.0137)	Silent	SNP	50324855	50324855	10475	15	G	A	A	48	48	MYO5C	A	2	2
CD276	80381	broad.mit.edu	36	15	71781820	71781820	+	Missense_Mutation	SNP	A	G	G			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:71781820A>G	uc002avv.1	+	c.251A>G	c.(250-252)GAC>GGC	p.D84G	CD276_uc010bjd.1_5'UTR|CD276_uc002avu.1_Missense_Mutation_p.D84G|CD276_uc002avw.1_Missense_Mutation_p.D84G|CD276_uc002avx.2_5'Flank	NM_001024736	NP_001019907	Q5ZPR3	CD276_HUMAN	CD276 antigen isoform a	84	Ig-like V-type 1.|Extracellular (Potential).				cell proliferation|immune response|positive regulation of interferon-gamma biosynthetic process|positive regulation of T cell proliferation|regulation of immune response|T cell activation	external side of plasma membrane|integral to membrane	receptor binding				0														0.8	26.704412	27.541202	8	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71781820	71781820	3120	15	A	G	G	10	10	CD276	G	4	4
CACNA1H	8912	broad.mit.edu	36	16	1210476	1210476	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1210476G>A	uc002cks.1	+	c.6543G>A	c.(6541-6543)GCG>GCA	p.A2181A	CACNA1H_uc002ckt.1_Silent_p.A2175A|CACNA1H_uc002cku.1_Silent_p.A876A|CACNA1H_uc010brj.1_Silent_p.A892A|CACNA1H_uc002ckv.1_Silent_p.A870A	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	2181	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)									0.4	50.645298	51.037264	18	27	GG		KEEP	---	---	---	---	capture			Silent	SNP	1210476	1210476	2661	16	G	A	A	38	38	CACNA1H	A	1	1
IL4R	3566	broad.mit.edu	36	16	27281367	27281367	+	Missense_Mutation	SNP	G	C	C			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27281367G>C	uc002don.1	+	c.1193G>C	c.(1192-1194)GGA>GCA	p.G398A	IL4R_uc010bxy.1_Missense_Mutation_p.G398A|IL4R_uc002doo.1_Missense_Mutation_p.G238A	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a	398	Cytoplasmic (Potential).				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2														0.477273	72.774845	72.794467	21	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27281367	27281367	7999	16	G	C	C	41	41	IL4R	C	3	3
ELMO3	79767	broad.mit.edu	36	16	65793032	65793032	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65793032G>A	uc002esa.1	+	c.1063G>A	c.(1063-1065)GAC>AAC	p.D355N	ELMO3_uc002esb.1_Missense_Mutation_p.D338N|ELMO3_uc002esc.1_Missense_Mutation_p.D189N	NM_024712	NP_078988	Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	302					apoptosis|phagocytosis	cytoplasm|cytoskeleton	SH3 domain binding				0		Ovarian(137;0.0563)												0.384615	53.28211	53.890393	20	32	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)	Missense_Mutation	SNP	65793032	65793032	5259	16	G	A	A	41	41	ELMO3	A	2	2
RLTPR	146206	broad.mit.edu	36	16	66239350	66239350	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:66239350C>T	uc002etn.1	+	c.1059C>T	c.(1057-1059)TCC>TCT	p.S353S	RLTPR_uc010cel.1_Silent_p.S353S	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin	353	LRR 6.									breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)												0.428571	18.348765	18.410829	6	8	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)	Silent	SNP	66239350	66239350	13871	16	C	T	T	23	23	RLTPR	T	1	1
C17orf46	124783	broad.mit.edu	36	17	40688430	40688430	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:40688430C>T	uc002iis.1	-	c.902G>A	c.(901-903)CGC>CAC	p.R301H	LOC100133991_uc010dah.1_Intron	NM_152343	NP_689556	Q96LK8	CQ046_HUMAN	hypothetical protein LOC124783	301										large_intestine(1)|ovary(1)	2														0.372093	137.192279	139.035911	48	81	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40688430	40688430	1913	17	C	T	T	27	27	C17orf46	T	1	1
SCN4A	6329	broad.mit.edu	36	17	59388584	59388584	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:59388584C>T	uc002jds.1	-	c.2046G>A	c.(2044-2046)TCG>TCA	p.S682S		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	682	Helical; Voltage-sensor; Name=S4 of repeat II; (Potential).|II.				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)									0.333333	14.571465	14.939742	5	10	CC		KEEP	---	---	---	---	capture			Silent	SNP	59388584	59388584	14402	17	C	T	T	19	19	SCN4A	T	1	1
EVPL	2125	broad.mit.edu	36	17	71523220	71523220	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71523220C>T	uc002jqi.2	-	c.1795G>A	c.(1795-1797)GTG>ATG	p.V599M		NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	599	Globular 1.				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			pancreas(2)|central_nervous_system(1)	3														0.325581	37.937128	39.096783	14	29	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71523220	71523220	5485	17	C	T	T	19	19	EVPL	T	1	1
TP53	7157	broad.mit.edu	36	17	7519280	7519280	+	Splice_Site_SNP	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519280C>T	uc002gim.2	-	c.376_splice	c.e5-1	p.Y126_splice	TP53_uc002gig.1_Splice_Site_SNP_p.Y126_splice|TP53_uc002gih.1_Splice_Site_SNP_p.Y126_splice|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'UTR|TP53_uc010cng.1_5'UTR|TP53_uc002gii.1_5'UTR|TP53_uc010cnh.1_Splice_Site_SNP_p.Y126_splice|TP53_uc010cni.1_Splice_Site_SNP_p.Y126_splice|TP53_uc002gij.2_Splice_Site_SNP_p.Y126_splice|TP53_uc010cnj.1_Splice_Site_SNP|TP53_uc002gin.2_Splice_Site_SNP_p.Y33_splice|TP53_uc002gio.2_Splice_Site_SNP	NM_001126112	NP_001119584			tumor protein p53 isoform a						activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.?(31)|p.0?(6)|p.V73fs*9(1)|p.Y126fs*11(1)|p.P13fs*18(1)|p.T125_Y126insX(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	(F36P-Tumor)|(BICR56-Tumor)|(OVCAR8-Tumor)|(BECKER-Tumor)|(CORL279-Tumor)|(SNU201-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.888889	27.533079	28.851826	8	1	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Splice_Site_SNP	SNP	7519280	7519280	16923	17	C	T	T	20	20	TP53	T	5	2
ZNF439	90594	broad.mit.edu	36	19	11839931	11839931	+	Silent	SNP	T	C	C			TCGA-41-5651-01	TCGA-41-5651-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11839931T>C	uc002mss.1	+	c.1047T>C	c.(1045-1047)TCT>TCC	p.S349S	ZNF439_uc002msr.1_Silent_p.S213S	NM_152262	NP_689475	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	349					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.275	59.234341	62.870242	22	58	TT		KEEP	---	---	---	---	capture			Silent	SNP	11839931	11839931	18504	19	T	C	C	55	55	ZNF439	C	4	4
