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
DDX10	1662	broad.mit.edu	36	11	108099016	108099016	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:108099016C>A	uc001pkm.1	+	c.1582C>A	c.(1582-1584)CAA>AAA	p.Q528K	DDX10_uc001pkl.1_Missense_Mutation_p.Q528K	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	528							ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)	2		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)								268				0.285714	8.709312	9.277968	4	10	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)	Missense_Mutation	SNP	108099016	108099016	4513	11	C	A	A	21	21	DDX10	A	3	3
OR5AR1	219493	broad.mit.edu	36	11	56187940	56187940	+	Missense_Mutation	SNP	T	G	G			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56187940T>G	uc001njc.1	+	c.203T>G	c.(202-204)TTT>TGT	p.F68C		NM_001004730	NP_001004730	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR,	68	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.331849	491.741489	502.980063	149	300	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56187940	56187940	11555	11	T	G	G	64	64	OR5AR1	G	4	4
OSBP	5007	broad.mit.edu	36	11	59132590	59132590	+	Silent	SNP	G	A	A			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59132590G>A	uc001noc.1	-	c.765C>T	c.(763-765)ATC>ATT	p.I255I		NM_002556	NP_002547	P22059	OSBP1_HUMAN	oxysterol binding protein	255					lipid transport	Golgi membrane	oxysterol binding			large_intestine(1)	1		all_epithelial(135;0.000236)												0.273077	184.901658	196.973591	71	189	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)	Silent	SNP	59132590	59132590	11684	11	G	A	A	45	45	OSBP	A	2	2
CTSF	8722	broad.mit.edu	36	11	66090446	66090446	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:66090446G>C	uc001oip.1	-	c.613C>G	c.(613-615)CGG>GGG	p.R205G		NM_003793	NP_003784	Q9UBX1	CATF_HUMAN	cathepsin F	205					proteolysis	lysosome	cysteine-type endopeptidase activity				0														0.415385	76.819971	77.224095	27	38	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66090446	66090446	4193	11	G	C	C	39	39	CTSF	C	3	3
SPTBN2	6712	broad.mit.edu	36	11	66229126	66229126	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:66229126C>T	uc001ojd.1	-	c.2197G>A	c.(2197-2199)GAG>AAG	p.E733K		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	733	Spectrin 4.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4														0.5	10.699074	10.699074	4	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66229126	66229126	15634	11	C	T	T	32	32	SPTBN2	T	2	2
SCARB1	949	broad.mit.edu	36	12	123862375	123862375	+	Silent	SNP	C	T	T			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:123862375C>T	uc001ugp.2	-	c.720G>A	c.(718-720)CTG>CTA	p.L240L	SCARB1_uc001ugm.2_Silent_p.L240L|SCARB1_uc001ugn.2_Silent_p.L240L|SCARB1_uc001ugo.2_Silent_p.L240L	NM_001082959	NP_001076428	Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1 isoform 2	240	Extracellular (Potential).				adhesion to symbiont|cell adhesion|cholesterol efflux|cholesterol homeostasis|cholesterol import|detection of lipopolysaccharide|high-density lipoprotein particle clearance|high-density lipoprotein particle remodeling|lipopolysaccharide transport|lipoprotein metabolic process|positive regulation of cholesterol storage|positive regulation of endothelial cell migration|positive regulation of nitric-oxide synthase activity|recognition of apoptotic cell|regulation of phagocytosis|reverse cholesterol transport|triglyceride homeostasis|wound healing	caveola	1-phosphatidylinositol binding|apolipoprotein A-I binding|high-density lipoprotein particle receptor activity|lipopolysaccharide receptor activity|low-density lipoprotein particle binding|phosphatidylserine binding|transporter activity			kidney(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)				Phosphatidylserine(DB00144)									0.366667	30.715691	31.185175	11	19	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Silent	SNP	123862375	123862375	14362	12	C	T	T	29	29	SCARB1	T	2	2
