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
MAP3K11	4296	broad.mit.edu	36	11	65123577	65123577	+	Silent	SNP	C	A	A			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65123577C>A	uc001oew.1	-	c.2070G>T	c.(2068-2070)CCG>CCT	p.P690P	MAP3K11_uc001oev.1_Silent_p.P106P|MAP3K11_uc001oex.1_Silent_p.P197P	NM_002419	NP_002410	Q16584	M3K11_HUMAN	mitogen-activated protein kinase kinase kinase	690	Pro-rich.				activation of JUN kinase activity|cell proliferation|G1 phase of mitotic cell cycle|microtubule-based process|protein autophosphorylation|protein oligomerization	centrosome|microtubule	ATP binding|JUN kinase kinase kinase activity|protein homodimerization activity			central_nervous_system(1)	1										130				0.146067	22.978434	33.644607	13	76	CC		KEEP	---	---	---	---	capture			Silent	SNP	65123577	65123577	9628	11	C	A	A	27	27	MAP3K11	A	3	3
BAZ2A	11176	broad.mit.edu	36	12	55281603	55281603	+	Silent	SNP	G	T	T			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55281603G>T	uc001slq.1	-	c.4071C>A	c.(4069-4071)TCC>TCA	p.S1357S	BAZ2A_uc001slo.1_Silent_p.S185S|BAZ2A_uc009zov.1_Silent_p.S327S|BAZ2A_uc009zow.1_Silent_p.S1325S|BAZ2A_uc001slp.1_Silent_p.S1355S	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1357	Pro-rich.				chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|transcription regulator activity|zinc ion binding				0														0.195122	9.163917	12.74725	8	33	GG		KEEP	---	---	---	---	capture			Silent	SNP	55281603	55281603	1352	12	G	T	T	47	47	BAZ2A	T	3	3
FGD6	55785	broad.mit.edu	36	12	94127228	94127228	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:94127228C>T	uc001tdp.2	-	c.1963G>A	c.(1963-1965)GGA>AGA	p.G655R	FGD6_uc009zsx.1_Intron	NM_018351	NP_060821	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	655					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3														0.371951	348.377308	353.096931	122	206	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94127228	94127228	6074	12	C	T	T	23	23	FGD6	T	1	1
FMN1	342184	broad.mit.edu	36	15	31146934	31146934	+	Silent	SNP	A	G	G			TCGA-28-5214-01	TCGA-28-5214-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:31146934A>G	uc001zhf.2	-	c.444T>C	c.(442-444)TCT>TCC	p.S148S	FMN1_uc001zhg.2_Silent_p.S148S	NM_001103184	NP_001096654	C9JFW6	C9JFW6_HUMAN	formin 1	Error:Variant_position_missing_in_C9JFW6_after_alignment										ovary(1)	1		all_lung(180;1.14e-07)												0.292208	125.59982	131.56419	45	109	AA		KEEP	---	---	---	---	capture		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Silent	SNP	31146934	31146934	6191	15	A	G	G	7	7	FMN1	G	4	4
VPS13C	54832	broad.mit.edu	36	15	59969824	59969824	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:59969824C>T	uc002agz.1	-	c.9173G>A	c.(9172-9174)CGC>CAC	p.R3058H	VPS13C_uc002aha.1_Missense_Mutation_p.R3015H|VPS13C_uc002ahb.1_Missense_Mutation_p.R3058H|VPS13C_uc002ahc.1_Missense_Mutation_p.R3015H	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	3058					protein localization					ovary(2)	2														0.264463	76.442933	82.514643	32	89	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59969824	59969824	17758	15	C	T	T	27	27	VPS13C	T	1	1