SLC1A6	6511	broad.mit.edu	36	19	14944572	14944572	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14944572G>A	uc002naa.1	-	c.151C>T	c.(151-153)CGC>TGC	p.R51C	SLC1A6_uc010dzu.1_Missense_Mutation_p.R51C|SLC1A6_uc002nab.2_Missense_Mutation_p.R51C|SLC1A6_uc002nac.2_Missense_Mutation_p.R51C|SLC1A6_uc002nad.1_Missense_Mutation_p.R51C	NM_005071	NP_005062	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity	51	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)	5					L-Glutamic Acid(DB00142)									0.238095	10.56264	11.880523	5	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14944572	14944572	14932	19	G	A	A	38	38	SLC1A6	A	1	1
NOTCH3	4854	broad.mit.edu	36	19	15142306	15142306	+	Silent	SNP	G	C	C			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15142306G>C	uc002nan.1	-	c.4950C>G	c.(4948-4950)GGC>GGG	p.G1650G		NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3	1650	Helical; (Potential).				Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			ovary(5)|lung(2)|central_nervous_system(1)	8										417				0.235294	7.791267	8.881627	4	13	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)		Silent	SNP	15142306	15142306	10953	19	G	C	C	38	38	NOTCH3	C	3	3
ATP1A3	478	broad.mit.edu	36	19	47181080	47181080	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47181080C>T	uc002osg.1	-	c.823G>A	c.(823-825)GCC>ACC	p.A275T	ATP1A3_uc002osh.2_Missense_Mutation_p.A275T	NM_152296	NP_689509	P13637	AT1A3_HUMAN	Na+/K+ -ATPase alpha 3 subunit	275	Cytoplasmic (Potential).				ATP biosynthetic process	endoplasmic reticulum|Golgi apparatus|sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(1)|pancreas(1)	2														0.5	6.450151	6.45015	2	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47181080	47181080	1149	19	C	T	T	27	27	ATP1A3	T	1	1
KLK3	354	broad.mit.edu	36	19	56053194	56053194	+	Missense_Mutation	SNP	G	T	T	rs61752561	unknown	TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56053194G>T	uc002pts.1	+	c.304G>T	c.(304-306)GAT>TAT	p.D102Y	KLK3_uc010eoe.1_Missense_Mutation_p.D102Y|KLK3_uc002ptr.1_Intron|KLK3_uc010eof.1_Intron	NM_001030047	NP_001025218	P07288	KLK3_HUMAN	prostate specific antigen isoform 3	102	Peptidase S1.				negative regulation of angiogenesis|proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)|kidney(1)	2		all_neural(266;0.057)				Colon(185;1767 2023 13025 30120 37630)				94				0.75	30.680666	31.362619	9	3	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)	Missense_Mutation	SNP	56053194	56053194	8719	19	G	T	T	37	37	KLK3	T	3	3
MUC16	94025	broad.mit.edu	36	19	8894637	8894637	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8894637G>A	uc002mkp.1	-	c.36300C>T	c.(36298-36300)AAC>AAT	p.N12100N		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12102	SEA 1.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.296296	41.879699	43.883362	16	38	GG		KEEP	---	---	---	---	capture			Silent	SNP	8894637	8894637	10367	19	G	A	A	40	40	MUC16	A	1	1
SPTA1	6708	broad.mit.edu	36	1	156894025	156894025	+	Nonsense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156894025G>A	uc001fst.1	-	c.2671C>T	c.(2671-2673)CGA>TGA	p.R891*		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	891	Spectrin 9.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.146789	23.278284	36.22756	16	93	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	156894025	156894025	15630	1	G	A	A	38	38	SPTA1	A	5	1
SPTA1	6708	broad.mit.edu	36	1	156904387	156904387	+	Missense_Mutation	SNP	C	G	G			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156904387C>G	uc001fst.1	-	c.1923G>C	c.(1921-1923)CAG>CAC	p.Q641H		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	641	Spectrin 7.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.666667	217.079515	219.219059	58	29	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156904387	156904387	15630	1	C	G	G	32	32	SPTA1	G	3	3
CCDC27	148870	broad.mit.edu	36	1	3670243	3670243	+	Missense_Mutation	SNP	C	A	A			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:3670243C>A	uc001akv.1	+	c.1435C>A	c.(1435-1437)CAA>AAA	p.Q479K		NM_152492	NP_689705	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	479											0	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)												0.363636	6.552936	6.749554	4	7	CC		KEEP	---	---	---	---	capture		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)	Missense_Mutation	SNP	3670243	3670243	2923	1	C	A	A	17	17	CCDC27	A	3	3
ZNF642	339559	broad.mit.edu	36	1	40717719	40717719	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:40717719G>A	uc001cfo.1	+	c.99G>A	c.(97-99)GAG>GAA	p.E33E	ZNF642_uc009vwb.1_Silent_p.E33E	NM_198494	NP_940896	Q49AA0	ZN642_HUMAN	zinc finger protein 642	33	SCAN box.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)												0.423077	32.819829	32.954223	11	15	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;8.81e-19)		Silent	SNP	40717719	40717719	18653	1	G	A	A	35	35	ZNF642	A	2	2
KIF16B	55614	broad.mit.edu	36	20	16202013	16202013	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:16202013G>A	uc002wpg.1	-	c.3839C>T	c.(3838-3840)ACA>ATA	p.T1280I	KIF16B_uc002wpe.1_Missense_Mutation_p.T632I|KIF16B_uc002wpf.1_Missense_Mutation_p.T621I|KIF16B_uc010gch.1_Missense_Mutation_p.T1229I	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23	1280	PX.				cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7														0.351852	51.304963	52.351905	19	35	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16202013	16202013	8589	20	G	A	A	48	48	KIF16B	A	2	2
SEC23B	10483	broad.mit.edu	36	20	18455120	18455120	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:18455120G>A	uc002wqz.1	+	c.938G>A	c.(937-939)CGT>CAT	p.R313H	SEC23B_uc002wra.1_Missense_Mutation_p.R313H|SEC23B_uc002wrb.1_Missense_Mutation_p.R313H|SEC23B_uc002wrc.1_Missense_Mutation_p.R313H	NM_006363	NP_116781	Q15437	SC23B_HUMAN	Sec23 homolog B	313			R -> H.		ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1														0.25	47.95848	52.507114	20	60	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18455120	18455120	14478	20	G	A	A	40	40	SEC23B	A	1	1
SLC12A5	57468	broad.mit.edu	36	20	44108018	44108018	+	Missense_Mutation	SNP	A	G	G			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:44108018A>G	uc002xrb.1	+	c.1664A>G	c.(1663-1665)GAC>GGC	p.D555G		NM_020708	NP_065759	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	578	Helical; (Potential).				potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)									0.294964	121.852307	127.062105	41	98	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44108018	44108018	14881	20	A	G	G	10	10	SLC12A5	G	4	4