TMEM132B	114795	broad.mit.edu	36	12	124704460	124704460	+	Nonsense_Mutation	SNP	G	T	T			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:124704460G>T	uc001uhe.1	+	c.2488G>T	c.(2488-2490)GAA>TAA	p.E830*	TMEM132B_uc001uhf.1_Nonsense_Mutation_p.E342*	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	830	Extracellular (Potential).					integral to membrane				ovary(5)|large_intestine(1)|breast(1)|pancreas(1)	8	all_neural(191;0.101)|Medulloblastoma(191;0.163)													0.210526	42.944427	50.312058	20	75	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)	Nonsense_Mutation	SNP	124704460	124704460	16577	12	G	T	T	41	41	TMEM132B	T	5	3
DDX11	1663	broad.mit.edu	36	12	31133692	31133692	+	Splice_Site_SNP	SNP	G	T	T			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:31133692G>T	uc001rjt.1	+	c.880_splice	c.e8+1	p.E294_splice	DDX11_uc001rjr.1_Splice_Site_SNP_p.E294_splice|DDX11_uc001rjs.1_Splice_Site_SNP_p.E294_splice|DDX11_uc001rju.1_5'UTR|DDX11_uc001rjv.1_Splice_Site_SNP_p.E294_splice|DDX11_uc001rjw.1_Splice_Site_SNP_p.E268_splice|DDX11_uc001rjx.1_5'UTR|DDX11_uc009zjn.1_Intron	NM_152438	NP_689651			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)										Multiple Myeloma(12;0.14)			0.333333	6.876802	7.181675	4	8	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	31133692	31133692	4514	12	G	T	T	44	44	DDX11	T	5	3
WIF1	11197	broad.mit.edu	36	12	63746710	63746710	+	Missense_Mutation	SNP	G	T	T			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:63746710G>T	uc001ssk.1	-	c.708C>A	c.(706-708)TTC>TTA	p.F236L		NM_007191	NP_009122	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1 precursor	236	EGF-like 2.				multicellular organismal development|Wnt receptor signaling pathway	extracellular region	protein tyrosine kinase activity			ovary(2)|lung(1)	3						Esophageal Squamous(148;1595 1816 48559 49439 49664)				284				0.213333	34.958902	40.653622	16	59	GG		KEEP	---	---	---	---	capture	LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)	Missense_Mutation	SNP	63746710	63746710	17940	12	G	T	T	33	33	WIF1	T	3	3
TRHDE	29953	broad.mit.edu	36	12	70953184	70953184	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:70953184C>T	uc001sxa.1	+	c.359C>T	c.(358-360)ACG>ATG	p.T120M	LOC283392_uc001swz.2_5'Flank	NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	120	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)	2														0.2	6.315732	7.571987	3	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70953184	70953184	17023	12	C	T	T	19	19	TRHDE	T	1	1
GPC6	10082	broad.mit.edu	36	13	93478087	93478087	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:93478087A>G	uc001vlt.1	+	c.815A>G	c.(814-816)AAC>AGC	p.N272S		NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor	272						anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)												0.960854	1075.993188	1098.196418	270	11	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	93478087	93478087	6876	13	A	G	G	2	2	GPC6	G	4	4
FANCM	57697	broad.mit.edu	36	14	44690462	44690462	+	Missense_Mutation	SNP	A	T	T			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr14:44690462A>T	uc001wwd.2	+	c.1031A>T	c.(1030-1032)AAC>ATC	p.N344I	FANCM_uc001wwc.2_Missense_Mutation_p.N344I|FANCM_uc010anf.1_Missense_Mutation_p.N318I	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	344					DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(2)|breast(1)	3										793				0.978022	326.287372	329.773041	89	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44690462	44690462	5907	14	A	T	T	2	2	FANCM	T	4	4