NR2F2	7026	broad.mit.edu	36	15	94678743	94678743	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:94678743C>T	uc002btq.1	+	c.877C>T	c.(877-879)CGG>TGG	p.R293W	NR2F2_uc002btp.1_Missense_Mutation_p.R160W	NM_021005	NP_066285	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	293	Interaction with ZFPM2 (By similarity).|Ligand-binding (By similarity).				lipid metabolic process|negative regulation of cyclin-dependent protein kinase activity|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|negative regulation of gene-specific transcription|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription|regulation of transcription involved in lymphatic endothelial cell fate commitment	nucleus	ligand-regulated transcription factor activity|promoter binding|protein homodimerization activity|retinoic acid binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription activator activity|transcription corepressor activity|zinc ion binding			ovary(1)|breast(1)	2	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)													0.378378	73.766177	74.731777	28	46	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(32;0.0856)		Missense_Mutation	SNP	94678743	94678743	11033	15	C	T	T	19	19	NR2F2	T	1	1
FOXN1	8456	broad.mit.edu	36	17	23888455	23888455	+	Silent	SNP	A	C	C			TCGA-28-5214-01	TCGA-28-5214-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:23888455A>C	uc010crm.1	+	c.1821A>C	c.(1819-1821)GCA>GCC	p.A607A	FOXN1_uc002hbj.1_Silent_p.A607A	NM_003593	NP_003584	O15353	FOXN1_HUMAN	forkhead box N1	607					defense response|embryo development|epithelial cell proliferation|keratinocyte differentiation|negative regulation of gene-specific transcription from RNA polymerase II promoter|organ morphogenesis|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|thymus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	Lung NSC(42;0.00431)													0.324324	76.380787	78.40431	24	50	AA		KEEP	---	---	---	---	capture			Silent	SNP	23888455	23888455	6265	17	A	C	C	6	6	FOXN1	C	4	4
GJC1	10052	broad.mit.edu	36	17	40237960	40237960	+	Missense_Mutation	SNP	A	G	G			TCGA-28-5214-01	TCGA-28-5214-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:40237960A>G	uc002ihj.1	-	c.752T>C	c.(751-753)CTT>CCT	p.L251P	GJC1_uc002ihk.1_Missense_Mutation_p.L251P|GJC1_uc002ihl.1_Missense_Mutation_p.L251P|GJC1_uc010czx.1_Missense_Mutation_p.L251P|GJC1_uc010czy.1_Missense_Mutation_p.L112P|GJC1_uc010czz.1_Missense_Mutation_p.L251P	NM_005497	NP_005488	P36383	CXG1_HUMAN	connexin 45	251	Cytoplasmic (Potential).				cellular membrane organization|gap junction assembly|muscle contraction|synaptic transmission|transport	connexon complex|integral to membrane					0		Prostate(33;0.0959)												0.238663	297.100393	323.222673	100	319	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40237960	40237960	6682	17	A	G	G	3	3	GJC1	G	4	4
MC4R	4160	broad.mit.edu	36	18	56190543	56190543	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:56190543C>T	uc002lie.1	-	c.20G>A	c.(19-21)CGT>CAT	p.R7H		NM_005912	NP_005903	P32245	MC4R_HUMAN	melanocortin 4 receptor	7	Extracellular (Potential).				feeding behavior|G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of bone resorption|positive regulation of cAMP biosynthetic process	integral to membrane|plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|ubiquitin protein ligase binding				0		Colorectal(73;0.0946)												0.351852	102.116052	104.207287	38	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56190543	56190543	9755	18	C	T	T	19	19	MC4R	T	1	1
ZNF564	163050	broad.mit.edu	36	19	12499084	12499084	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12499084G>A	uc002mty.1	-	c.838C>T	c.(838-840)CCC>TCC	p.P280S	ZNF709_uc002mtx.2_Intron	NM_144976	NP_659413	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	280					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.152838	59.595686	85.988789	35	194	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12499084	12499084	18590	19	G	A	A	44	44	ZNF564	A	2	2
