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
DNAJB12	54788	broad.mit.edu	36	10	73766425	73766425	+	Missense_Mutation	SNP	T	A	A			TCGA-12-1089-01	TCGA-12-1089-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:73766425T>A	uc001jsz.1	-	c.869A>T	c.(868-870)CAC>CTC	p.H290L	DNAJB12_uc001jsy.1_Non-coding_Transcript|DNAJB12_uc001jta.1_Missense_Mutation_p.H290L	NM_017626	NP_060096	Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	290					protein folding	endoplasmic reticulum|integral to membrane	heat shock protein binding|unfolded protein binding				0														0.4	8.093654	8.182129	4	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73766425	73766425	4800	10	T	A	A	59	59	DNAJB12	A	4	4
PTEN	5728	broad.mit.edu	36	10	89707742	89707742	+	Nonsense_Mutation	SNP	A	T	T			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89707742A>T	uc001kfb.1	+	c.787A>T	c.(787-789)AAG>TAG	p.K263*		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	263	C2 tensin-type.			KMLKKDK->AAGAADA: Reduces the growth suppression activity and cells show anchorage-independent growth. Reduces binding to phospholipid membranes in vitro. Phosphatase activity towards PtdIns(3,4,5)P3 is not affected.	apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.K263*(2)|p.G165_*404del(1)|p.D252_K263>AKE(1)|p.G165_K342del(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)				31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.595745	175.108329	175.86211	56	38	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	89707742	89707742	13192	10	A	T	T	5	5	PTEN	T	5	4
C10orf12	26148	broad.mit.edu	36	10	98732364	98732365	+	Missense_Mutation	DNP	TC	GA	GA			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:98732364_98732365TC>GA	uc001kmv.1	+	c.1227_1228TC>GA	c.(1225-1230)AGTCTG>AGGATG	p.409_410SL>RM	C10orf12_uc009xvg.1_Missense_Mutation_p.719_720SL>RM	NM_015652	NP_056467	Q8N655	CJ012_HUMAN	hypothetical protein LOC26148	409_410											0		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)										0.227273	8.460494	9.966502	5	17	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	98732364	98732365	1624	10	TC	GA	GA	58	58	C10orf12	GA	4	4
RPS25	6230	broad.mit.edu	36	11	118393912	118393912	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118393912G>T	uc001pun.1	-	c.65C>A	c.(64-66)CCA>CAA	p.P22Q	TRAPPC4_uc001puo.1_5'Flank|TRAPPC4_uc001pup.1_5'Flank	NM_001028	NP_001019	P62851	RS25_HUMAN	ribosomal protein S25	22					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)										0.135294	19.389008	41.349994	23	147	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118393912	118393912	14116	11	G	T	T	47	47	RPS25	T	3	3
PUS3	83480	broad.mit.edu	36	11	125269086	125269086	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:125269086C>T	uc001qcy.1	-	c.1250G>A	c.(1249-1251)CGT>CAT	p.R417H	HYLS1_uc001qcw.1_Intron|HYLS1_uc001qcx.2_Intron	NM_031307	NP_112597	Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	417						nucleus	RNA binding			ovary(1)	1	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)										0.141414	42.469984	67.037682	28	170	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125269086	125269086	13290	11	C	T	T	19	19	PUS3	T	1	1
NAV2	89797	broad.mit.edu	36	11	19927141	19927141	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:19927141G>A	uc009yhw.1	+	c.2653G>A	c.(2653-2655)GGC>AGC	p.G885S	NAV2_uc001mpp.1_Missense_Mutation_p.G798S|NAV2_uc001mpr.2_Missense_Mutation_p.G862S	NM_182964	NP_892009	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 1	885						nucleus	ATP binding|helicase activity			ovary(1)|pancreas(1)	2														0.210526	8.13761	9.576362	4	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19927141	19927141	10580	11	G	A	A	39	39	NAV2	A	1	1
OR51A2	401667	broad.mit.edu	36	11	4933050	4933050	+	Missense_Mutation	SNP	A	T	T			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4933050A>T	uc001lzu.1	-	c.470T>A	c.(469-471)CTG>CAG	p.L157Q		NM_001004748	NP_001004748	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A,	157	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.274038	142.776381	152.354341	57	151	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4933050	4933050	11496	11	A	T	T	7	7	OR51A2	T	4	4
RIN1	9610	broad.mit.edu	36	11	65857334	65857334	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65857334G>T	uc001ohn.1	-	c.1846C>A	c.(1846-1848)CGC>AGC	p.R616S	RIN1_uc009yrd.1_Missense_Mutation_p.R309S	NM_004292	NP_004283	Q13671	RIN1_HUMAN	ras inhibitor RIN1	616	Ras and 14-3-3 protein binding region.				endocytosis|signal transduction	cytoplasm|cytoskeleton|plasma membrane	GTPase activator activity|protein binding			lung(1)	1														0.6	7.221845	7.264858	3	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65857334	65857334	13848	11	G	T	T	38	38	RIN1	T	3	3
DEAF1	10522	broad.mit.edu	36	11	681587	681588	+	Missense_Mutation	DNP	CT	TG	TG			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:681587_681588CT>TG	uc001lqq.1	-	c.300_301AG>CA	c.(298-303)ACAGTG>ACCATG	p.V101M		NM_021008	NP_066288	O75398	DEAF1_HUMAN	deformed epidermal autoregulatory factor 1	101	Ala-rich.				embryonic skeletal system development|germ cell development|neural tube closure|regulation of mammary gland epithelial cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|cytoplasm|extracellular region|nucleus	protein binding|zinc ion binding				0		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)										0.153846	8.802754	16.272118	10	55	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	681587	681588	4551	11	CT	TG	TG	20	20	DEAF1	TG	2	2
FGF23	8074	broad.mit.edu	36	12	4350074	4350074	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:4350074G>A	uc001qmq.1	-	c.452C>T	c.(451-453)CCA>CTA	p.P151L		NM_020638	NP_065689	Q9GZV9	FGF23_HUMAN	fibroblast growth factor 23 precursor	151					cell differentiation|insulin receptor signaling pathway|negative regulation of bone mineralization|negative regulation of hormone secretion|negative regulation of osteoblast differentiation|positive regulation of vitamin D 24-hydroxylase activity|regulation of phosphate transport|vitamin D catabolic process	extracellular space	growth factor activity			ovary(2)|skin(1)	3			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)|STAD - Stomach adenocarcinoma(119;0.206)											0.145833	32.975571	50.362912	21	123	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4350074	4350074	6089	12	G	A	A	47	47	FGF23	A	2	2
ITGA7	3679	broad.mit.edu	36	12	54368089	54368089	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54368089C>A	uc001shh.1	-	c.3128G>T	c.(3127-3129)TGG>TTG	p.W1043L	ITGA7_uc001shf.1_Missense_Mutation_p.W17L|ITGA7_uc009znw.1_Missense_Mutation_p.W286L|ITGA7_uc009znx.1_Missense_Mutation_p.W920L|ITGA7_uc001shg.1_Missense_Mutation_p.W1039L	NM_002206	NP_002197	Q13683	ITA7_HUMAN	integrin alpha 7 isoform 2 precursor	1083	Helical; (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development|regulation of cell shape	integrin complex	receptor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4										261				0.227273	7.057732	8.567777	5	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54368089	54368089	8185	12	C	A	A	21	21	ITGA7	A	3	3
FREM2	341640	broad.mit.edu	36	13	38161584	38161584	+	Silent	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:38161584G>A	uc001uwv.1	+	c.2103G>A	c.(2101-2103)CCG>CCA	p.P701P		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	701	CSPG 4.|Extracellular (Potential).				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)	10		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)										0.194444	47.419721	56.822456	21	87	GG		KEEP	---	---	---	---	capture			Silent	SNP	38161584	38161584	6292	13	G	A	A	39	39	FREM2	A	1	1
DYNC1H1	1778	broad.mit.edu	36	14	101540966	101540966	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:101540966A>G	uc001yks.1	+	c.5164A>G	c.(5164-5166)ACG>GCG	p.T1722A		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	1722	Stem (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10														0.375	6.520348	6.630989	3	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101540966	101540966	5027	14	A	G	G	14	14	DYNC1H1	G	4	4