OPRL1	4987	broad.mit.edu	36	20	62199845	62199845	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:62199845C>T	uc002yic.1	+	c.480C>T	c.(478-480)GAC>GAT	p.D160D	OPRL1_uc002yid.1_Silent_p.D160D|OPRL1_uc002yif.2_Silent_p.D155D	NM_182647	NP_872588	P41146	OPRX_HUMAN	opiate receptor-like 1	160	Cytoplasmic (Potential).				elevation of cytosolic calcium ion concentration|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception	integral to plasma membrane	protein binding|X-opioid receptor activity			central_nervous_system(1)	1	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)													0.266667	35.939856	38.92293	16	44	CC		KEEP	---	---	---	---	capture			Silent	SNP	62199845	62199845	11292	20	C	T	T	19	19	OPRL1	T	1	1
ITSN1	6453	broad.mit.edu	36	21	34152927	34152927	+	Missense_Mutation	SNP	A	C	C			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:34152927A>C	uc002yta.1	+	c.3851A>C	c.(3850-3852)AAC>ACC	p.N1284T	DONSON_uc002ysn.1_Intron|ITSN1_uc002ytb.1_Missense_Mutation_p.N1279T|ITSN1_uc002ytj.2_Missense_Mutation_p.N1279T|ITSN1_uc010gmm.1_Non-coding_Transcript	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l	1284	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)	3														0.176471	36.483977	44.858842	15	70	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34152927	34152927	8230	21	A	C	C	2	2	ITSN1	C	4	4
IGSF5	150084	broad.mit.edu	36	21	40059534	40059534	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:40059534C>T	uc002yyo.1	+	c.303C>T	c.(301-303)GGC>GGT	p.G101G		NM_001080444	NP_001073913	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily 5 like	101	Ig-like V-type 1.|Extracellular (Potential).					integral to membrane|tight junction					0		Prostate(19;5.35e-06)												0.4375	20.62265	20.677114	7	9	CC		KEEP	---	---	---	---	capture			Silent	SNP	40059534	40059534	7903	21	C	T	T	27	27	IGSF5	T	1	1
ITGB2	3689	broad.mit.edu	36	21	45144810	45144810	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:45144810G>A	uc002zgd.1	-	c.750C>T	c.(748-750)ATC>ATT	p.I250I	ITGB2_uc002zge.1_Silent_p.I250I|ITGB2_uc002zgf.2_Silent_p.I250I|ITGB2_uc010gpw.1_Silent_p.I193I|ITGB2_uc002zgg.1_Silent_p.I250I	NM_001127491	NP_001120963	P05107	ITB2_HUMAN	integrin, beta 2 precursor	250	Extracellular (Potential).|VWFA.				apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(3)|central_nervous_system(3)|breast(2)	8					Simvastatin(DB00641)									0.4	46.591751	46.941596	16	24	GG		KEEP	---	---	---	---	capture		Colorectal(79;0.0669)	Silent	SNP	45144810	45144810	8198	21	G	A	A	37	37	ITGB2	A	1	1
SEC14L3	266629	broad.mit.edu	36	22	29186050	29186050	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:29186050G>A	uc003ahy.1	-	c.1161C>T	c.(1159-1161)GAC>GAT	p.D387D	SEC14L3_uc003ahz.1_Silent_p.D310D|SEC14L3_uc003aia.1_Silent_p.D328D|SEC14L3_uc003aib.1_Silent_p.D328D	NM_174975	NP_777635	Q9UDX4	S14L3_HUMAN	SEC14-like 3	387						integral to membrane|intracellular	lipid binding|transporter activity			ovary(3)|pancreas(1)	4					Vitamin E(DB00163)	Esophageal Squamous(108;290 1516 3584 23771 37333)								0.475	58.138536	58.158737	19	21	GG		KEEP	---	---	---	---	capture			Silent	SNP	29186050	29186050	14469	22	G	A	A	40	40	SEC14L3	A	1	1
PES1	23481	broad.mit.edu	36	22	29310618	29310618	+	Missense_Mutation	SNP	T	C	C			TCGA-41-5651-01	TCGA-41-5651-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:29310618T>C	uc003aij.1	-	c.455A>G	c.(454-456)AAG>AGG	p.K152R	PES1_uc003aik.1_Missense_Mutation_p.K152R|PES1_uc003ail.1_Missense_Mutation_p.K152R|PES1_uc003aim.1_Missense_Mutation_p.K152R|PES1_uc003ain.1_Missense_Mutation_p.K13R|PES1_uc003aio.1_Missense_Mutation_p.K13R	NM_014303	NP_055118	O00541	PESC_HUMAN	pescadillo homolog 1, containing BRCT domain	152	Sufficient for nucleolar localization.				cell proliferation|maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|regulation of cell cycle	chromosome|nucleoplasm|PeBoW complex|preribosome, large subunit precursor	protein binding				0														0.388889	23.121537	23.316052	7	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29310618	29310618	12154	22	T	C	C	56	56	PES1	C	4	4
IL18RAP	8807	broad.mit.edu	36	2	102406215	102406215	+	Nonsense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102406215C>T	uc002tbx.1	+	c.46C>T	c.(46-48)CGA>TGA	p.R16*	IL18RAP_uc010fiz.1_5'UTR|IL18RAP_uc002tby.1_Nonsense_Mutation_p.R16*	NM_003853	NP_003844	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	16					cell surface receptor linked signaling pathway|inflammatory response|innate immune response	integral to membrane	transmembrane receptor activity			ovary(2)	2														0.388889	119.533133	120.69775	42	66	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	102406215	102406215	7949	2	C	T	T	27	27	IL18RAP	T	5	1
ACOXL	55289	broad.mit.edu	36	2	111566998	111566998	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:111566998C>T	uc002tgr.2	+	c.1616C>T	c.(1615-1617)ACG>ATG	p.T539M	ACOXL_uc010fkc.1_Missense_Mutation_p.T332M	NM_001105516	NP_001098986	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 2	539					fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0										368				0.432432	47.896539	48.043259	16	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111566998	111566998	162	2	C	T	T	19	19	ACOXL	T	1	1
ABCA12	26154	broad.mit.edu	36	2	215563839	215563839	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:215563839C>T	uc002vew.1	-	c.3456G>A	c.(3454-3456)TCG>TCA	p.S1152S	ABCA12_uc002vev.1_Silent_p.S834S	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	1152	Helical; (Potential).				cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|breast(1)|central_nervous_system(1)|pancreas(1)	9		Renal(323;0.127)				Ovarian(66;664 1488 5121 34295)								0.489362	75.331678	75.335977	23	24	CC		KEEP	---	---	---	---	capture		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)	Silent	SNP	215563839	215563839	31	2	C	T	T	23	23	ABCA12	T	1	1