EML2	24139	broad.mit.edu	36	19	50829560	50829560	+	Nonsense_Mutation	SNP	G	T	T			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50829560G>T	uc002pcq.1	-	c.792C>A	c.(790-792)TAC>TAA	p.Y264*	EML2_uc002pcn.1_Nonsense_Mutation_p.Y63*|EML2_uc002pco.1_Non-coding_Transcript|EML2_uc002pcp.1_Intron|EML2_uc010ekj.1_Nonsense_Mutation_p.Y63*|EML2_uc010ekk.1_5'Flank	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like	63					sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)												0.28	6.746629	7.893221	7	18	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)	Nonsense_Mutation	SNP	50829560	50829560	5289	19	G	T	T	44	44	EML2	T	5	3
SYNGR4	23546	broad.mit.edu	36	19	53570778	53570778	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:53570778C>T	uc002piz.1	+	c.428C>T	c.(427-429)GCC>GTC	p.A143V		NM_012451	NP_036583	O95473	SNG4_HUMAN	synaptogyrin 4	143	MARVEL.					integral to membrane					0		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)												0.210526	107.949085	127.116167	52	195	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)	Missense_Mutation	SNP	53570778	53570778	15972	19	C	T	T	26	26	SYNGR4	T	2	2
LILRA1	11024	broad.mit.edu	36	19	59798054	59798054	+	Silent	SNP	T	C	C			TCGA-28-5214-01	TCGA-28-5214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59798054T>C	uc002qgh.1	+	c.183T>C	c.(181-183)TAT>TAC	p.Y61Y		NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,	61	Ig-like C2-type 1.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			ovary(1)	1														0.278523	253.426947	266.556457	83	215	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0348)	Silent	SNP	59798054	59798054	9110	19	T	C	C	49	49	LILRA1	C	4	4
CPSF3L	54973	broad.mit.edu	36	1	1246239	1246239	+	Silent	SNP	G	A	A			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1246239G>A	uc001aee.1	-	c.126C>T	c.(124-126)GAC>GAT	p.D42D	CPSF3L_uc001aef.1_Silent_p.D48D|CPSF3L_uc009vjz.1_Silent_p.D42D|CPSF3L_uc001aeg.1_De_novo_Start_OutOfFrame|CPSF3L_uc001aeh.1_Silent_p.D42D|CPSF3L_uc001aei.1_Intron|CPSF3L_uc001aej.1_Missense_Mutation_p.T15I|CPSF3L_uc001aek.1_Intron|CPSF3L_uc001aem.1_Silent_p.D42D|CPSF3L_uc001ael.1_De_novo_Start_InFrame|CPSF3L_uc001aen.1_Silent_p.D42D	NM_017871	NP_060341	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor	42						Golgi apparatus|nucleus	hydrolase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)												0.338889	164.557073	168.622825	61	119	GG		KEEP	---	---	---	---	capture		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)	Silent	SNP	1246239	1246239	3965	1	G	A	A	40	40	CPSF3L	A	1	1
LOR	4014	broad.mit.edu	36	1	151500124	151500124	+	Silent	SNP	T	C	C			TCGA-28-5214-01	TCGA-28-5214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:151500124T>C	uc001fbm.1	+	c.75T>C	c.(73-75)GGT>GGC	p.G25G	LOR_uc009wof.1_Silent_p.G25G	NM_000427	NP_000418	P23490	LORI_HUMAN	loricrin	25					keratinization|peptide cross-linking	cornified envelope|cytoplasm|insoluble fraction|nucleoplasm	protein binding, bridging|structural constituent of cytoskeleton				0	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)													0.151515	7.169577	10.995643	5	28	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.171)		Silent	SNP	151500124	151500124	9269	1	T	C	C	59	59	LOR	C	4	4
USH2A	7399	broad.mit.edu	36	1	214128586	214128586	+	Silent	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:214128586C>T	uc001hku.1	-	c.8028G>A	c.(8026-8028)CCG>CCA	p.P2676P		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2676	Extracellular (Potential).|Fibronectin type-III 13.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22														0.441176	217.69643	218.209711	75	95	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	Silent	SNP	214128586	214128586	17598	1	C	T	T	31	31	USH2A	T	1	1