ACIN1	22985	broad.mit.edu	36	14	22617237	22617238	+	Missense_Mutation	DNP	AG	TA	TA			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:22617237_22617238AG>TA	uc001wit.2	-	c.2259_2260CT>TA	c.(2257-2262)ACCTCT>ACTACT	p.S754T	ACIN1_uc001wis.2_Missense_Mutation_p.S436T|ACIN1_uc010akg.1_Missense_Mutation_p.S754T	NM_014977	NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	754					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)			GBM - Glioblastoma multiforme(265;0.00816)										0.172414	6.452945	9.400909	5	24	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	22617237	22617238	143	14	AG	TA	TA	11	11	ACIN1	TA	4	4
TRAPPC6B	122553	broad.mit.edu	36	14	38690796	38690796	+	Splice_Site_SNP	SNP	T	A	A			TCGA-12-1089-01	TCGA-12-1089-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:38690796T>A	uc001wut.1	-	c.e5_splice_site			TRAPPC6B_uc001wuu.1_Splice_Site_SNP|TRAPPC6B_uc001wuv.1_Splice_Site_SNP	NM_001079537	NP_001073005			trafficking protein particle complex 6B isoform						vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0128)										0.25	6.788137	7.701731	4	12	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	38690796	38690796	17008	14	T	A	A	53	53	TRAPPC6B	A	5	4
ATG2B	55102	broad.mit.edu	36	14	95868675	95868675	+	Silent	SNP	C	G	G			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:95868675C>G	uc001yfi.1	-	c.1278G>C	c.(1276-1278)GGG>GGC	p.G426G		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	426										ovary(1)|kidney(1)	2		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)										0.266667	6.387246	7.130409	4	11	CC		KEEP	---	---	---	---	capture			Silent	SNP	95868675	95868675	1113	14	C	G	G	22	22	ATG2B	G	3	3
NDNL2	56160	broad.mit.edu	36	15	27348858	27348858	+	Missense_Mutation	SNP	A	C	C			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:27348858A>C	uc001zco.1	-	c.344T>G	c.(343-345)GTC>GGC	p.V115G	FAM189A1_uc010azk.1_Intron	NM_138704	NP_619649	Q96MG7	MAGG1_HUMAN	necdin-like 2	115	MAGE.				regulation of growth	cytoplasm|nucleus					0		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)										0.237569	73.004013	84.432008	43	138	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27348858	27348858	10647	15	A	C	C	10	10	NDNL2	C	4	4
MAP1A	4130	broad.mit.edu	36	15	41601624	41601624	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:41601624G>T	uc001zrt.1	+	c.661G>T	c.(661-663)GGC>TGC	p.G221C		NM_002373	NP_002364	P78559	MAP1A_HUMAN	microtubule-associated protein 1A	221						cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(3)|breast(3)|pancreas(2)	8		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)									0.10303	14.767216	40.660603	17	148	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41601624	41601624	9610	15	G	T	T	35	35	MAP1A	T	3	3
PRTG	283659	broad.mit.edu	36	15	53752966	53752966	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:53752966G>T	uc002adg.1	-	c.1747C>A	c.(1747-1749)CCT>ACT	p.P583T	PRTG_uc002adh.2_Missense_Mutation_p.P85T	NM_173814	NP_776175	Q2VWP7	PRTG_HUMAN	protogenin	583	Fibronectin type-III 2.				multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)	2				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)										0.26383	158.050472	169.899998	62	173	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53752966	53752966	13089	15	G	T	T	44	44	PRTG	T	3	3
C15orf42	90381	broad.mit.edu	36	15	87939753	87939753	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:87939753G>T	uc002boe.1	+	c.1807G>T	c.(1807-1809)GCT>TCT	p.A603S		NM_152259	NP_689472	Q7Z2Z1	TICRR_HUMAN	leucine-rich repeat kinase 1	603					cell cycle|DNA repair|DNA replication|formation of translation preinitiation complex|G2/M transition checkpoint|response to ionizing radiation|S-M checkpoint	nucleus	chromatin binding|protein binding			ovary(4)|central_nervous_system(2)	6	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)											0.263158	32.799742	35.693083	15	42	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87939753	87939753	1846	15	G	T	T	42	42	C15orf42	T	3	3
NUTF2	10204	broad.mit.edu	36	16	66459981	66459981	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:66459981G>T	uc002eup.1	+	c.248G>T	c.(247-249)AGC>ATC	p.S83I	NUTF2_uc002euq.2_5'Flank	NM_005796	NP_005787	P61970	NTF2_HUMAN	nuclear transport factor 2	83	NTF2.				protein transport	cytosol|nuclear pore	protein binding|transporter activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00443)|Epithelial(162;0.0199)|all cancers(182;0.129)										0.25	8.563444	9.70279	5	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66459981	66459981	11184	16	G	T	T	34	34	NUTF2	T	3	3
MYH13	8735	broad.mit.edu	36	17	10189619	10189619	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10189619C>T	uc002gmk.1	-	c.1303G>A	c.(1303-1305)GAG>AAG	p.E435K		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	435	Myosin head-like.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.801917	1674.415946	1727.531201	502	124	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10189619	10189619	10427	17	C	T	T	31	31	MYH13	T	1	1
OR1A1	8383	broad.mit.edu	36	17	3065778	3065778	+	Silent	SNP	A	G	G			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:3065778A>G	uc002fve.1	+	c.114A>G	c.(112-114)ACA>ACG	p.T38T		NM_014565	NP_055380	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A,	38	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.279476	330.004716	350.038788	128	330	AA		KEEP	---	---	---	---	capture			Silent	SNP	3065778	3065778	11355	17	A	G	G	8	8	OR1A1	G	4	4
KRTAP9-4	85280	broad.mit.edu	36	17	36659542	36659542	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36659542G>A	uc002hwi.1	+	c.44G>A	c.(43-45)AGG>AAG	p.R15K		NM_033191	NP_149461	Q9BYQ2	KRA94_HUMAN	keratin associated protein 9-4	15	2.|15 X 5 AA repeats of C-C-[RQVGE]-[SPTN]- [TASPF].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)											0.121622	11.919827	22.305026	9	65	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36659542	36659542	8898	17	G	A	A	35	35	KRTAP9-4	A	2	2
SGCA	6442	broad.mit.edu	36	17	45601529	45601529	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:45601529G>A	uc002iqi.1	+	c.662G>A	c.(661-663)CGC>CAC	p.R221H	SGCA_uc002iqj.1_Intron	NM_000023	NP_000014	Q16586	SGCA_HUMAN	sarcoglycan, alpha isoform 1 precursor	221	Extracellular (Potential).				muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(2)	2												OREG0024558	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.387097	27.586677	27.934494	12	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45601529	45601529	14690	17	G	A	A	38	38	SGCA	A	1	1
PRR11	55771	broad.mit.edu	36	17	54627513	54627513	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:54627513G>A	uc002ixf.1	+	c.784G>A	c.(784-786)GTC>ATC	p.V262I	PRR11_uc002ixg.1_Non-coding_Transcript	NM_018304	NP_060774	Q96HE9	PRR11_HUMAN	proline rich 11	262										ovary(2)	2	Medulloblastoma(34;0.0922)|all_neural(34;0.101)													0.352113	75.557397	76.925215	25	46	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54627513	54627513	13026	17	G	A	A	40	40	PRR11	A	1	1
ABCA8	10351	broad.mit.edu	36	17	64391532	64391532	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:64391532G>C	uc002jhq.1	-	c.3702C>G	c.(3700-3702)TTC>TTG	p.F1234L	ABCA8_uc002jhp.1_Missense_Mutation_p.F1194L	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	1194						integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)	2	Breast(10;4.56e-13)													0.116279	6.543923	12.777518	5	38	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64391532	64391532	39	17	G	C	C	33	33	ABCA8	C	3	3