GLB1L	79411	broad.mit.edu	36	2	219816493	219816493	+	Missense_Mutation	SNP	A	T	T			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219816493A>T	uc002vkm.1	-	c.47T>A	c.(46-48)CTC>CAC	p.L16H	GLB1L_uc002vkl.1_5'Flank|GLB1L_uc002vkn.1_Missense_Mutation_p.L16H|STK16_uc002vko.1_5'Flank|STK16_uc010fwf.1_5'Flank|STK16_uc002vkp.1_5'Flank|STK16_uc002vkq.1_5'Flank|STK16_uc002vkr.1_5'Flank	NM_024506	NP_078782	Q6UWU2	GLB1L_HUMAN	galactosidase, beta 1-like	16					carbohydrate metabolic process	extracellular region	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds				0		all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559)												0.448276	73.838236	73.973719	26	32	AA		KEEP	---	---	---	---	capture		Epithelial(149;1.3e-11)|all cancers(144;2.07e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Missense_Mutation	SNP	219816493	219816493	6696	2	A	T	T	11	11	GLB1L	T	4	4
ACSL3	2181	broad.mit.edu	36	2	223489443	223489443	+	Missense_Mutation	SNP	A	G	G			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:223489443A>G	uc002vni.1	+	c.541A>G	c.(541-543)ATG>GTG	p.M181V	ACSL3_uc002vnj.1_Missense_Mutation_p.M181V	NM_004457	NP_976251	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	181	Cytoplasmic (Potential).				long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|fatty-acyl-CoA synthase activity|long-chain fatty acid-CoA ligase activity|protein binding			ovary(2)	2		Renal(207;0.0183)			Icosapent(DB00159)									0.428571	61.346722	61.532926	18	24	AA		KEEP	---	---	---	---	capture		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Missense_Mutation	SNP	223489443	223489443	179	2	A	G	G	16	16	ACSL3	G	4	4
UGT1A5	54579	broad.mit.edu	36	2	234345770	234345770	+	Silent	SNP	C	T	T	rs28900406	by-cluster,by-frequency	TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:234345770C>T	uc002vuw.1	+	c.1431C>T	c.(1429-1431)CCC>CCT	p.P477P	UGT1A8_uc002vup.1_Silent_p.P473P|UGT1A10_uc002vur.1_Silent_p.P473P|UGT1A9_uc002vus.1_Silent_p.P473P|UGT1A7_uc002vut.1_Silent_p.P473P|UGT1A6_uc002vuu.1_Silent_p.P208P|UGT1A6_uc002vuv.2_Silent_p.P475P|UGT1A4_uc002vux.1_Silent_p.P477P|UGT1A3_uc002vuy.1_Silent_p.P477P|UGT1A10_uc002vva.1_Non-coding_Transcript|UGT1A1_uc002vvb.1_Silent_p.P476P	NM_019078	NP_061951	P35504	UD15_HUMAN	UDP glycosyltransferase 1 family, polypeptide A5	477					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase 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)												0.415385	83.024242	83.427492	27	38	CC		KEEP	---	---	---	---	capture		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)	Silent	SNP	234345770	234345770	17506	2	C	T	T	23	23	UGT1A5	T	1	1
C2orf78	388960	broad.mit.edu	36	2	73897195	73897195	+	Silent	SNP	T	C	C			TCGA-41-5651-01	TCGA-41-5651-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:73897195T>C	uc002sjr.1	+	c.2337T>C	c.(2335-2337)GGT>GGC	p.G779G		NM_001080474	NP_001073943	A6NCI8	CB078_HUMAN	hypothetical protein LOC388960	779										ovary(2)	2														0.4	10.20639	10.398632	8	12	TT		KEEP	---	---	---	---	capture			Silent	SNP	73897195	73897195	2285	2	T	C	C	58	58	C2orf78	C	4	4
C2orf65	130951	broad.mit.edu	36	2	74695726	74695726	+	Missense_Mutation	SNP	T	C	C			TCGA-41-5651-01	TCGA-41-5651-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:74695726T>C	uc002smy.1	-	c.299A>G	c.(298-300)CAG>CGG	p.Q100R	C2orf65_uc002smz.1_Missense_Mutation_p.Q100R	NM_138804	NP_620159	Q8TC57	CB065_HUMAN	hypothetical protein LOC130951	100					chromatin assembly|female gamete generation|RNA processing|spermatogenesis	integral to membrane				ovary(1)|pancreas(1)	2														0.6	135.237485	135.84537	42	28	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74695726	74695726	2272	2	T	C	C	55	55	C2orf65	C	4	4
PIK3CA	5290	broad.mit.edu	36	3	180399575	180399575	+	Missense_Mutation	SNP	T	G	G			TCGA-41-5651-01	TCGA-41-5651-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:180399575T>G	uc003fjk.1	+	c.268T>G	c.(268-270)TGT>GGT	p.C90G		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	90					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1506)|large_intestine(749)|endometrium(244)|urinary_tract(195)|ovary(136)|skin(112)|stomach(89)|thyroid(77)|central_nervous_system(69)|lung(61)|upper_aerodigestive_tract(48)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|kidney(2)|prostate(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3437	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)					Colon(199;1504 1750 3362 26421 31210 32040)		57		621	TCGA GBM(8;5.49e-07)			0.4	94.329563	94.986098	30	45	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Missense_Mutation	SNP	180399575	180399575	12337	3	T	G	G	63	63	PIK3CA	G	4	4
ABCC5	10057	broad.mit.edu	36	3	185162003	185162003	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:185162003G>A	uc003fmg.1	-	c.2369C>T	c.(2368-2370)CCG>CTG	p.P790L	ABCC5_uc010hxl.1_Missense_Mutation_p.P790L|ABCC5_uc003fmf.1_Missense_Mutation_p.P318L	NM_005688	NP_005679	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C, member 5	790						integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)													0.47619	31.149631	31.159897	10	11	GG		KEEP	---	---	---	---	capture	Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Missense_Mutation	SNP	185162003	185162003	57	3	G	A	A	39	39	ABCC5	A	1	1
CYP8B1	1582	broad.mit.edu	36	3	42891207	42891207	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:42891207G>A	uc003cmh.1	-	c.1106C>T	c.(1105-1107)TCC>TTC	p.S369F	CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmg.2_Intron|CCBP2_uc010hie.1_Intron|CYP8B1_uc010hif.1_Missense_Mutation_p.S369F	NM_004391	NP_004382	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B,	369					bile acid biosynthetic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity			ovary(2)	2														0.482759	84.458694	84.475135	28	30	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)	Missense_Mutation	SNP	42891207	42891207	4363	3	G	A	A	41	41	CYP8B1	A	2	2
ACY1	95	broad.mit.edu	36	3	51995710	51995710	+	Silent	SNP	T	C	C			TCGA-41-5651-01	TCGA-41-5651-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:51995710T>C	uc003dcp.1	+	c.576T>C	c.(574-576)AGT>AGC	p.S192S	ACY1_uc003dcq.1_Silent_p.S192S	NM_000666	NP_000657	Q03154	ACY1_HUMAN	aminoacylase 1	192					cellular amino acid metabolic process|proteolysis	cytosol	aminoacylase activity|metal ion binding|metallopeptidase activity			breast(1)	1					L-Aspartic Acid(DB00128)									0.388235	106.384923	107.304598	33	52	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Silent	SNP	51995710	51995710	227	3	T	C	C	58	58	ACY1	C	4	4