MACF1	23499	broad.mit.edu	36	1	39606492	39606492	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:39606492C>T	uc009vvr.1	+	c.8177C>T	c.(8176-8178)GCG>GTG	p.A2726V	MACF1_uc009vvo.1_Missense_Mutation_p.A2224V|MACF1_uc009vvp.1_Missense_Mutation_p.A2224V|MACF1_uc001cda.1_Missense_Mutation_p.A2132V|MACF1_uc001cdb.1_Missense_Mutation_p.A1311V|MACF1_uc001cdc.1_Missense_Mutation_p.A1311V|MACF1_uc009vvs.1_Missense_Mutation_p.A2726V	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	2224	Potential.				cell cycle arrest	cytoplasm|cytoskeleton	actin filament binding|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)	14	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)												0.345029	154.165806	157.795652	59	112	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		Missense_Mutation	SNP	39606492	39606492	9521	1	C	T	T	27	27	MACF1	T	1	1
NPHP4	261734	broad.mit.edu	36	1	5859941	5859941	+	Silent	SNP	T	C	C			TCGA-28-5214-01	TCGA-28-5214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:5859941T>C	uc001alq.1	-	c.2616A>G	c.(2614-2616)AAA>AAG	p.K872K	NPHP4_uc001als.1_Non-coding_Transcript|NPHP4_uc009vlt.1_Non-coding_Transcript|NPHP4_uc001alt.1_Non-coding_Transcript	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	872					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cilium|membrane|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)												0.366667	35.309373	35.781109	11	19	TT		KEEP	---	---	---	---	capture		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)	Silent	SNP	5859941	5859941	10985	1	T	C	C	60	60	NPHP4	C	4	4
EPHX4	253152	broad.mit.edu	36	1	92301252	92301252	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:92301252G>A	uc001don.1	+	c.910G>A	c.(910-912)GGA>AGA	p.G304R		NM_173567	NP_775838	Q8IUS5	EPHX4_HUMAN	abhydrolase domain containing 7	304						integral to membrane	hydrolase activity			central_nervous_system(1)	1						GBM(140;473 1857 5172 22066 49719)								0.320635	298.158722	307.163972	101	214	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92301252	92301252	5375	1	G	A	A	43	43	EPHX4	A	2	2
PCDP1	200373	broad.mit.edu	36	2	120101755	120101755	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:120101755C>T	uc002tmb.1	+	c.715C>T	c.(715-717)CGG>TGG	p.R239W		NM_001029996	NP_001025167	Q4G0U5	PCDP1_HUMAN	primary ciliary dyskinesia protein 1	525						cilium	calmodulin binding				0	Colorectal(110;0.196)													0.356287	340.73965	346.812906	119	215	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	120101755	120101755	11992	2	C	T	T	23	23	PCDP1	T	1	1
GPR128	84873	broad.mit.edu	36	3	101832263	101832263	+	Missense_Mutation	SNP	A	G	G			TCGA-28-5214-01	TCGA-28-5214-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:101832263A>G	uc003duc.1	+	c.254A>G	c.(253-255)TAT>TGT	p.Y85C		NM_032787	NP_116176	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	85	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3						Pancreas(87;185 1975 7223 18722)								0.443396	172.820591	173.11494	47	59	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101832263	101832263	6915	3	A	G	G	16	16	GPR128	G	4	4
SCN11A	11280	broad.mit.edu	36	3	38867228	38867228	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:38867228C>T	uc010hhm.1	-	c.4075G>A	c.(4075-4077)GTG>ATG	p.V1359M	SCN11A_uc003cis.1_Missense_Mutation_p.V24M	NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	1359					response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Cocaine(DB00907)									0.312925	121.196831	125.776335	46	101	CC		KEEP	---	---	---	---	capture		Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Missense_Mutation	SNP	38867228	38867228	14395	3	C	T	T	19	19	SCN11A	T	1	1