MPPE1	65258	broad.mit.edu	36	18	11883476	11883476	+	Silent	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:11883476G>A	uc002kqj.1	-	c.381C>T	c.(379-381)AGC>AGT	p.S127S	MPPE1_uc002kqf.1_Silent_p.S127S|MPPE1_uc002kqn.1_Silent_p.S127S|MPPE1_uc002kqg.1_Non-coding_Transcript|MPPE1_uc002kqh.1_Non-coding_Transcript|MPPE1_uc002kqi.1_Non-coding_Transcript|MPPE1_uc002kqk.1_Silent_p.S127S|MPPE1_uc002kql.1_Silent_p.S127S|MPPE1_uc002kqm.1_Silent_p.S127S|MPPE1_uc010dla.1_Silent_p.S127S	NM_023075	NP_075563	Q53F39	MPPE1_HUMAN	metallophosphoesterase 1 precursor	127					ER to Golgi vesicle-mediated transport|GPI anchor biosynthetic process	cis-Golgi network|endoplasmic reticulum exit site|ER-Golgi intermediate compartment membrane|integral to membrane	GPI anchor binding|manganese ion binding|phosphoric diester hydrolase activity				0														0.180556	26.532367	33.439768	13	59	GG		KEEP	---	---	---	---	capture			Silent	SNP	11883476	11883476	10132	18	G	A	A	46	46	MPPE1	A	2	2
DSG4	147409	broad.mit.edu	36	18	27247132	27247132	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1089-01	TCGA-12-1089-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:27247132T>C	uc002kwr.1	+	c.2756T>C	c.(2755-2757)GTG>GCG	p.V919A	DSG4_uc002kwq.1_Missense_Mutation_p.V900A	NM_177986	NP_817123	Q86SJ6	DSG4_HUMAN	desmoglein 4 isoform 2	900	Cytoplasmic (Potential).|Desmoglein repeat 1.				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8			OV - Ovarian serous cystadenocarcinoma(10;0.00504)											0.264706	606.457814	650.705731	234	650	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27247132	27247132	4963	18	T	C	C	59	59	DSG4	C	4	4
ATP8B1	5205	broad.mit.edu	36	18	53468665	53468665	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:53468665C>A	uc002lgw.1	-	c.3463G>T	c.(3463-3465)GTG>TTG	p.V1155L		NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1	1155	Helical; (Potential).				ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(4)|ovary(2)|central_nervous_system(2)	8		Colorectal(73;0.229)								950				0.09331	22.221256	116.787811	53	515	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53468665	53468665	1213	18	C	A	A	17	17	ATP8B1	A	3	3
MUM1	84939	broad.mit.edu	36	19	1311279	1311279	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1311279G>T	uc002lsa.1	+	c.362G>T	c.(361-363)CGA>CTA	p.R121L	MUM1_uc002lrz.1_Missense_Mutation_p.R120L|MUM1_uc010dsi.1_Missense_Mutation_p.R52L|MUM1_uc002lsb.1_Missense_Mutation_p.R52L|MUM1_uc002lsc.1_Missense_Mutation_p.R52L	NM_032853	NP_116242	Q2TAK8	MUM1_HUMAN	melanoma ubiquitous mutated protein	120					chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)								OREG0025088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.145833	147.810106	223.103764	91	533	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1311279	1311279	10379	19	G	T	T	37	37	MUM1	T	3	3
ZNF676	163223	broad.mit.edu	36	19	22155911	22155911	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:22155911A>G	uc002nqs.1	-	c.448T>C	c.(448-450)TTT>CTT	p.F150L		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	150					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)												0.357143	14.871442	15.122933	5	9	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22155911	22155911	18678	19	A	G	G	4	4	ZNF676	G	4	4
MRPL54	116541	broad.mit.edu	36	19	3716273	3716273	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3716273C>A	uc002lyq.2	+	c.228C>A	c.(226-228)AAC>AAA	p.N76K		NM_172251	NP_758455	Q6P161	RM54_HUMAN	mitochondrial ribosomal protein L54	76						mitochondrion|ribosome					0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)										0.203125	28.43664	33.678223	13	51	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3716273	3716273	10211	19	C	A	A	17	17	MRPL54	A	3	3
HAUS5	23354	broad.mit.edu	36	19	40801753	40801753	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40801753G>A	uc002oam.1	+	c.1141G>A	c.(1141-1143)GCC>ACC	p.A381T		NM_015302	NP_056117	O94927	HAUS5_HUMAN	hypothetical protein LOC23354	381	Potential.				cell division|centrosome organization|mitosis|spindle assembly	HAUS complex|microtubule|microtubule organizing center|spindle					0														1	11.948737	11.830916	3	0	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40801753	40801753	7251	19	G	A	A	42	42	HAUS5	A	2	2
AURKC	6795	broad.mit.edu	36	19	62435796	62435796	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:62435796C>T	uc002qoe.1	+	c.371C>T	c.(370-372)CCA>CTA	p.P124L	AURKC_uc002qoc.1_Missense_Mutation_p.P105L|AURKC_uc002qod.1_Missense_Mutation_p.P90L|AURKC_uc010etv.1_Missense_Mutation_p.P121L	NM_001015878	NP_003151	Q9UQB9	AURKC_HUMAN	aurora kinase C isoform 1	124	Protein kinase.				cell cycle|cytokinesis|protein phosphorylation	centrosome|nucleus	ATP binding|protein serine/threonine kinase activity			lung(4)|ovary(2)	6		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)						92				0.151163	22.21841	32.245889	13	73	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62435796	62435796	1245	19	C	T	T	21	21	AURKC	T	2	2
FSTL3	10272	broad.mit.edu	36	19	632446	632446	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:632446G>A	uc002lpk.1	+	c.619G>A	c.(619-621)GGC>AGC	p.G207S	FSTL3_uc010drt.1_Non-coding_Transcript	NM_005860	NP_005851	O95633	FSTL3_HUMAN	follistatin-like 3 glycoprotein precursor	207	Kazal-like 2.				hemopoietic progenitor cell differentiation|negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of osteoclast differentiation|ossification|positive regulation of cell-cell adhesion|positive regulation of transcription from RNA polymerase II promoter|regulation of gene-specific transcription from RNA polymerase II promoter|transcription, DNA-dependent	extracellular space|nucleus	activin binding|fibronectin binding				0		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)						26				0.4375	20.61865	20.673687	7	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	632446	632446	6329	19	G	A	A	39	39	FSTL3	A	1	1
ANGPTL7	10218	broad.mit.edu	36	1	11177569	11177569	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11177569A>G	uc001ase.1	+	c.943A>G	c.(943-945)AAG>GAG	p.K315E	MTOR_uc001asd.1_Intron	NM_021146	NP_066969	O43827	ANGL7_HUMAN	angiopoietin-like 7	315	Fibrinogen C-terminal.				response to oxidative stress|signal transduction	extracellular region	receptor binding				0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.39e-06)|COAD - Colon adenocarcinoma(227;0.000244)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0487)										0.181818	6.526824	9.67666	6	27	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11177569	11177569	622	1	A	G	G	13	13	ANGPTL7	G	4	4
EPHA2	1969	broad.mit.edu	36	1	16324400	16324401	+	Missense_Mutation	DNP	TC	CT	CT			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:16324400_16324401TC>CT	uc001aya.1	-	c.2827_2828GA>AG	c.(2827-2829)GAC>AGC	p.D943S		NM_004431	NP_004422	P29317	EPHA2_HUMAN	ephrin receptor EphA2	943	SAM.|Cytoplasmic (Potential).|Negatively regulates interaction with ARHGEF16.				activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|ephrin receptor signaling pathway|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|protein phosphorylation|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus	focal adhesion|integral to plasma membrane|leading edge membrane	ATP binding|ephrin receptor activity|protein binding			ovary(2)|central_nervous_system(2)|stomach(1)|lung(1)	6		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)					485				0.238095	7.862297	9.181976	5	16	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	16324400	16324401	5360	1	TC	CT	CT	58	58	EPHA2	CT	4	4
IGSF21	84966	broad.mit.edu	36	1	18564571	18564571	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:18564571G>A	uc001bau.1	+	c.808G>A	c.(808-810)GTG>ATG	p.V270M	IGSF21_uc001bav.1_Missense_Mutation_p.V91M	NM_032880	NP_116269	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	270						extracellular region				ovary(2)|large_intestine(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)										0.423077	34.922566	35.056322	11	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18564571	18564571	7900	1	G	A	A	40	40	IGSF21	A	1	1