ACTN1	87	broad.mit.edu	36	14	68419376	68419376	+	Silent	SNP	G	A	A			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:68419376G>A	uc001xkm.1	-	c.1785C>T	c.(1783-1785)ATC>ATT	p.I595I	ACTN1_uc001xkk.1_Silent_p.I191I|ACTN1_uc001xkl.1_Silent_p.I595I|ACTN1_uc001xkn.1_Silent_p.I595I	NM_001102	NP_001093	P12814	ACTN1_HUMAN	actinin, alpha 1 isoform b	595	Interaction with DDN.|Spectrin 3.				focal adhesion assembly|negative regulation of cellular component movement|platelet activation|platelet degranulation|regulation of apoptosis	actin cytoskeleton|cytosol|extracellular region|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|sarcomere	actin binding|calcium ion binding|integrin binding|vinculin binding			central_nervous_system(1)	1														0.147541	26.372446	40.928542	18	104	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)	Silent	SNP	68419376	68419376	205	14	G	A	A	45	45	ACTN1	A	2	2
TTLL5	23093	broad.mit.edu	36	14	75329134	75329134	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:75329134G>A	uc010ask.1	+	c.3154G>A	c.(3154-3156)GCT>ACT	p.A1052T	TTLL5_uc001xrx.1_Missense_Mutation_p.A1037T|TTLL5_uc001xrz.2_Missense_Mutation_p.A612T|TTLL5_uc001xsa.1_Missense_Mutation_p.A111T	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1037					protein modification process|transcription, DNA-dependent	cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3														0.178571	7.054701	9.784175	5	23	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.029)	Missense_Mutation	SNP	75329134	75329134	17285	14	G	A	A	34	34	TTLL5	A	2	2
DICER1	23405	broad.mit.edu	36	14	94627382	94627382	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:94627382T>C	uc001ydw.2	-	c.5438A>G	c.(5437-5439)GAG>GGG	p.E1813G	DICER1_uc010avh.1_Missense_Mutation_p.E711G|DICER1_uc001ydv.2_Missense_Mutation_p.E1803G|DICER1_uc001ydx.2_Missense_Mutation_p.E1813G	NM_030621	NP_803187	Q9UPY3	DICER_HUMAN	dicer1	1813	RNase III 2.	Magnesium or manganese 2.		E->A: Decreased activity. Loss of activity; when associated with E-1444.	negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-microRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			ovary(1)|pancreas(1)|lung(1)|skin(1)	4		all_cancers(154;0.0621)|all_epithelial(191;0.223)								741				0.956522	1758.208451	1799.859663	440	20	TT		KEEP	---	---	---	---	capture		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)	Missense_Mutation	SNP	94627382	94627382	4700	14	T	C	C	54	54	DICER1	C	4	4
NOX5	79400	broad.mit.edu	36	15	67134797	67134797	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:67134797T>A	uc002ars.1	+	c.2069T>A	c.(2068-2070)CTG>CAG	p.L690Q	NOX5_uc002arp.1_Missense_Mutation_p.L672Q|NOX5_uc002arq.1_Missense_Mutation_p.L644Q|NOX5_uc010bid.1_Missense_Mutation_p.L655Q|NOX5_uc002arr.1_Missense_Mutation_p.L662Q|NOX5_uc010bie.1_Missense_Mutation_p.L490Q|NOX5_uc010bif.1_Non-coding_Transcript	NM_024505	NP_078781	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	690	Extracellular (Potential).				angiogenesis|angiogenesis|cytokine secretion|cytokinesis|electron transport chain|endothelial cell proliferation|induction of apoptosis|positive regulation of reactive oxygen species metabolic process|regulation of fusion of sperm to egg plasma membrane|regulation of proton transport|superoxide anion generation	endoplasmic reticulum|endoplasmic reticulum|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|hydrogen ion channel activity|NADP binding|superoxide-generating NADPH oxidase activity			breast(1)|pancreas(1)	2														0.12766	16.23208	28.943059	12	82	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67134797	67134797	10963	15	T	A	A	55	55	NOX5	A	4	4