FSTL5	56884	broad.mit.edu	36	4	162797005	162797005	+	Silent	SNP	T	C	C			TCGA-28-5214-01	TCGA-28-5214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:162797005T>C	uc003iqh.1	-	c.819A>G	c.(817-819)CAA>CAG	p.Q273Q	FSTL5_uc003iqi.1_Silent_p.Q272Q|FSTL5_uc010iqv.1_Silent_p.Q272Q	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	273	Ig-like 1.					extracellular region	calcium ion binding			ovary(2)|pancreas(2)|large_intestine(1)|central_nervous_system(1)	6	all_hematologic(180;0.24)													0.267176	108.067788	114.478923	35	96	TT		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(41;0.179)	Silent	SNP	162797005	162797005	6331	4	T	C	C	56	56	FSTL5	C	4	4
CORIN	10699	broad.mit.edu	36	4	47374715	47374715	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:47374715C>T	uc003gxm.1	-	c.1246G>A	c.(1246-1248)GTC>ATC	p.V416I		NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin	416	Extracellular (Potential).				peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)	1														0.35514	103.612176	105.593834	38	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47374715	47374715	3890	4	C	T	T	19	19	CORIN	T	1	1
UGT2B15	7366	broad.mit.edu	36	4	69218670	69218670	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:69218670C>A	uc003heb.1	-	c.262G>T	c.(262-264)GAT>TAT	p.D88Y		NM_001076	NP_001067	P54855	UDB15_HUMAN	UDP glycosyltransferase 2 family, polypeptide	88					steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0														0.735294	307.941873	314.73904	100	36	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69218670	69218670	17516	4	C	A	A	32	32	UGT2B15	A	3	3
PCDHGA9	56107	broad.mit.edu	36	5	140764099	140764099	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140764099G>A	uc003lkh.1	+	c.1396G>A	c.(1396-1398)GCC>ACC	p.A466T	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkg.1_Missense_Mutation_p.A466T	NM_018921	NP_061744	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9 isoform 1	466	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.314286	84.732526	87.957553	33	72	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140764099	140764099	11981	5	G	A	A	38	38	PCDHGA9	A	1	1
RNF130	55819	broad.mit.edu	36	5	179326435	179326435	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:179326435C>T	uc003mll.1	-	c.1127G>A	c.(1126-1128)GGA>GAA	p.G376E	RNF130_uc003mlm.1_Missense_Mutation_p.G376E	NM_018434	NP_060904	Q86XS8	GOLI_HUMAN	ring finger protein 130	376	Cytoplasmic (Potential).				apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)				GBM(24;432 554 38471 39699 51728)				168				0.337662	71.02098	72.818207	26	51	CC		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Missense_Mutation	SNP	179326435	179326435	13915	5	C	T	T	30	30	RNF130	T	2	2
CDH9	1007	broad.mit.edu	36	5	27023970	27023970	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:27023970C>G	uc003jgs.1	-	c.228G>C	c.(226-228)AAG>AAC	p.K76N	CDH9_uc010iug.1_Missense_Mutation_p.K76N	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	76	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)	5						Melanoma(8;187 585 15745 40864 52829)								0.27451	33.422684	35.762275	14	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27023970	27023970	3246	5	C	G	G	24	24	CDH9	G	3	3