UCHL5	51377	broad.mit.edu	36	1	191265356	191265357	+	Missense_Mutation	DNP	TA	CC	CC			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:191265356_191265357TA>CC	uc001gsm.1	-	c.300_301TA>GG	c.(298-303)TGTACC>TGGGCC	p.100_101CT>WA	UCHL5_uc001gsn.1_Non-coding_Transcript|UCHL5_uc001gso.1_Missense_Mutation_p.100_101CT>WA|UCHL5_uc001gsp.1_Missense_Mutation_p.100_101CT>WA|UCHL5_uc001gsq.1_Missense_Mutation_p.100_101CT>WA	NM_015984	NP_057068	Q9Y5K5	UCHL5_HUMAN	ubiquitin C-terminal hydrolase UCH37	100_101					protein deubiquitination|regulation of proteasomal protein catabolic process|ubiquitin-dependent protein catabolic process	cytosol|nucleus|proteasome complex	endopeptidase inhibitor activity|omega peptidase activity|proteasome binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1														0.5	8.624452	8.624452	3	3	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	191265356	191265357	17480	1	TA	CC	CC	57	57	UCHL5	CC	4	4
GABRD	2563	broad.mit.edu	36	1	1946861	1946861	+	Silent	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1946861C>T	uc001aip.2	+	c.294C>T	c.(292-294)AGC>AGT	p.S98S		NM_000815	NP_000806	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	98	Extracellular (Probable).					cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)										0.139241	16.279698	26.21004	11	68	CC		KEEP	---	---	---	---	capture			Silent	SNP	1946861	1946861	6420	1	C	T	T	25	25	GABRD	T	2	2
PPP1R12B	4660	broad.mit.edu	36	1	200684769	200684769	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:200684769C>T	uc001gxz.1	+	c.1697C>T	c.(1696-1698)ACA>ATA	p.T566I	PPP1R12B_uc001gya.1_Missense_Mutation_p.T566I	NM_032105	NP_115288	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)	566					regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)											0.73444	583.758113	595.729615	177	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	200684769	200684769	12790	1	C	T	T	17	17	PPP1R12B	T	2	2
OR2T33	391195	broad.mit.edu	36	1	246503464	246503464	+	Silent	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246503464G>A	uc001ied.1	-	c.276C>T	c.(274-276)CGC>CGT	p.R92R		NM_001004695	NP_001004695	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T,	92	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)											0.276873	241.244982	254.999552	85	222	GG		KEEP	---	---	---	---	capture			Silent	SNP	246503464	246503464	11430	1	G	A	A	38	38	OR2T33	A	1	1
OR14C36	127066	broad.mit.edu	36	1	246578835	246578835	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246578835G>C	uc001ieg.1	+	c.136G>C	c.(136-138)GTC>CTC	p.V46L		NM_001001918	NP_001001918	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C,	46	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2														0.34058	141.632651	144.708815	47	91	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	246578835	246578835	11352	1	G	C	C	40	40	OR14C36	C	3	3
TRIM62	55223	broad.mit.edu	36	1	33396558	33396558	+	Splice_Site_SNP	SNP	T	C	C			TCGA-12-1089-01	TCGA-12-1089-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:33396558T>C	uc001bxb.1	-	c.e4_splice_site				NM_018207	NP_060677			tripartite motif-containing 62							intracellular	zinc ion binding				0		Myeloproliferative disorder(586;0.0393)												0.25	6.79005	7.70202	4	12	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	33396558	33396558	17083	1	T	C	C	55	55	TRIM62	C	5	4
NFYC	4802	broad.mit.edu	36	1	41004862	41004862	+	Missense_Mutation	SNP	T	A	A			TCGA-12-1089-01	TCGA-12-1089-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:41004862T>A	uc001cge.2	+	c.728T>A	c.(727-729)CTG>CAG	p.L243Q	NFYC_uc001cfz.2_Missense_Mutation_p.L243Q|NFYC_uc009vwd.1_Missense_Mutation_p.L243Q|NFYC_uc001cfx.2_Missense_Mutation_p.L243Q|NFYC_uc001cfy.2_Missense_Mutation_p.L243Q|NFYC_uc001cgb.2_Missense_Mutation_p.L243Q|NFYC_uc001cgd.2_Missense_Mutation_p.L243Q	NM_014223	NP_055038	Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma isoform 2	243					protein folding|regulation of transcription from RNA polymerase II promoter	CCAAT-binding factor complex	protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|kidney(1)	3	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)											0.225806	9.601377	11.75267	7	24	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41004862	41004862	10791	1	T	A	A	55	55	NFYC	A	4	4
PTPRF	5792	broad.mit.edu	36	1	43830138	43830138	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:43830138C>G	uc001cjr.1	+	c.1600C>G	c.(1600-1602)CTG>GTG	p.L534V	PTPRF_uc001cjs.1_Missense_Mutation_p.L534V|PTPRF_uc001cju.1_Missense_Mutation_p.L105V|PTPRF_uc009vwt.1_Missense_Mutation_p.L105V|PTPRF_uc001cjv.1_Missense_Mutation_p.L105V	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	534	Extracellular (Potential).|Fibronectin type-III 3.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|lung(1)|kidney(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)												0.444444	7.882582	7.908704	4	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43830138	43830138	13258	1	C	G	G	28	28	PTPRF	G	3	3
IPO13	9670	broad.mit.edu	36	1	44188238	44188238	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:44188238G>C	uc001ckx.1	+	c.647G>C	c.(646-648)AGC>ACC	p.S216T		NM_014652	NP_055467	O94829	IPO13_HUMAN	importin 13	216	HEAT 2.				protein import into nucleus	cytoplasm|nucleus	protein binding|protein transporter activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)												0.6	7.022091	7.065148	3	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44188238	44188238	8095	1	G	C	C	34	34	IPO13	C	3	3
ZSWIM5	57643	broad.mit.edu	36	1	45278750	45278750	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:45278750C>T	uc001cnd.2	-	c.1657G>A	c.(1657-1659)GGT>AGT	p.G553S		NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM domain containing 5	553							zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)													0.690265	247.467378	251.109027	78	35	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45278750	45278750	18848	1	C	T	T	21	21	ZSWIM5	T	2	2
ZNF217	7764	broad.mit.edu	36	20	51626932	51626932	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:51626932G>A	uc002xwq.2	-	c.1778C>T	c.(1777-1779)TCA>TTA	p.S593L	ZNF217_uc010gij.1_Missense_Mutation_p.S585L	NM_006526	NP_006517	O75362	ZN217_HUMAN	zinc finger protein 217	593					regulation of transcription, DNA-dependent	histone deacetylase complex	promoter binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			skin(2)|large_intestine(1)|lung(1)|ovary(1)	5	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)						p.S593*(NCIH854-Tumor)	185				0.138298	71.738823	119.338163	52	324	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51626932	51626932	18363	20	G	A	A	45	45	ZNF217	A	2	2
GNAS	2778	broad.mit.edu	36	20	56861884	56861884	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:56861884G>A	uc002xzw.1	+	c.169G>A	c.(169-171)GAG>AAG	p.E57K	GNAS_uc002xzt.1_Intron|GNAS_uc002xzu.2_Intron|GNAS_uc010gjq.1_Intron|GNAS_uc002xzv.1_Non-coding_Transcript|GNAS-AS_uc002xzs.1_5'Flank	NM_080425	NP_536350	P63092	GNAS2_HUMAN	GNAS complex locus XLas	Error:Variant_position_missing_in_P63092_after_alignment					activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|large_intestine(5)|parathyroid(5)|kidney(5)|lung(2)|testis(1)|autonomic_ganglia(1)	279	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			Colon(117;935 1597 6045 8307 46442)				461	TSP Lung(22;0.16)			0.532258	103.575781	103.632042	33	29	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56861884	56861884	6779	20	G	A	A	37	37	GNAS	A	1	1
TRABD	80305	broad.mit.edu	36	22	48978126	48978126	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1089-01	TCGA-12-1089-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:48978126T>C	uc003bjv.1	+	c.653T>C	c.(652-654)TTC>TCC	p.F218S	TRABD_uc003bjq.1_Missense_Mutation_p.F218S|TRABD_uc003bjr.1_Missense_Mutation_p.F102S|TRABD_uc003bjs.1_Missense_Mutation_p.F218S|TRABD_uc003bjt.1_Missense_Mutation_p.F218S|TRABD_uc003bju.1_Missense_Mutation_p.F218S|TRABD_uc003bjw.1_Missense_Mutation_p.F218S	NM_025204	NP_079480	Q9H4I3	TRABD_HUMAN	TraB domain containing	218											0		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)										0.208333	6.354683	8.256326	5	19	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48978126	48978126	16979	22	T	C	C	62	62	TRABD	C	4	4