PIGQ	9091	broad.mit.edu	36	16	568419	568419	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:568419A>G	uc002cho.1	+	c.982A>G	c.(982-984)ATG>GTG	p.M328V	PIGQ_uc010bqw.1_Missense_Mutation_p.M328V|PIGQ_uc002chn.1_Missense_Mutation_p.M328V	NM_148920	NP_683721	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	328	Leu-rich.				C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)												0.241379	7.050226	8.888464	7	22	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	568419	568419	12320	16	A	G	G	12	12	PIGQ	G	4	4
WWP2	11060	broad.mit.edu	36	16	68531331	68531331	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:68531331T>C	uc002exu.1	+	c.2600T>C	c.(2599-2601)TTT>TCT	p.F867S	WWP2_uc002exv.1_Missense_Mutation_p.F867S|WWP2_uc002exw.1_Missense_Mutation_p.F428S	NM_007014	NP_008945	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase	867	HECT.				entry of virus into host cell|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			skin(1)	1														0.956522	79.901454	81.893078	22	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	68531331	68531331	17990	16	T	C	C	64	64	WWP2	C	4	4
NF1	4763	broad.mit.edu	36	17	26581462	26581462	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26581462C>T	uc002hgg.1	+	c.3049C>T	c.(3049-3051)CAA>TAA	p.Q1017*	NF1_uc002hgh.1_Nonsense_Mutation_p.Q1017*|NF1_uc002hgi.1_Nonsense_Mutation_p.Q50*|NF1_uc010csn.1_Nonsense_Mutation_p.Q877*	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1017					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(3)|p.Q1017*(1)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)								847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.942029	216.374933	226.752238	65	4	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	Nonsense_Mutation	SNP	26581462	26581462	10756	17	C	T	T	29	29	NF1	T	5	2
GAS2L2	246176	broad.mit.edu	36	17	31096752	31096752	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:31096752C>G	uc002hjv.1	-	c.1877G>C	c.(1876-1878)AGG>ACG	p.R626T		NM_139285	NP_644814	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	626					cell cycle arrest	cytoplasm|cytoskeleton				ovary(1)|skin(1)	2		Ovarian(249;0.17)												0.928571	722.662236	764.977628	208	16	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	Missense_Mutation	SNP	31096752	31096752	6511	17	C	G	G	24	24	GAS2L2	G	3	3
TUBG2	27175	broad.mit.edu	36	17	38071228	38071228	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:38071228A>G	uc002iao.1	+	c.700A>G	c.(700-702)ACC>GCC	p.T234A	TUBG2_uc002iap.1_Missense_Mutation_p.T81A|TUBG2_uc002iaq.1_Missense_Mutation_p.T76A|TUBG2_uc002iar.1_Missense_Mutation_p.T81A|TUBG2_uc002ias.1_Missense_Mutation_p.T76A	NM_016437	NP_057521	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	234					G2/M transition of mitotic cell cycle|microtubule-based process|protein polymerization	cytosol	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1		Breast(137;0.00116)												0.222222	64.473258	74.064959	30	105	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.141)	Missense_Mutation	SNP	38071228	38071228	17320	17	A	G	G	6	6	TUBG2	G	4	4
WNK4	65266	broad.mit.edu	36	17	38193394	38193394	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:38193394C>A	uc002ibj.1	+	c.1814C>A	c.(1813-1815)CCT>CAT	p.P605H	WNK4_uc002ibk.1_Missense_Mutation_p.P377H	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	605					intracellular protein kinase cascade|protein phosphorylation	tight junction	ATP binding|protein serine/threonine kinase activity			ovary(3)|skin(3)|stomach(1)	7		Breast(137;0.000143)				Esophageal Squamous(6;201 374 4964 23855 42828)				263				0.28	67.459682	71.811249	28	72	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.0749)	Missense_Mutation	SNP	38193394	38193394	17954	17	C	A	A	24	24	WNK4	A	3	3