HIVEP1	3096	broad.mit.edu	36	6	12231437	12231437	+	Silent	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:12231437C>T	uc003nac.1	+	c.3423C>T	c.(3421-3423)TCC>TCT	p.S1141S		NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	1141					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)	5	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)												0.351351	155.857553	158.741368	52	96	CC		KEEP	---	---	---	---	capture			Silent	SNP	12231437	12231437	7477	6	C	T	T	22	22	HIVEP1	T	2	2
PGK2	5232	broad.mit.edu	36	6	49862347	49862347	+	Silent	SNP	G	A	A			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:49862347G>A	uc003ozu.1	-	c.513C>T	c.(511-513)CGC>CGT	p.R171R		NM_138733	NP_620061	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	171		Substrate (By similarity).			glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			ovary(1)	1	Lung NSC(77;0.0402)													0.310345	139.273047	144.856008	54	120	GG		KEEP	---	---	---	---	capture			Silent	SNP	49862347	49862347	12214	6	G	A	A	38	38	PGK2	A	1	1
PIK3CG	5294	broad.mit.edu	36	7	106296295	106296295	+	Silent	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106296295C>T	uc003vdv.2	+	c.1053C>T	c.(1051-1053)ACC>ACT	p.T351T	PIK3CG_uc003vdu.1_Silent_p.T351T|PIK3CG_uc003vdw.1_Silent_p.T351T	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	351					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21									p.T351T(COLO792-Tumor)	292				0.21519	155.500594	179.110244	68	248	CC		KEEP	---	---	---	---	capture			Silent	SNP	106296295	106296295	12340	7	C	T	T	23	23	PIK3CG	T	1	1
PRSS1	5644	broad.mit.edu	36	7	142139869	142139869	+	Silent	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142139869C>T	uc003wak.2	+	c.468C>T	c.(466-468)GAC>GAT	p.D156D	PRSS2_uc003wal.2_Intron|PRSS1_uc003wam.2_Silent_p.D96D	NM_002769	NP_002760	P07477	TRY1_HUMAN	protease, serine, 1 preproprotein	156	Peptidase S1.				digestion|proteolysis	extracellular space	metal ion binding|protein binding|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)												0.239567	359.712104	399.771406	155	492	CC		KEEP	---	---	---	---	capture	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Silent	SNP	142139869	142139869	13064	7	C	T	T	19	19	PRSS1	T	1	1
INHBA	3624	broad.mit.edu	36	7	41696450	41696450	+	Missense_Mutation	SNP	T	A	A			TCGA-28-5214-01	TCGA-28-5214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:41696450T>A	uc003thq.1	-	c.604A>T	c.(604-606)AGT>TGT	p.S202C	INHBA_uc003thr.1_Missense_Mutation_p.S202C	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor	202					cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway|regulation of gene-specific transcription from RNA polymerase II promoter	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity|transcription activator activity			lung(5)|ovary(1)	6										102	TSP Lung(11;0.080)			0.213836	67.761404	79.800947	34	125	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41696450	41696450	8042	7	T	A	A	54	54	INHBA	A	4	4
TMEM120A	83862	broad.mit.edu	36	7	75455539	75455539	+	Missense_Mutation	SNP	A	C	C			TCGA-28-5214-01	TCGA-28-5214-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:75455539A>C	uc003ued.1	-	c.530T>G	c.(529-531)ATC>AGC	p.I177S	TMEM120A_uc003ueb.1_5'Flank|TMEM120A_uc003uec.1_Missense_Mutation_p.I81S|TMEM120A_uc003uee.1_Missense_Mutation_p.I81S	NM_031925	NP_114131	Q9BXJ8	T120A_HUMAN	transmembrane protein 120A	177	Helical; (Potential).					integral to membrane					0														0.205128	79.723008	92.300033	32	124	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75455539	75455539	16564	7	A	C	C	12	12	TMEM120A	C	4	4