GREB1	9687	broad.mit.edu	36	2	11690483	11690483	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:11690483A>G	uc002rbk.1	+	c.4834A>G	c.(4834-4836)ATC>GTC	p.I1612V	GREB1_uc002rbp.1_Missense_Mutation_p.I610V	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	GREB1 protein isoform a	1612						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		Ovarian(39;850 945 2785 23371 33093)								0.206897	6.82301	9.14838	6	23	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11690483	11690483	7037	2	A	G	G	8	8	GREB1	G	4	4
CCDC93	54520	broad.mit.edu	36	2	118409624	118409624	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:118409624C>T	uc002tlj.1	-	c.1645G>A	c.(1645-1647)GCC>ACC	p.A549T		NM_019044	NP_061917	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	549										large_intestine(1)|ovary(1)	2														0.428571	62.877792	63.092997	21	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118409624	118409624	2997	2	C	T	T	26	26	CCDC93	T	2	2
GORASP2	26003	broad.mit.edu	36	2	171519501	171519501	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:171519501G>A	uc002ugk.1	+	c.662G>A	c.(661-663)GGT>GAT	p.G221D	GORASP2_uc002ugj.1_Missense_Mutation_p.G153D|GORASP2_uc002ugl.1_Missense_Mutation_p.G153D|GORASP2_uc002ugm.1_Missense_Mutation_p.G3D	NM_015530	NP_056345	Q9H8Y8	GORS2_HUMAN	golgi reassembly stacking protein 2	221						Golgi membrane				breast(1)|central_nervous_system(1)	2														0.361702	51.063981	51.854307	17	30	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	171519501	171519501	6849	2	G	A	A	44	44	GORASP2	A	2	2
TNS1	7145	broad.mit.edu	36	2	218459517	218459517	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:218459517A>G	uc002vgt.2	-	c.589T>C	c.(589-591)TTT>CTT	p.F197L	TNS1_uc010fvk.1_Missense_Mutation_p.F322L|TNS1_uc002vgr.2_Missense_Mutation_p.F197L|TNS1_uc002vgs.2_Missense_Mutation_p.F197L|TNS1_uc010fvi.1_5'Flank|TNS1_uc010fvj.1_Missense_Mutation_p.F265L|TNS1_uc002vgu.2_Missense_Mutation_p.F228L	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin	197	C2 tensin-type.					cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)								OREG0015188	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.15	24.561178	36.308228	15	85	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	218459517	218459517	16884	2	A	G	G	3	3	TNS1	G	4	4
KNG1	3827	broad.mit.edu	36	3	187918148	187918148	+	Silent	SNP	G	T	T			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:187918148G>T	uc010hyt.1	+	c.123G>T	c.(121-123)CTG>CTT	p.L41L	KNG1_uc003fqr.1_Silent_p.L41L	NM_001102416	NP_001095886	P01042	KNG1_HUMAN	kininogen 1 isoform 1	41	Cystatin 1.				blood coagulation, intrinsic pathway|diuresis|elevation of cytosolic calcium ion concentration|inflammatory response|natriuresis|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|smooth muscle contraction|vasodilation	extracellular space|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding				0	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)	Ouabain(DB01092)									0.32	13.978305	14.705251	8	17	GG		KEEP	---	---	---	---	capture			Silent	SNP	187918148	187918148	8741	3	G	T	T	45	45	KNG1	T	3	3
GADL1	339896	broad.mit.edu	36	3	30794691	30794691	+	Nonsense_Mutation	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:30794691C>T	uc003cep.1	-	c.824G>A	c.(823-825)TGG>TAG	p.W275*		NM_207359	NP_997242	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	459					carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)									0.142857	58.84771	86.3808	32	192	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	30794691	30794691	6436	3	C	T	T	21	21	GADL1	T	5	2
TRAK1	22906	broad.mit.edu	36	3	42209648	42209648	+	Nonsense_Mutation	SNP	G	T	T			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:42209648G>T	uc003cky.1	+	c.847G>T	c.(847-849)GAG>TAG	p.E283*	TRAK1_uc003ckz.2_Nonsense_Mutation_p.E209*|TRAK1_uc003cla.1_Nonsense_Mutation_p.E225*	NM_001042646	NP_001036111	Q9UPV9	TRAK1_HUMAN	OGT(O-Glc-NAc transferase)-interacting protein	283	Potential.|HAP1 N-terminal.				endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1						GBM(44;195 884 22595 31865 41850)								0.163265	6.955451	12.263605	8	41	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	42209648	42209648	16993	3	G	T	T	41	41	TRAK1	T	5	3
SLIT2	9353	broad.mit.edu	36	4	20200423	20200423	+	Silent	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:20200423C>T	uc003gpr.1	+	c.3147C>T	c.(3145-3147)CAC>CAT	p.H1049H	SLIT2_uc003gps.1_Silent_p.H1041H	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2	1049	EGF-like 4.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|initiation of Roundabout signal transduction|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|ovary(3)	7														0.732106	1215.816013	1239.591902	358	131	CC		KEEP	---	---	---	---	capture			Silent	SNP	20200423	20200423	15238	4	C	T	T	19	19	SLIT2	T	1	1
PF4	5196	broad.mit.edu	36	4	75065854	75065854	+	Silent	SNP	T	C	C			TCGA-12-1089-01	TCGA-12-1089-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:75065854T>C	uc003hhi.1	-	c.237A>G	c.(235-237)GGA>GGG	p.G79G		NM_002619	NP_002610	P02776	PLF4_HUMAN	platelet factor 4 (chemokine (C-X-C motif)	79					cytokine-mediated signaling pathway|immune response|leukocyte chemotaxis|negative regulation of angiogenesis|negative regulation of apoptosis|negative regulation of cytolysis|negative regulation of megakaryocyte differentiation|negative regulation of MHC class II biosynthetic process|platelet activation|platelet degranulation|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|positive regulation of macrophage differentiation|positive regulation of tumor necrosis factor production	extracellular space|platelet alpha granule lumen	chemokine activity|heparin binding				0	Breast(15;0.00136)		all cancers(17;0.0034)|Lung(101;0.196)		Drotrecogin alfa(DB00055)									0.130435	13.427061	22.597139	9	60	TT		KEEP	---	---	---	---	capture			Silent	SNP	75065854	75065854	12174	4	T	C	C	62	62	PF4	C	4	4
CCDC158	339965	broad.mit.edu	36	4	77524423	77524423	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:77524423G>A	uc003hkb.2	-	c.568C>T	c.(568-570)CGG>TGG	p.R190W	CCDC158_uc010ijg.1_Non-coding_Transcript|CCDC158_uc003hkd.2_Missense_Mutation_p.R190W	NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	hypothetical protein LOC339965	190										ovary(2)|pancreas(1)	3														0.387097	149.881861	151.263177	48	76	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77524423	77524423	2912	4	G	A	A	39	39	CCDC158	A	1	1
GRIA1	2890	broad.mit.edu	36	5	153006918	153006918	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:153006918G>A	uc003luy.2	+	c.458G>A	c.(457-459)CGG>CAG	p.R153Q	GRIA1_uc003lva.2_Missense_Mutation_p.R153Q|GRIA1_uc003luz.2_Missense_Mutation_p.R58Q|GRIA1_uc010jia.1_Missense_Mutation_p.R133Q	NM_000827	NP_000818	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	153	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(1)	5		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)									0.395722	231.81072	233.589951	74	113	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153006918	153006918	7045	5	G	A	A	39	39	GRIA1	A	1	1
AIM1	202	broad.mit.edu	36	6	107075209	107075209	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:107075209G>A	uc003prh.1	+	c.2209G>A	c.(2209-2211)GAA>AAA	p.E737K		NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1	737							sugar binding			breast(4)|ovary(2)|large_intestine(1)	7	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)						659				0.693989	821.946206	834.24855	254	112	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107075209	107075209	433	6	G	A	A	37	37	AIM1	A	1	1