BRPF1	7862	broad.mit.edu	36	3	9758816	9758816	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:9758816C>T	uc003bsf.1	+	c.1962C>T	c.(1960-1962)AGC>AGT	p.S654S	BRPF1_uc003bse.1_Silent_p.S654S|BRPF1_uc003bsg.1_Silent_p.S654S	NM_001003694	NP_001003694	P55201	BRPF1_HUMAN	bromodomain and PHD finger-containing protein 1	654	Required for RUNX1 and RUNX2 transcriptional activation.|Interaction with MEAF6 and ING5.|Bromo.				histone H3 acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|MOZ/MORF histone acetyltransferase complex|plasma membrane	DNA binding|transcription activator activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Medulloblastoma(99;0.227)													0.529412	53.245605	53.270829	18	16	CC		KEEP	---	---	---	---	capture			Silent	SNP	9758816	9758816	1551	3	C	T	T	27	27	BRPF1	T	1	1
GABRA4	2557	broad.mit.edu	36	4	46661755	46661755	+	Missense_Mutation	SNP	C	A	A			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:46661755C>A	uc003gxg.1	-	c.1123G>T	c.(1123-1125)GCC>TCC	p.A375S		NM_000809	NP_000800	P48169	GBRA4_HUMAN	gamma-aminobutyric acid A receptor, alpha 4	375	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|breast(1)	3					Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	Ovarian(6;283 369 8234 12290 33402)								0.466667	21.123263	21.137818	7	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46661755	46661755	6414	4	C	A	A	28	28	GABRA4	A	3	3
PKD2L2	27039	broad.mit.edu	36	5	137285276	137285276	+	Missense_Mutation	SNP	C	G	G			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:137285276C>G	uc003lby.2	+	c.1381C>G	c.(1381-1383)CAA>GAA	p.Q461E	PKD2L2_uc003lbw.1_Missense_Mutation_p.Q461E|PKD2L2_uc003lbx.2_Intron	NM_014386	NP_055201	Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	461	Extracellular (Potential).					integral to membrane	calcium ion binding|ion channel activity				0														0.555556	52.628384	52.700977	15	12	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)		Missense_Mutation	SNP	137285276	137285276	12393	5	C	G	G	25	25	PKD2L2	G	3	3
ODZ2	57451	broad.mit.edu	36	5	167484467	167484467	+	Silent	SNP	A	G	G			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:167484467A>G	uc010jjd.1	+	c.2043A>G	c.(2041-2043)GGA>GGG	p.G681G	ODZ2_uc003lzr.2_Silent_p.G449G|ODZ2_uc003lzt.2_Silent_p.G45G|ODZ2_uc010jje.1_5'UTR	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)												0.4	11.089	11.178736	4	6	AA		KEEP	---	---	---	---	capture	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)	Silent	SNP	167484467	167484467	11240	5	A	G	G	11	11	ODZ2	G	4	4
CDH12	1010	broad.mit.edu	36	5	21852981	21852981	+	Missense_Mutation	SNP	C	A	A			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:21852981C>A	uc010iuc.1	-	c.832G>T	c.(832-834)GTT>TTT	p.V278F	CDH12_uc003jgk.1_Missense_Mutation_p.V278F	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	278	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2														0.583333	65.278253	65.495932	21	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21852981	21852981	3227	5	C	A	A	20	20	CDH12	A	3	3
PRDM9	56979	broad.mit.edu	36	5	23562744	23562744	+	Missense_Mutation	SNP	C	G	G			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:23562744C>G	uc003jgo.1	+	c.1790C>G	c.(1789-1791)ACT>AGT	p.T597S		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	597	C2H2-type 4.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6														0.130435	9.517397	15.629282	6	40	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23562744	23562744	12906	5	C	G	G	20	20	PRDM9	G	3	3
HEATR7B2	133558	broad.mit.edu	36	5	41085204	41085204	+	Missense_Mutation	SNP	A	T	T			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41085204A>T	uc003jmj.2	-	c.1436T>A	c.(1435-1437)ATG>AAG	p.M479K	HEATR7B2_uc003jmi.2_Missense_Mutation_p.M34K	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	479							binding			ovary(6)|central_nervous_system(2)	8														0.473684	28.776698	28.787845	9	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41085204	41085204	7318	5	A	T	T	8	8	HEATR7B2	T	4	4
MAP1B	4131	broad.mit.edu	36	5	71530180	71530180	+	Missense_Mutation	SNP	G	T	T			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:71530180G>T	uc003kbw.2	+	c.5242G>T	c.(5242-5244)GAT>TAT	p.D1748Y	MAP1B_uc010iyw.1_Missense_Mutation_p.D1765Y|MAP1B_uc010iyx.1_Missense_Mutation_p.D1622Y|MAP1B_uc010iyy.1_Missense_Mutation_p.D1622Y	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1748						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)				Melanoma(17;367 822 11631 31730 47712)								0.3625	75.444036	76.778377	29	51	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)	Missense_Mutation	SNP	71530180	71530180	9611	5	G	T	T	33	33	MAP1B	T	3	3
LHFPL2	10184	broad.mit.edu	36	5	77820491	77820491	+	Silent	SNP	C	G	G			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:77820491C>G	uc003kfo.1	-	c.672G>C	c.(670-672)CTG>CTC	p.L224L		NM_005779	NP_005770	Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2	224						integral to membrane					0		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)												0.4375	98.492729	98.71047	28	36	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)	Silent	SNP	77820491	77820491	9091	5	C	G	G	29	29	LHFPL2	G	3	3
KIF25	3834	broad.mit.edu	36	6	168186201	168186201	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:168186201C>T	uc003qwk.1	+	c.941C>T	c.(940-942)CCG>CTG	p.P314L	KIF25_uc003qwl.1_Intron	NM_030615	NP_085118	Q9UIL4	KIF25_HUMAN	kinesin family member 25 isoform 1	314					microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(1)|pancreas(1)	2		Breast(66;1.07e-05)|Ovarian(120;0.0728)												0.40625	37.8696	38.115099	13	19	CC		KEEP	---	---	---	---	capture		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)	Missense_Mutation	SNP	168186201	168186201	8604	6	C	T	T	23	23	KIF25	T	1	1
HLA-DOB	3112	broad.mit.edu	36	6	32890120	32890120	+	Missense_Mutation	SNP	G	C	C			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32890120G>C	uc003oca.1	-	c.598C>G	c.(598-600)CTT>GTT	p.L200V		NM_002120	NP_002111	P13765	DOB_HUMAN	major histocompatibility complex, class II, DO	200	Beta-2.|Extracellular (Potential).|Ig-like C1-type.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endosome membrane|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0														0.462963	75.731043	75.798758	25	29	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32890120	32890120	7492	6	G	C	C	35	35	HLA-DOB	C	3	3