C18orf34	374864	broad.mit.edu	36	18	29127222	29127222	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:29127222T>A	uc002kxn.2	-	c.1075A>T	c.(1075-1077)ATA>TTA	p.I359L	C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Missense_Mutation_p.I359L|C18orf34_uc002kxp.2_Missense_Mutation_p.I359L	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	359	Potential.									ovary(1)	1														0.534413	426.914472	427.168888	132	115	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29127222	29127222	1963	18	T	A	A	50	50	C18orf34	A	4	4
MBD1	4152	broad.mit.edu	36	18	46060341	46060341	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:46060341T>C	uc002lem.2	-	c.20A>G	c.(19-21)GAC>GGC	p.D7G	MBD1_uc002lef.2_5'Flank|MBD1_uc010dow.1_Missense_Mutation_p.D7G|MBD1_uc002leg.2_Missense_Mutation_p.D7G|MBD1_uc002leh.2_Missense_Mutation_p.D7G|MBD1_uc002lei.2_Missense_Mutation_p.D7G|MBD1_uc002lej.2_Missense_Mutation_p.D7G|MBD1_uc002lek.2_Missense_Mutation_p.D7G|MBD1_uc002lel.2_Missense_Mutation_p.D7G|MBD1_uc002len.2_Missense_Mutation_p.D7G|MBD1_uc010dox.1_Missense_Mutation_p.D7G|MBD1_uc002leo.2_Missense_Mutation_p.D7G	NM_015846	NP_056671	Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1 isoform 1	7	MBD.				negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|nuclear speck	methyl-CpG binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription repressor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.230769	7.644578	9.375481	6	20	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46060341	46060341	9726	18	T	C	C	58	58	MBD1	C	4	4
CC2D1A	54862	broad.mit.edu	36	19	13901917	13901917	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:13901917C>G	uc002mxo.1	+	c.2737C>G	c.(2737-2739)CTG>GTG	p.L913V	CC2D1A_uc002mxp.1_Missense_Mutation_p.L912V|CC2D1A_uc010dzh.1_Missense_Mutation_p.L482V	NM_017721	NP_060191	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	913					positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0														0.25	11.401162	13.002659	7	21	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)		Missense_Mutation	SNP	13901917	13901917	2846	19	C	G	G	28	28	CC2D1A	G	3	3
C19orf2	8725	broad.mit.edu	36	19	35167976	35167976	+	Silent	SNP	G	A	A			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:35167976G>A	uc002nsr.1	+	c.159G>A	c.(157-159)AAG>AAA	p.K53K	C19orf2_uc002nsq.2_Silent_p.K35K|C19orf2_uc002nss.1_Silent_p.K13K|C19orf2_uc002nst.1_5'UTR	NM_003796	NP_003787	O94763	RMP_HUMAN	RPB5-mediating protein isoform a	53					protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)				Melanoma(75;661 1306 1472 28422 37948)								0.293878	429.722003	448.344842	144	346	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)	Silent	SNP	35167976	35167976	1973	19	G	A	A	35	35	C19orf2	A	2	2
WDR88	126248	broad.mit.edu	36	19	38343185	38343185	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:38343185T>A	uc002nui.1	+	c.1023T>A	c.(1021-1023)TTT>TTA	p.F341L		NM_173479	NP_775750	Q6ZMY6	WDR88_HUMAN	PQQ repeat and WD repeat domain containing	341	WD 6.									ovary(1)|breast(1)|central_nervous_system(1)	3	Esophageal squamous(110;0.137)													0.318182	520.513615	537.99751	189	405	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38343185	38343185	17909	19	T	A	A	63	63	WDR88	A	4	4