C6orf174	387104	broad.mit.edu	36	6	127838982	127838982	+	Missense_Mutation	SNP	T	A	A			TCGA-12-1089-01	TCGA-12-1089-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:127838982T>A	uc003qbf.1	-	c.1882A>T	c.(1882-1884)AAC>TAC	p.N628Y	KIAA0408_uc003qbc.1_5'Flank|KIAA0408_uc003qbd.1_5'UTR|KIAA0408_uc003qbe.1_Non-coding_Transcript	NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104	628	Potential.					integral to membrane				breast(3)|ovary(2)	5				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)										0.205882	9.499638	12.238111	7	27	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127838982	127838982	2450	6	T	A	A	63	63	C6orf174	A	4	4
FAM120B	84498	broad.mit.edu	36	6	170469442	170469442	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:170469442G>A	uc003qxp.1	+	c.1039G>A	c.(1039-1041)GCT>ACT	p.A347T	FAM120B_uc003qxo.1_Missense_Mutation_p.A347T	NM_032448	NP_115824	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	347					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)										0.130952	118.234497	207.273978	88	584	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	170469442	170469442	5614	6	G	A	A	46	46	FAM120B	A	2	2
KIAA1949	170954	broad.mit.edu	36	6	30754993	30754993	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30754993C>G	uc003nrb.2	-	c.1764G>C	c.(1762-1764)GAG>GAC	p.E588D	KIAA1949_uc003nra.1_Missense_Mutation_p.E588D	NM_133471	NP_597728	Q6NYC8	PHTNS_HUMAN	phostensin	588						cytoplasm|cytoskeleton	actin binding				0														0.222222	6.903122	8.173951	4	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30754993	30754993	8574	6	C	G	G	28	28	KIAA1949	G	3	3
CDC5L	988	broad.mit.edu	36	6	44521463	44521463	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:44521463A>G	uc003oxl.1	+	c.2185A>G	c.(2185-2187)ATG>GTG	p.M729V		NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like	729	Interaction with PLRG1.				cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)	5	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)							515				0.38	311.679734	314.832522	95	155	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44521463	44521463	3211	6	A	G	G	16	16	CDC5L	G	4	4
TBX18	9096	broad.mit.edu	36	6	85503274	85503274	+	Missense_Mutation	SNP	A	C	C			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:85503274A>C	uc003pkl.1	-	c.1672T>G	c.(1672-1674)TCA>GCA	p.S558A	TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	558					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)						300				0.285714	6.588768	7.1699	4	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	85503274	85503274	16179	6	A	C	C	11	11	TBX18	C	4	4
RELN	5649	broad.mit.edu	36	7	103416974	103416975	+	Missense_Mutation	DNP	CC	TT	TT			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103416974_103416975CC>TT	uc003vca.1	-	c.65_66GG>AA	c.(64-66)AGG>AAA	p.R22K	RELN_uc010liz.1_Missense_Mutation_p.R22K	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	22					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.545455	40.5931	40.662188	18	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	103416974	103416975	13689	7	CC	TT	TT	22	22	RELN	TT	2	2
MGAM	8972	broad.mit.edu	36	7	141399167	141399167	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:141399167G>A	uc003vwy.1	+	c.3073G>A	c.(3073-3075)GTT>ATT	p.V1025I		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	1025	Lumenal (Potential).				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)									0.487768	1003.978854	1004.063432	319	335	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	141399167	141399167	9931	7	G	A	A	40	40	MGAM	A	1	1
EPHA1	2041	broad.mit.edu	36	7	142806878	142806878	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142806878C>T	uc003wcz.1	-	c.823G>A	c.(823-825)GAA>AAA	p.E275K		NM_005232	NP_005223	P21709	EPHA1_HUMAN	ephrin receptor EphA1	275	Extracellular (Potential).|Cys-rich.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(3)|lung(1)|breast(1)	5	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)								379				0.175439	22.415901	28.076958	10	47	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142806878	142806878	5358	7	C	T	T	31	31	EPHA1	T	1	1
HEATR2	54919	broad.mit.edu	36	7	786194	786194	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:786194G>A	uc010krz.1	+	c.2318G>A	c.(2317-2319)TGT>TAT	p.C773Y	HEATR2_uc003siz.2_Missense_Mutation_p.C641Y|HEATR2_uc003sjb.2_Missense_Mutation_p.C153Y|HEATR2_uc003sjc.2_Missense_Mutation_p.C198Y	NM_017802	NP_060272	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	773	HEAT 9.						protein binding				0		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)										0.234973	205.752009	229.284114	86	280	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	786194	786194	7311	7	G	A	A	48	48	HEATR2	A	2	2
UBR5	51366	broad.mit.edu	36	8	103368870	103368870	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:103368870C>T	uc003ykr.1	-	c.4924G>A	c.(4924-4926)GTT>ATT	p.V1642I	UBR5_uc003yks.1_Missense_Mutation_p.V1642I	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	1642					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(5)|ovary(3)|large_intestine(3)|kidney(1)|central_nervous_system(1)	13	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			Ovarian(131;96 1741 5634 7352 27489)				1024				0.285047	171.291838	180.163777	61	153	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	103368870	103368870	17463	8	C	T	T	19	19	UBR5	T	1	1
RIMS2	9699	broad.mit.edu	36	8	105070711	105070711	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:105070711G>A	uc003yls.2	+	c.2264G>A	c.(2263-2265)CGG>CAG	p.R755Q	RIMS2_uc003ylp.2_Missense_Mutation_p.R977Q|RIMS2_uc003ylw.2_Missense_Mutation_p.R769Q|RIMS2_uc003ylq.2_Missense_Mutation_p.R769Q|RIMS2_uc003ylr.2_Missense_Mutation_p.R816Q	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1039					intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)							728				0.28125	45.825958	48.577209	18	46	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105070711	105070711	13845	8	G	A	A	39	39	RIMS2	A	1	1
CHD7	55636	broad.mit.edu	36	8	61937403	61937403	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:61937403C>T	uc003xue.1	+	c.7925C>T	c.(7924-7926)ACA>ATA	p.T2642I		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2642					central nervous system development|chromatin assembly or disassembly|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	chromatin|nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|lung(1)|breast(1)|pancreas(1)	8		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)											0.233577	82.22981	91.130006	32	105	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61937403	61937403	3464	8	C	T	T	17	17	CHD7	T	2	2
PREX2	80243	broad.mit.edu	36	8	69127932	69127932	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:69127932A>G	uc003xxv.1	+	c.990A>G	c.(988-990)ATA>ATG	p.I330M	PREX2_uc003xxu.1_Missense_Mutation_p.I330M	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	330	PH.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			large_intestine(4)|pancreas(3)|lung(2)|skin(2)|ovary(1)|kidney(1)	13										1011				0.130973	110.922017	185.708048	74	491	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69127932	69127932	12920	8	A	G	G	14	14	PREX2	G	4	4
ATP6V0D2	245972	broad.mit.edu	36	8	87231612	87231612	+	Silent	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:87231612G>A	uc003ydp.1	+	c.795G>A	c.(793-795)AAG>AAA	p.K265K		NM_152565	NP_689778	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0	265					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	apical plasma membrane|endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex	hydrogen ion transmembrane transporter activity|protein binding				0														0.214128	221.62723	255.827944	97	356	GG		KEEP	---	---	---	---	capture			Silent	SNP	87231612	87231612	1193	8	G	A	A	33	33	ATP6V0D2	A	2	2
PALM2-AKAP2	445815	broad.mit.edu	36	9	111940324	111940324	+	Silent	SNP	T	A	A			TCGA-12-1089-01	TCGA-12-1089-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:111940324T>A	uc004bei.2	+	c.3375T>A	c.(3373-3375)GCT>GCA	p.A1125A	PALM2-AKAP2_uc004bek.2_Silent_p.A893A|PALM2-AKAP2_uc004bej.2_Silent_p.A893A|PALM2-AKAP2_uc004bel.1_Silent_p.A703A|AKAP2_uc004bem.1_Silent_p.A751A|PALM2-AKAP2_uc010mtw.1_Silent_p.A711A|PALM2-AKAP2_uc004ben.1_Silent_p.A662A	NM_001004065	NP_001004065	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 1	662							enzyme binding			ovary(3)|central_nervous_system(2)	5														0.25	10.401857	12.003195	7	21	TT		KEEP	---	---	---	---	capture			Silent	SNP	111940324	111940324	11826	9	T	A	A	55	55	PALM2-AKAP2	A	4	4