DNAH8	1769	broad.mit.edu	36	6	38948378	38948378	+	Missense_Mutation	SNP	A	G	G			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:38948378A>G	uc003ooe.1	+	c.6428A>G	c.(6427-6429)AAG>AGG	p.K2143R		NM_001371	NP_001362	Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy polypeptide 8	2143	AAA 2 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(5)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	17										2979				0.4375	91.482706	91.701738	28	36	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38948378	38948378	4790	6	A	G	G	3	3	DNAH8	G	4	4
LRFN2	57497	broad.mit.edu	36	6	40468403	40468403	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:40468403C>T	uc003oph.1	-	c.1627G>A	c.(1627-1629)GTG>ATG	p.V543M		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III	543	Helical; (Potential).					cell junction|integral to membrane|postsynaptic membrane				ovary(2)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)													0.304348	19.516563	20.301976	7	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40468403	40468403	9311	6	C	T	T	19	19	LRFN2	T	1	1
TREML1	340205	broad.mit.edu	36	6	41229549	41229549	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:41229549C>T	uc003opw.1	-	c.301G>A	c.(301-303)GAG>AAG	p.E101K	TREML1_uc003opx.1_Missense_Mutation_p.E101K|TREML1_uc010jxk.1_Intron	NM_178174	NP_835468	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid	101	Ig-like V-type.|Extracellular (Potential).				calcium-mediated signaling|innate immune response|platelet activation	cell surface|integral to membrane|plasma membrane|platelet alpha granule	protein binding|receptor activity			breast(1)	1	Ovarian(28;0.0418)|Colorectal(47;0.196)													0.428571	53.356209	53.539872	18	24	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41229549	41229549	17016	6	C	T	T	31	31	TREML1	T	1	1
TDRD6	221400	broad.mit.edu	36	6	46766160	46766160	+	Missense_Mutation	SNP	C	G	G			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:46766160C>G	uc003oyj.1	+	c.2336C>G	c.(2335-2337)TCT>TGT	p.S779C	TDRD6_uc010jze.1_Missense_Mutation_p.S773C	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	779					cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)	5														0.4	53.591734	53.941703	16	24	CC		KEEP	---	---	---	---	capture	Lung(136;0.192)		Missense_Mutation	SNP	46766160	46766160	16261	6	C	G	G	32	32	TDRD6	G	3	3
POLR2J3	548644	broad.mit.edu	36	7	101995701	101995701	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:101995701G>A	uc003vac.2	-	c.177C>T	c.(175-177)GGC>GGT	p.G59G	POLR2J3_uc003vab.2_Silent_p.G59G|POLR2J3_uc003uzw.2_Intron|UPK3BL_uc003uzy.2_Intron	NM_001097615	NP_001091084	Q9H1A7	RPB1C_HUMAN	polymerase (RNA) II (DNA directed) polypeptide	59						nucleus	DNA binding|DNA-directed RNA polymerase activity|protein dimerization activity				0														0.114804	43.258237	91.61665	38	293	GG		KEEP	---	---	---	---	capture			Silent	SNP	101995701	101995701	12653	7	G	A	A	34	34	POLR2J3	A	2	2
KIAA1549	57670	broad.mit.edu	36	7	138244370	138244370	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:138244370G>A	uc003vuk.2	-	c.3033C>T	c.(3031-3033)TTC>TTT	p.F1011F	KIAA1549_uc003vul.2_5'Flank	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670	1061						integral to membrane			KIAA1549/BRAF(211)	central_nervous_system(211)|pancreas(1)	212						NSCLC(119;1534 1718 44213 46230 50068)				967				0.269231	9.211023	10.553034	7	19	GG		KEEP	---	---	---	---	capture			Silent	SNP	138244370	138244370	8553	7	G	A	A	33	33	KIAA1549	A	2	2
CNTNAP2	26047	broad.mit.edu	36	7	147475612	147475612	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:147475612G>A	uc003weu.1	+	c.2651G>A	c.(2650-2652)CGG>CAG	p.R884Q		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	884	Laminin G-like 3.|Extracellular (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)												0.242991	67.601259	74.041134	26	81	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0319)		Missense_Mutation	SNP	147475612	147475612	3785	7	G	A	A	39	39	CNTNAP2	A	1	1
UBE3C	9690	broad.mit.edu	36	7	156655816	156655816	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:156655816G>A	uc010lqs.1	+	c.253G>A	c.(253-255)GCT>ACT	p.A85T	UBE3C_uc003wnf.2_Missense_Mutation_p.A42T|UBE3C_uc003wng.2_Missense_Mutation_p.A85T	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	85					protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			large_intestine(1)|ovary(1)	2		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)												0.344	114.927059	117.595341	43	82	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)	Missense_Mutation	SNP	156655816	156655816	17439	7	G	A	A	38	38	UBE3C	A	1	1
GHRHR	2692	broad.mit.edu	36	7	30981135	30981135	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:30981135C>T	uc003tbx.1	+	c.837C>T	c.(835-837)TCC>TCT	p.S279S	GHRHR_uc003tbw.1_Silent_p.S279S|GHRHR_uc003tby.1_Silent_p.S215S|GHRHR_uc003tbz.1_Missense_Mutation_p.P46S	NM_000823	NP_000814	Q02643	GHRHR_HUMAN	growth hormone releasing hormone receptor	279	Extracellular (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of cell proliferation|positive regulation of growth hormone secretion|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of multicellular organism growth|response to estrogen stimulus|response to glucocorticoid stimulus	cell surface|integral to membrane|nuclear inner membrane|nuclear matrix|nuclear outer membrane|plasma membrane|stored secretory granule	growth factor binding|growth hormone-releasing hormone receptor activity|peptide hormone binding			large_intestine(1)|ovary(1)	2					Sermorelin(DB00010)							OREG0017943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.357143	88.125611	89.636016	30	54	CC		KEEP	---	---	---	---	capture			Silent	SNP	30981135	30981135	6641	7	C	T	T	22	22	GHRHR	T	2	2
ZDHHC4	55146	broad.mit.edu	36	7	6594930	6594930	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:6594930G>A	uc003sqh.1	+	c.899G>A	c.(898-900)CGT>CAT	p.R300H	ZDHHC4_uc003sqi.1_Missense_Mutation_p.R300H|ZDHHC4_uc003sqj.1_Missense_Mutation_p.R300H|ZDHHC4_uc003sqk.1_Missense_Mutation_p.R300H|ZDHHC4_uc003sql.1_Missense_Mutation_p.R300H|ZDHHC4_uc003sqm.1_Missense_Mutation_p.R300H|ZDHHC4_uc003sqn.1_Missense_Mutation_p.R300H|C7orf26_uc003sqo.1_5'Flank|C7orf26_uc003sqp.1_5'Flank|C7orf26_uc003sqq.1_5'Flank	NM_018106	NP_060576	Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	300						integral to membrane	acyltransferase activity|zinc ion binding			breast(1)|pancreas(1)	2		Ovarian(82;0.232)												0.274725	58.612407	62.791744	25	66	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)	Missense_Mutation	SNP	6594930	6594930	18205	7	G	A	A	40	40	ZDHHC4	A	1	1