SMURF1	57154	broad.mit.edu	36	7	98473948	98473948	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98473948G>A	uc003upu.1	-	c.1765C>T	c.(1765-1767)CGG>TGG	p.R589W	SMURF1_uc003upv.1_Missense_Mutation_p.R563W|SMURF1_uc003upt.1_Missense_Mutation_p.R135W	NM_020429	NP_065162	Q9HCE7	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 isoform	589	HECT.				BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			ovary(1)	1	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)									444				0.231884	75.637784	84.719361	32	106	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)		Missense_Mutation	SNP	98473948	98473948	15319	7	G	A	A	39	39	SMURF1	A	1	1
NRBP2	340371	broad.mit.edu	36	8	144990027	144990027	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144990027C>T	uc003yzw.1	-	c.764G>A	c.(763-765)AGC>AAC	p.S255N	NRBP2_uc003yzv.2_Missense_Mutation_p.S220N|NRBP2_uc010mfl.1_Silent_p.Q285Q|NRBP2_uc010mfm.1_Intron|NRBP2_uc003yzx.1_Non-coding_Transcript|NRBP2_uc003yzy.1_Missense_Mutation_p.S220N|NRBP2_uc003yzz.1_Silent_p.Q143Q	NM_178564	NP_848659	Q9NSY0	NRBP2_HUMAN	nuclear receptor binding protein 2	463					negative regulation of neuron apoptosis|neuron differentiation|protein phosphorylation	cytoplasm	ATP binding|protein kinase activity			central_nervous_system(2)	2	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)									69				0.210526	8.588349	10.062348	4	15	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)		Missense_Mutation	SNP	144990027	144990027	11048	8	C	T	T	28	28	NRBP2	T	2	2
EPB41L4B	54566	broad.mit.edu	36	9	111055599	111055599	+	Missense_Mutation	SNP	T	C	C			TCGA-28-5214-01	TCGA-28-5214-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:111055599T>C	uc004bdz.1	-	c.1222A>G	c.(1222-1224)ACC>GCC	p.T408A	EPB41L4B_uc004bea.1_Missense_Mutation_p.T408A	NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	408						cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2														0.319298	255.43451	263.698888	91	194	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111055599	111055599	5349	9	T	C	C	59	59	EPB41L4B	C	4	4
FUT7	2529	broad.mit.edu	36	9	139045459	139045459	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139045459G>C	uc004ckq.2	-	c.553C>G	c.(553-555)CTG>GTG	p.L185V	ABCA2_uc010nby.1_5'Flank|ABCA2_uc010nbz.1_5'Flank|ABCA2_uc004ckl.1_5'Flank|ABCA2_uc004ckm.1_5'Flank|C9orf139_uc004ckp.1_Intron	NM_004479	NP_004470	Q11130	FUT7_HUMAN	fucosyltransferase 7	185	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity				0	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0511)												0.216216	9.655731	12.572178	8	29	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)	Missense_Mutation	SNP	139045459	139045459	6360	9	G	C	C	34	34	FUT7	C	3	3
LINGO2	158038	broad.mit.edu	36	9	27939565	27939565	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:27939565G>A	uc003zqu.1	-	c.1105C>T	c.(1105-1107)CGA>TGA	p.R369*	LINGO2_uc010mjf.1_Nonsense_Mutation_p.R369*|LINGO2_uc003zqv.1_Nonsense_Mutation_p.R369*|LINGO2_uc010mjg.1_Nonsense_Mutation_p.R369*	NM_152570	NP_689783	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	369	LRRCT.|Extracellular (Potential).					integral to membrane				ovary(1)|central_nervous_system(1)	2	Melanoma(11;0.242)	all_neural(11;2.78e-09)												0.378947	96.883298	98.101929	36	59	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)	Nonsense_Mutation	SNP	27939565	27939565	9142	9	G	A	A	38	38	LINGO2	A	5	1
SMARCA1	6594	broad.mit.edu	36	X	128485000	128485000	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:128485000G>C	uc004eun.2	-	c.29C>G	c.(28-30)GCC>GGC	p.A10G	SMARCA1_uc004eup.2_Missense_Mutation_p.A10G	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	10					ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of gene-specific transcription|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding|transcription regulator activity			ovary(3)|skin(1)	4														0.259259	7.793369	9.327489	7	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128485000	128485000	15266	23	G	C	C	42	42	SMARCA1	C	3	3