PTPRD	5789	broad.mit.edu	36	9	8507927	8507927	+	Silent	SNP	A	G	G			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:8507927A>G	uc003zkk.1	-	c.1464T>C	c.(1462-1464)TAT>TAC	p.Y488Y	PTPRD_uc003zkp.1_Silent_p.Y488Y|PTPRD_uc003zkq.1_Silent_p.Y488Y|PTPRD_uc003zkr.1_Silent_p.Y482Y|PTPRD_uc003zks.1_Silent_p.Y478Y|PTPRD_uc003zkl.1_Silent_p.Y488Y|PTPRD_uc003zkm.1_Silent_p.Y475Y|PTPRD_uc003zko.1_Silent_p.Y485Y|PTPRD_uc003zkn.1_Silent_p.Y488Y	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	488	Fibronectin type-III 2.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(10)|large_intestine(3)|ovary(2)|urinary_tract(1)	16		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)						1253	TSP Lung(15;0.13)			0.375	277.721748	281.119776	93	155	AA		KEEP	---	---	---	---	capture			Silent	SNP	8507927	8507927	13256	9	A	G	G	4	4	PTPRD	G	4	4
BEX4	56271	broad.mit.edu	36	X	102357874	102357874	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1089-01	TCGA-12-1089-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:102357874C>A	uc004ejv.2	+	c.137C>A	c.(136-138)CCT>CAT	p.P46H	BEX4_uc004ejw.2_Missense_Mutation_p.P46H|BEX4_uc010noj.1_Missense_Mutation_p.P46H	NM_001080425	NP_001121160	Q9NWD9	BEX4_HUMAN	BEX family member 4	46						cytoplasm|nucleus				skin(1)	1														0.333333	8.962877	9.335454	5	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102357874	102357874	1436	23	C	A	A	24	24	BEX4	A	3	3
ELF4	2000	broad.mit.edu	36	X	129029115	129029115	+	Silent	SNP	G	A	A			TCGA-12-1089-01	TCGA-12-1089-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:129029115G>A	uc004evd.2	-	c.1254C>T	c.(1252-1254)ACC>ACT	p.T418T	ELF4_uc004eve.2_Silent_p.T418T	NM_001421	NP_001412	Q99607	ELF4_HUMAN	E74-like factor 4	418					natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter	PML body	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity			ovary(1)	1										86				0.71875	151.167283	153.917651	46	18	GG		KEEP	---	---	---	---	capture			Silent	SNP	129029115	129029115	5247	23	G	A	A	43	43	ELF4	A	2	2
ZFX	7543	broad.mit.edu	36	X	24138705	24138705	+	Missense_Mutation	SNP	A	T	T			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:24138705A>T	uc004dbf.1	+	c.1709A>T	c.(1708-1710)CAT>CTT	p.H570L	ZFX_uc004dbe.1_3'UTR|ZFX_uc010nfz.1_Missense_Mutation_p.H226L	NM_003410	NP_003401	P17010	ZFX_HUMAN	zinc finger protein, X-linked	570	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|transcription regulator activity|zinc ion binding			ovary(2)	2						Esophageal Squamous(20;306 562 7346 32868 37983)								0.170732	6.393562	10.616267	7	34	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24138705	24138705	18251	23	A	T	T	8	8	ZFX	T	4	4
MAGEB1	4112	broad.mit.edu	36	X	30178572	30178572	+	Missense_Mutation	SNP	A	C	C			TCGA-12-1089-01	TCGA-12-1089-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:30178572A>C	uc004dcc.1	+	c.41A>C	c.(40-42)AAA>ACA	p.K14T	MAGEB1_uc004dcd.1_Missense_Mutation_p.K14T|MAGEB1_uc004dce.1_Missense_Mutation_p.K14T|MAGEB1_uc010ngh.1_Missense_Mutation_p.K14T	NM_002363	NP_803134	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	14											0														0.666667	11.600251	11.74739	4	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30178572	30178572	9553	23	A	C	C	1	1	MAGEB1	C	4	4
STARD8	9754	broad.mit.edu	36	X	67860891	67860891	+	Missense_Mutation	SNP	T	A	A			TCGA-12-1089-01	TCGA-12-1089-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:67860891T>A	uc004dxb.1	+	c.3214T>A	c.(3214-3216)TAC>AAC	p.Y1072N	STARD8_uc004dxa.1_Missense_Mutation_p.Y992N|STARD8_uc004dxc.2_Missense_Mutation_p.Y992N	NM_014725	NP_055540	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain	992	START.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion	GTPase activator activity			breast(3)|ovary(2)|pancreas(1)	6														0.909091	135.145787	142.055634	40	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67860891	67860891	15782	23	T	A	A	57	57	STARD8	A	4	4
AMPD3	272	broad.mit.edu	36	11	10483843	10483844	+	Frame_Shift_Ins	INS	-	G	G			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:10483843_10483844insG	uc001min.1	+	c.2167_2168insG	c.(2167-2169)TTTfs	p.F723fs	AMPD3_uc009yfw.1_Non-coding_Transcript|AMPD3_uc001mio.1_Frame_Shift_Ins_p.F714fs|AMPD3_uc001mip.1_Frame_Shift_Ins_p.F721fs|AMPD3_uc009yfz.1_Non-coding_Transcript	NM_000480	NP_001020560	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3 isoform 1A	714					AMP catabolic process|purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			large_intestine(1)|ovary(1)	2				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)										0.30			50	116				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	10483843	10483844	590	11	-	G	G	60	60	AMPD3	G	5	5
MUC5B	727897	broad.mit.edu	36	11	1217302	1217303	+	Frame_Shift_Ins	INS	-	G	G			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1217302_1217303insG	uc001ltb.2	+	c.3522_3523insG	c.(3520-3525)TGCGGGfs	p.C1174fs	MUC5B_uc009yct.1_3'UTR	NM_002458	NP_002449	Q9HC84	MUC5B_HUMAN	mucin 5, subtype B, tracheobronchial	1171_1172	Cys-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	1217302	1217303	10373	11	-	G	G	27	27	MUC5B	G	5	5
MRPL17	63875	broad.mit.edu	36	11	6660923	6660931	+	Splice_Site_Del	DEL	TCCTCACCT	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6660923_6660931delTCCTCACCT	uc001men.2	-	c.e1_splice_site				NM_022061	NP_071344			mitochondrial ribosomal protein L17						translation	ribosome	protein domain specific binding|structural constituent of ribosome				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)										0.32			6	13				---	---	---	---	capture_indel			Splice_Site_Del	DEL	6660923	6660931	10175	11	TCCTCACCT	-	-	54	54	MRPL17	-	5	5
GOLGA3	2802	broad.mit.edu	36	12	131893915	131893915	+	Frame_Shift_Del	DEL	T	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:131893915_131893915delT	uc001ukz.1	-	c.1211_1211delA	c.(1210-1212)CAGfs	p.Q404fs	GOLGA3_uc009zyx.1_Non-coding_Transcript|GOLGA3_uc001ula.1_Frame_Shift_Del_p.Q404fs|GOLGA3_uc001ulb.2_Frame_Shift_Del_p.Q404fs	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	404	Potential.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)										0.47			8	9				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	131893915	131893915	6823	12	T	-	-	55	55	GOLGA3	-	5	5
EDNRB	1910	broad.mit.edu	36	13	77390228	77390229	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:77390228_77390229delTT	uc001vkp.1	-	c.730_731delAA	c.(730-732)AAGfs	p.K244fs	EDNRB_uc001vko.2_Frame_Shift_Del_p.K161fs|EDNRB_uc010aez.1_Frame_Shift_Del_p.K161fs|EDNRB_uc001vkq.1_Frame_Shift_Del_p.K161fs|EDNRB_uc010afa.1_Frame_Shift_Del_p.K161fs	NM_001122659	NP_001116131	P24530	EDNRB_HUMAN	endothelin receptor type B isoform 1 precursor	161	Helical; Name=2; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of neuron maturation|vein smooth muscle contraction	integral to plasma membrane	endothelin-B receptor activity|peptide hormone binding				0		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)					117				0.37			91	155				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	77390228	77390229	5107	13	TT	-	-	56	56	EDNRB	-	5	5
HYDIN	54768	broad.mit.edu	36	16	69399405	69399406	+	Frame_Shift_Del	DEL	CC	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:69399405_69399406delCC	uc002ezr.1	-	c.14941_14942delGG	c.(14941-14943)GGCfs	p.G4981fs	HYDIN_uc010cfy.1_Non-coding_Transcript	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	4982										ovary(1)	1		Ovarian(137;0.0654)												0.41			22	32				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	69399405	69399406	7767	16	CC	-	-	26	26	HYDIN	-	5	5