PKHD1L1	93035	broad.mit.edu	36	8	110523469	110523469	+	Missense_Mutation	SNP	C	A	A			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:110523469C>A	uc003yne.1	+	c.4262C>A	c.(4261-4263)ACA>AAA	p.T1421K		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L	1421	Extracellular (Potential).|IPT/TIG 7.				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14														0.617647	70.082057	70.494557	21	13	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)		Missense_Mutation	SNP	110523469	110523469	12397	8	C	A	A	17	17	PKHD1L1	A	3	3
DEPDC6	64798	broad.mit.edu	36	8	121046832	121046832	+	Splice_Site_SNP	SNP	G	T	T			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:121046832G>T	uc003yow.2	+	c.604_splice	c.e4+1	p.V202_splice		NM_022783	NP_073620			DEP domain containing 6						intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis	intracellular	protein binding				0	Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)													0.318182	61.354337	63.292253	21	45	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00185)		Splice_Site_SNP	SNP	121046832	121046832	4622	8	G	T	T	44	44	DEPDC6	T	5	3
ADCY8	114	broad.mit.edu	36	8	132071891	132071891	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:132071891C>T	uc003ytd.2	-	c.1040G>A	c.(1039-1041)CGC>CAC	p.R347H	ADCY8_uc010mds.1_Missense_Mutation_p.R347H	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	347	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|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			large_intestine(1)|central_nervous_system(1)	2	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)													0.489655	210.225243	210.238379	71	74	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.000538)		Missense_Mutation	SNP	132071891	132071891	301	8	C	T	T	27	27	ADCY8	T	1	1
ADAM28	10863	broad.mit.edu	36	8	24255206	24255206	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:24255206C>T	uc003xdy.1	+	c.1821C>T	c.(1819-1821)GGC>GGT	p.G607G	ADAM28_uc010lua.1_Silent_p.G294G	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1	607	Extracellular (Potential).|Cys-rich.				proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(2)|lung(1)|central_nervous_system(1)	4		Prostate(55;0.0959)				NSCLC(193;488 2149 22258 34798 40734)			p.G607G(PF382-Tumor)	410				0.414634	50.968701	51.22927	17	24	CC		KEEP	---	---	---	---	capture		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)	Silent	SNP	24255206	24255206	247	8	C	T	T	27	27	ADAM28	T	1	1
PXDNL	137902	broad.mit.edu	36	8	52550252	52550252	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:52550252C>T	uc003xqu.2	-	c.527G>A	c.(526-528)CGT>CAT	p.R176H		NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like	176					hydrogen peroxide catabolic process|oxidation-reduction process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)												0.464286	37.043039	37.076431	13	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52550252	52550252	13306	8	C	T	T	19	19	PXDNL	T	1	1
C8orf38	137682	broad.mit.edu	36	8	96116924	96116924	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:96116924G>A	uc003yhj.1	+	c.364G>A	c.(364-366)GAA>AAA	p.E122K	C8orf38_uc003yhe.1_Non-coding_Transcript|C8orf38_uc003yhf.1_Missense_Mutation_p.E30K|C8orf38_uc003yhi.1_Missense_Mutation_p.E70K|C8orf38_uc003yhk.1_Non-coding_Transcript|C8orf38_uc003yhl.1_Missense_Mutation_p.E30K	NM_152416	NP_689629	Q330K2	CH038_HUMAN	hypothetical protein LOC137682	122					biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)													0.560976	73.427829	73.560299	23	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	96116924	96116924	2534	8	G	A	A	41	41	C8orf38	A	2	2
SNX30	401548	broad.mit.edu	36	9	114619914	114619914	+	Missense_Mutation	SNP	C	G	G			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:114619914C>G	uc004bgj.2	+	c.457C>G	c.(457-459)CCC>GCC	p.P153A		NM_001012994	NP_001013012	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	153	PX.				cell communication|protein transport	cytoplasm	phosphatidylinositol binding				0														0.5	45.875039	45.875039	13	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	114619914	114619914	15400	9	C	G	G	30	30	SNX30	G	3	3
OR1J1	347168	broad.mit.edu	36	9	124279316	124279316	+	Silent	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:124279316G>A	uc004bmk.1	-	c.711C>T	c.(709-711)GCC>GCT	p.A237A	OR1J2_uc004bmj.1_Intron	NM_001004451	NP_001004451	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J,	237	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1														0.295455	35.350638	37.002356	13	31	GG		KEEP	---	---	---	---	capture			Silent	SNP	124279316	124279316	11365	9	G	A	A	35	35	OR1J1	A	2	2
SDCCAG3	10807	broad.mit.edu	36	9	138419440	138419440	+	Missense_Mutation	SNP	A	G	G			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138419440A>G	uc004chi.1	-	c.929T>C	c.(928-930)ATG>ACG	p.M310T	SDCCAG3_uc004chj.1_Missense_Mutation_p.M287T|SDCCAG3_uc004chk.1_Missense_Mutation_p.M237T	NM_001039707	NP_001034796	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	310	Potential.					cytoplasm					0		Myeloproliferative disorder(178;0.0511)												0.323529	64.529596	66.407736	22	46	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)	Missense_Mutation	SNP	138419440	138419440	14443	9	A	G	G	8	8	SDCCAG3	G	4	4
ACO1	48	broad.mit.edu	36	9	32420435	32420435	+	Missense_Mutation	SNP	G	T	T			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:32420435G>T	uc003zqw.2	+	c.1589G>T	c.(1588-1590)GGA>GTA	p.G530V	ACO1_uc010mjh.1_Missense_Mutation_p.G364V|ACO1_uc003zqx.2_Missense_Mutation_p.G530V|ACO1_uc003zqy.2_Non-coding_Transcript	NM_002197	NP_002188	P21399	ACOC_HUMAN	aconitase 1	530					citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0														0.402597	85.405251	86.04471	31	46	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)	Missense_Mutation	SNP	32420435	32420435	147	9	G	T	T	41	41	ACO1	T	3	3
DAPK1	1612	broad.mit.edu	36	9	89409902	89409902	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:89409902C>T	uc004apc.1	+	c.276C>T	c.(274-276)ATC>ATT	p.I92I	DAPK1_uc004apd.1_Silent_p.I92I	NM_004938	NP_004929	P53355	DAPK1_HUMAN	death-associated protein kinase 1	92	Protein kinase.				apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade|protein phosphorylation	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2										862				0.53125	51.869625	51.896315	17	15	CC		KEEP	---	---	---	---	capture			Silent	SNP	89409902	89409902	4402	9	C	T	T	32	32	DAPK1	T	2	2