MAGEA8	4107	broad.mit.edu	36	X	148774496	148774496	+	Silent	SNP	G	A	A			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:148774496G>A	uc004fdw.1	+	c.792G>A	c.(790-792)GCG>GCA	p.A264A	MAGEA8_uc010ntd.1_Silent_p.A264A	NM_005364	NP_005355	P43361	MAGA8_HUMAN	melanoma antigen family A, 8	264	MAGE.										0	Acute lymphoblastic leukemia(192;6.56e-05)													0.691489	395.183815	401.321446	130	58	GG		KEEP	---	---	---	---	capture			Silent	SNP	148774496	148774496	9550	23	G	A	A	38	38	MAGEA8	A	1	1
STARD8	9754	broad.mit.edu	36	X	67856971	67856971	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5214-01	TCGA-28-5214-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:67856971G>C	uc004dxb.1	+	c.2030G>C	c.(2029-2031)CGC>CCC	p.R677P	STARD8_uc004dxa.1_Missense_Mutation_p.R597P|STARD8_uc004dxc.2_Missense_Mutation_p.R597P	NM_014725	NP_055540	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain	597	Rho-GAP.				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														0.363636	6.891419	7.072738	4	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67856971	67856971	15782	23	G	C	C	38	38	STARD8	C	3	3
CDX4	1046	broad.mit.edu	36	X	72584052	72584052	+	Nonsense_Mutation	SNP	C	T	T			TCGA-28-5214-01	TCGA-28-5214-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:72584052C>T	uc004ebj.1	+	c.238C>T	c.(238-240)CGA>TGA	p.R80*		NM_005193	NP_005184	O14627	CDX4_HUMAN	caudal type homeobox 4	80						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0	Renal(35;0.156)													0.642857	107.008975	108.016098	36	20	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	72584052	72584052	3313	23	C	T	T	27	27	CDX4	T	5	1
FNBP4	23360	broad.mit.edu	36	11	47745240	47745245	+	In_Frame_Del	DEL	GGTGGT	-	-			TCGA-28-5214-01	TCGA-28-5214-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:47745240_47745245delGGTGGT	uc009ylv.1	-	c.172_177delACCACC	c.(172-177)ACCACCdel	p.TT58del	FNBP4_uc001ngj.1_5'UTR|FNBP4_uc001ngl.2_Non-coding_Transcript	NM_015308	NP_056123	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	58_59										ovary(1)	1														0.50			3	3				---	---	---	---	capture_indel			In_Frame_Del	DEL	47745240	47745245	6209	11	GGTGGT	-	-	39	39	FNBP4	-	5	5
PRR21	643905	broad.mit.edu	36	2	240630917	240630930	+	Frame_Shift_Del	DEL	TGGATGAAGGGCCA	-	-			TCGA-28-5214-01	TCGA-28-5214-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:240630917_240630930delTGGATGAAGGGCCA	uc002vys.1	-	c.143_156delTGGCCCTTCATCCA	c.(142-156)ATGGCCCTTCATCCAfs	p.M48fs		NM_001080835	NP_001074304	Q8WXC7	PRR21_HUMAN	hypothetical protein LOC643905	48_52	Pro-rich.									ovary(1)	1														0.33			16	33				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	240630917	240630930	13040	2	TGGATGAAGGGCCA	-	-	59	59	PRR21	-	5	5
IK	3550	broad.mit.edu	36	5	140013720	140013720	+	Frame_Shift_Del	DEL	G	-	-			TCGA-28-5214-01	TCGA-28-5214-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140013720_140013720delG	uc003lgq.1	+	c.418_418delG	c.(418-420)GCAfs	p.A140fs		NM_006083	NP_006074	Q13123	RED_HUMAN	RED protein	140					cell-cell signaling|immune response	extracellular space|nucleus|soluble fraction				large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.33			19	38				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	140013720	140013720	7909	5	G	-	-	46	46	IK	-	5	5