MTMR4	9110	broad.mit.edu	36	17	53945275	53945277	+	In_Frame_Del	DEL	CTC	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:53945275_53945277delCTC	uc002iwj.1	-	c.28_30delGAG	c.(28-30)GAGdel	p.E10del	MTMR4_uc010dcx.1_In_Frame_Del_p.E24del	NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	10						cytoplasm|membrane	protein tyrosine phosphatase activity|zinc ion binding			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.41			67	95				---	---	---	---	capture_indel			In_Frame_Del	DEL	53945275	53945277	10339	17	CTC	-	-	20	20	MTMR4	-	5	5
KCTD3	51133	broad.mit.edu	36	1	213860378	213860382	+	Frame_Shift_Del	DEL	AAAAT	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:213860378_213860382delAAAAT	uc001hks.1	+	c.2243_2247delAAAAT	c.(2242-2247)GAAAATfs	p.E748fs	KCTD3_uc001hkt.1_Frame_Shift_Del_p.E746fs|KCTD3_uc009xdn.1_Frame_Shift_Del_p.E472fs	NM_016121	NP_057205	Q9Y597	KCTD3_HUMAN	potassium channel tetramerisation domain	748_749						voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			ovary(2)	2				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)										0.30			30	69				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	213860378	213860382	8416	1	AAAAT	-	-	9	9	KCTD3	-	5	5
NEURL2	140825	broad.mit.edu	36	20	43952611	43952614	+	Frame_Shift_Del	DEL	CGAG	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:43952611_43952614delCGAG	uc002xqg.1	-	c.424_427delCTCG	c.(424-429)CTCGTGfs	p.L142fs	C20orf165_uc002xqf.1_5'Flank|CTSA_uc002xqh.1_5'Flank|CTSA_uc002xqj.2_5'Flank|CTSA_uc002xqi.1_5'Flank|CTSA_uc002xqk.2_5'Flank	NM_080749	NP_542787	Q9BR09	NEUL2_HUMAN	neuralized-like protein 2	142_143	NHR.				intracellular signal transduction						0		Myeloproliferative disorder(115;0.0122)												0.39			7	11				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	43952611	43952614	10746	20	CGAG	-	-	19	19	NEURL2	-	5	5
ZC3H7B	23264	broad.mit.edu	36	22	40065873	40065882	+	Frame_Shift_Del	DEL	CTCCATCCCT	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:40065873_40065882delCTCCATCCCT	uc003azw.1	+	c.924_933delCTCCATCCCT	c.(922-933)GGCTCCATCCCTfs	p.G308fs	ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	324_327					interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1														0.74			253	91				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	40065873	40065882	18161	22	CTCCATCCCT	-	-	28	28	ZC3H7B	-	5	5
SPEG	10290	broad.mit.edu	36	2	220040177	220040180	+	Frame_Shift_Del	DEL	CCTG	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220040177_220040180delCCTG	uc010fwg.1	+	c.2919_2922delCCTG	c.(2917-2922)CCCCTGfs	p.P973fs		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	973_974	Ig-like 4.				muscle organ development|negative regulation of cell proliferation|protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity			ovary(4)|stomach(2)|central_nervous_system(1)	7		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)						482		OREG0004000	type=REGULATORY REGION|Gene=APEG1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.40			4	6				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	220040177	220040180	15548	2	CCTG	-	-	22	22	SPEG	-	5	5
SLC23A1	9963	broad.mit.edu	36	5	138741079	138741080	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:138741079_138741080delAG	uc003leg.1	-	c.1471_1472delCT	c.(1471-1473)CTTfs	p.L491fs	SLC23A1_uc003leh.1_Frame_Shift_Del_p.L487fs	NM_152685	NP_689898	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (nucleobase	487					brain development|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|response to toxin|transepithelial L-ascorbic acid transport|water-soluble vitamin metabolic process	apical plasma membrane|cytoplasm|integral to plasma membrane|intracellular organelle|membrane fraction	dehydroascorbic acid transporter activity|L-ascorbate:sodium symporter activity|nucleobase transmembrane transporter activity|protein binding|sodium-dependent L-ascorbate transmembrane transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)									0.51			42	40				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	138741079	138741080	14959	5	AG	-	-	3	3	SLC23A1	-	5	5
C6orf118	168090	broad.mit.edu	36	6	165631568	165631569	+	Frame_Shift_Ins	INS	-	TA	TA			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:165631568_165631569insTA	uc003qum.2	-	c.948_949insTA	c.(946-951)GCTCAAfs	p.A316fs		NM_144980	NP_659417	Q5T5N4	CF118_HUMAN	hypothetical protein LOC168090	316_317											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)										0.59			36	25				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	165631568	165631569	2425	6	-	TA	TA	45	45	C6orf118	TA	5	5
C9orf50	375759	broad.mit.edu	36	9	131415249	131415263	+	In_Frame_Del	DEL	GCTTCGCGGCCTCTG	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:131415249_131415263delGCTTCGCGGCCTCTG	uc004byc.2	-	c.1132_1146delCAGAGGCCGCGAAGC	c.(1132-1146)CAGAGGCCGCGAAGCdel	p.QRPRS378del	C9orf50_uc004byb.2_Non-coding_Transcript	NM_199350	NP_955382	Q5SZB4	CI050_HUMAN	hypothetical protein LOC375759	378_382										ovary(1)|central_nervous_system(1)	2		Ovarian(14;0.00556)												0.96			505	19				---	---	---	---	capture_indel			In_Frame_Del	DEL	131415249	131415263	2602	9	GCTTCGCGGCCTCTG	-	-	46	46	C9orf50	-	5	5
RGAG1	57529	broad.mit.edu	36	X	109583253	109583255	+	In_Frame_Del	DEL	TCA	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:109583253_109583255delTCA	uc004eor.1	+	c.2752_2754delTCA	c.(2752-2754)TCAdel	p.S918del		NM_020769	NP_065820	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	918										lung(2)|ovary(1)	3														0.32			15	32				---	---	---	---	capture_indel			In_Frame_Del	DEL	109583253	109583255	13747	23	TCA	-	-	54	54	RGAG1	-	5	5
KLHL13	90293	broad.mit.edu	36	X	116917351	116917354	+	Frame_Shift_Del	DEL	TGAG	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:116917351_116917354delTGAG	uc004eql.1	-	c.1513_1516delCTCA	c.(1513-1518)CTCATGfs	p.L505fs	KLHL13_uc004eqk.1_Frame_Shift_Del_p.L454fs|KLHL13_uc004eqm.1_Frame_Shift_Del_p.L454fs	NM_033495	NP_277030	Q9P2N7	KLH13_HUMAN	kelch-like 13	505_506	Kelch 4.				cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex				kidney(1)	1														0.35			24	44				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	116917351	116917354	8681	23	TGAG	-	-	51	51	KLHL13	-	5	5
MAGEC1	9947	broad.mit.edu	36	X	140822031	140822031	+	Frame_Shift_Del	DEL	C	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140822031_140822031delC	uc004fbt.1	+	c.1175_1175delC	c.(1174-1176)TCCfs	p.S392fs	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	392							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.49			25	26				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	140822031	140822031	9561	23	C	-	-	30	30	MAGEC1	-	5	5
MXRA5	25878	broad.mit.edu	36	X	3239260	3239261	+	Frame_Shift_Del	DEL	AT	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3239260_3239261delAT	uc004crg.2	-	c.6983_6984delAT	c.(6982-6984)AATfs	p.N2328fs		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican	2328	Ig-like C2-type 7.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.36			37	66				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	3239260	3239261	10397	23	AT	-	-	12	12	MXRA5	-	5	5
WDR45	11152	broad.mit.edu	36	X	48820304	48820304	+	Frame_Shift_Del	DEL	G	-	-			TCGA-12-1089-01	TCGA-12-1089-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:48820304_48820304delG	uc004dmo.1	-	c.638_638delC	c.(637-639)GCAfs	p.A213fs	PRAF2_uc004dmi.1_5'Flank|WDR45_uc004dmj.1_Frame_Shift_Del_p.A151fs|WDR45_uc004dmk.1_Frame_Shift_Del_p.A190fs|WDR45_uc004dml.1_Frame_Shift_Del_p.A191fs|WDR45_uc004dmm.1_Frame_Shift_Del_p.A155fs|WDR45_uc010nim.1_Frame_Shift_Del_p.A190fs|WDR45_uc004dmn.1_Frame_Shift_Del_p.A81fs|WDR45_uc004dmp.1_Frame_Shift_Del_p.A191fs	NM_007075	NP_009006	Q9Y484	WIPI4_HUMAN	WD repeat domain 45 isoform 1	190	WD 2.				autophagy|response to starvation	organelle membrane	phosphatidylinositol-3,5-bisphosphate binding			ovary(1)	1														0.47			9	10				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	48820304	48820304	17870	23	G	-	-	46	46	WDR45	-	5	5