RPL36A	6173	broad.mit.edu	36	X	100533109	100533109	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:100533109G>A	uc004ehk.1	+	c.10G>A	c.(10-12)GTC>ATC	p.V4I	BTK_uc010nno.1_5'Flank|RPL36A_uc004ehj.1_Missense_Mutation_p.V4I	NM_021029	NP_066357	P83881	RL36A_HUMAN	ribosomal protein L36a	4					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	protein binding|structural constituent of ribosome				0														0.277512	150.515488	159.792086	58	151	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100533109	100533109	14066	23	G	A	A	40	40	RPL36A	A	1	1
KIAA1210	57481	broad.mit.edu	36	X	118123016	118123016	+	Missense_Mutation	SNP	C	A	A			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:118123016C>A	uc004era.2	-	c.1035G>T	c.(1033-1035)AAG>AAT	p.K345N		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	345										ovary(4)|skin(1)	5														0.268182	149.883889	160.593423	59	161	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118123016	118123016	8522	23	C	A	A	24	24	KIAA1210	A	3	3
FRMD7	90167	broad.mit.edu	36	X	131047292	131047292	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:131047292G>A	uc004ewn.1	-	c.643C>T	c.(643-645)CGG>TGG	p.R215W		NM_194277	NP_919253	Q6ZUT3	FRMD7_HUMAN	nystagmus 1 protein	215	FERM.				regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding				0	Acute lymphoblastic leukemia(192;0.000127)													0.282051	84.315533	89.317784	33	84	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131047292	131047292	6305	23	G	A	A	40	40	FRMD7	A	1	1
ATP2B3	492	broad.mit.edu	36	X	152471814	152471814	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152471814C>T	uc004fht.1	+	c.1951C>T	c.(1951-1953)CGG>TGG	p.R651W	ATP2B3_uc004fhs.1_Missense_Mutation_p.R651W	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	651	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.293103	46.354749	48.576045	17	41	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152471814	152471814	1160	23	C	T	T	23	23	ATP2B3	T	1	1
CXorf21	80231	broad.mit.edu	36	X	30487671	30487671	+	Silent	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:30487671C>T	uc004dcg.1	-	c.723G>A	c.(721-723)GCG>GCA	p.A241A	CXorf21_uc010ngi.1_Silent_p.A241A	NM_025159	NP_079435	Q9HAI6	CX021_HUMAN	hypothetical protein LOC80231	241										ovary(1)	1														0.264957	78.368872	84.213125	31	86	CC		KEEP	---	---	---	---	capture			Silent	SNP	30487671	30487671	4261	23	C	T	T	19	19	CXorf21	T	1	1
GRIPAP1	56850	broad.mit.edu	36	X	48724700	48724700	+	Missense_Mutation	SNP	G	A	A			TCGA-41-5651-01	TCGA-41-5651-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48724700G>A	uc004dly.1	-	c.1369C>T	c.(1369-1371)CGG>TGG	p.R457W	GRIPAP1_uc004dlz.1_Missense_Mutation_p.R347W|GRIPAP1_uc004dma.1_Missense_Mutation_p.R404W	NM_020137	NP_064522	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1 isoform 1	457	Potential.					early endosome				breast(2)|kidney(1)	3														0.247788	67.856512	74.389108	28	85	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48724700	48724700	7068	23	G	A	A	40	40	GRIPAP1	A	1	1
ITIH5L	347365	broad.mit.edu	36	X	54802148	54802148	+	Missense_Mutation	SNP	C	T	T			TCGA-41-5651-01	TCGA-41-5651-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:54802148C>T	uc004dtj.1	-	c.1084G>A	c.(1084-1086)GTC>ATC	p.V362I		NM_198510	NP_940912	Q6UXX5	ITH5L_HUMAN	inter-alpha (globulin) inhibitor H5-like	362	VWFA.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			lung(2)|ovary(1)|breast(1)|skin(1)	5										249				0.428571	9.02445	9.055458	3	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54802148	54802148	8212	23	C	T	T	19	19	ITIH5L	T	1	1
TAF1	6872	broad.mit.edu	36	X	70529947	70529947	+	Silent	SNP	A	C	C			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70529947A>C	uc004dzt.2	+	c.3183A>C	c.(3181-3183)GGA>GGC	p.G1061G	TAF1_uc004dzu.2_Silent_p.G1040G|TAF1_uc004dzv.2_Silent_p.G214G	NM_004606	NP_004597	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 1	1040					G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|response to DNA damage stimulus|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(5)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	15	Renal(35;0.156)	all_lung(315;0.000321)								472				0.307692	60.172817	62.743551	24	54	AA		KEEP	---	---	---	---	capture			Silent	SNP	70529947	70529947	16034	23	A	C	C	11	11	TAF1	C	4	4
ABCB7	22	broad.mit.edu	36	X	74208101	74208101	+	Missense_Mutation	SNP	A	T	T			TCGA-41-5651-01	TCGA-41-5651-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:74208101A>T	uc004ebz.1	-	c.1178T>A	c.(1177-1179)ATA>AAA	p.I393K	ABCB7_uc004eca.1_Missense_Mutation_p.I392K|ABCB7_uc010nls.1_Missense_Mutation_p.I353K|ABCB7_uc010nlt.1_Missense_Mutation_p.I352K	NM_004299	NP_004290	O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B, member 7	392	ABC transmembrane type-1.|Helical; (Potential).				cellular iron ion homeostasis	integral to membrane|mitochondrial inner membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|heme transporter activity			ovary(1)	1														0.211538	25.297349	29.297665	11	41	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74208101	74208101	47	23	A	T	T	16	16	ABCB7	T	4	4
ITPKB	3707	broad.mit.edu	36	1	224991499	224991507	+	In_Frame_Del	DEL	CTGCCGCTG	-	-			TCGA-41-5651-01	TCGA-41-5651-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:224991499_224991507delCTGCCGCTG	uc001hqg.1	-	c.276_284delCAGCGGCAG	c.(274-285)AGCAGCGGCAGT>AGT	p.92_95SSGS>S	ITPKB_uc001hqh.2_In_Frame_Del_p.92_95SSGS>S	NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B	92_95							ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)				Colon(84;110 1851 5306 33547)								0.36			5	9				---	---	---	---	capture_indel			In_Frame_Del	DEL	224991499	224991507	8222	1	CTGCCGCTG	-	-	20	20	ITPKB	-	5	5
AHDC1	27245	broad.mit.edu	36	1	27750092	27750092	+	Frame_Shift_Del	DEL	G	-	-			TCGA-41-5651-01	TCGA-41-5651-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27750092_27750092delG	uc009vsy.1	-	c.1122_1122delC	c.(1120-1122)CCCfs	p.P374fs	AHDC1_uc009vsz.1_Frame_Shift_Del_p.P374fs|AHDC1_uc001boh.1_Frame_Shift_Del_p.P247fs|AHDC1_uc009vta.1_Frame_Shift_Del_p.P374fs	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	374	Pro-rich.						DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	27750092	27750092	415	1	G	-	-	39	39	AHDC1	-	5	5