KCTD15	79047	broad.mit.edu	36	19	38983943	38983943	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:38983943C>T	uc002nuw.2	+	c.98C>T	c.(97-99)ACC>ATC	p.T33I	KCTD15_uc002nuv.1_Missense_Mutation_p.T33I|KCTD15_uc002nux.2_Missense_Mutation_p.T33I|KCTD15_uc002nuy.2_Missense_Mutation_p.T33I	NM_024076	NP_076981	Q96SI1	KCD15_HUMAN	potassium channel tetramerisation domain	33						voltage-gated potassium channel complex	voltage-gated potassium channel activity			pancreas(1)	1	Esophageal squamous(110;0.162)					Melanoma(36;646 1094 5145 14504 45302)|GBM(25;193 541 1518 14388 52178)								0.112462	31.840984	80.680648	37	292	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38983943	38983943	8408	19	C	T	T	18	18	KCTD15	T	2	2
DMRTC2	63946	broad.mit.edu	36	19	47043729	47043729	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47043729G>A	uc002ors.1	+	c.310G>A	c.(310-312)GAA>AAA	p.E104K	DMRTC2_uc002orr.1_5'UTR	NM_001040283	NP_001035373	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2	104					cell differentiation|regulation of transcription, DNA-dependent|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0														0.25	7.152121	8.30572	5	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47043729	47043729	4773	19	G	A	A	41	41	DMRTC2	A	2	2
ZNF470	388566	broad.mit.edu	36	19	61780269	61780269	+	Silent	SNP	A	G	G			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61780269A>G	uc002qnl.2	+	c.660A>G	c.(658-660)CAA>CAG	p.Q220Q	ZNF470_uc010etn.1_Intron	NM_001001668	NP_001001668	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	220					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)												0.164062	51.491935	65.209608	21	107	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0294)	Silent	SNP	61780269	61780269	18523	19	A	G	G	3	3	ZNF470	G	4	4
ZNF324	25799	broad.mit.edu	36	19	63675310	63675310	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63675310G>A	uc002qsw.1	+	c.1639G>A	c.(1639-1641)GTC>ATC	p.V547I	ZNF324_uc002qsx.1_Missense_Mutation_p.V324I	NM_014347	NP_055162	O75467	Z324A_HUMAN	zinc finger protein 324	547					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)												0.390625	68.057257	68.728746	25	39	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)	Missense_Mutation	SNP	63675310	63675310	18436	19	G	A	A	40	40	ZNF324	A	1	1
MUC16	94025	broad.mit.edu	36	19	8827754	8827754	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8827754C>G	uc002mkp.1	-	c.43199G>C	c.(43198-43200)CGG>CCG	p.R14400P	MUC16_uc010dwh.1_Non-coding_Transcript|MUC16_uc010dwi.1_Non-coding_Transcript|MUC16_uc010dwj.1_Missense_Mutation_p.R1200P	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	14498	SEA 16.|Extracellular (Potential).			Missing (in Ref. 3; AAK74120).	cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.214286	6.350958	7.382459	3	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8827754	8827754	10367	19	C	G	G	23	23	MUC16	G	3	3
IFI16	3428	broad.mit.edu	36	1	157253036	157253036	+	Silent	SNP	C	G	G			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:157253036C>G	uc001ftg.1	+	c.471C>G	c.(469-471)GCC>GCG	p.A157A	IFI16_uc001fti.2_Silent_p.A157A|IFI16_uc001ftf.1_Silent_p.A157A	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	157					cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nucleolus|nucleoplasm	double-stranded DNA binding|transcription repressor activity			ovary(1)	1	all_hematologic(112;0.0429)													0.137931	32.357299	54.475054	24	150	CC		KEEP	---	---	---	---	capture			Silent	SNP	157253036	157253036	7812	1	C	G	G	23	23	IFI16	G	3	3
NR5A2	2494	broad.mit.edu	36	1	198284334	198284334	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:198284334G>C	uc001gvb.1	+	c.875G>C	c.(874-876)AGT>ACT	p.S292T	NR5A2_uc001gvc.1_Missense_Mutation_p.S246T|NR5A2_uc009wzh.1_Missense_Mutation_p.S252T	NM_205860	NP_995582	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	292					embryo development|positive regulation of gene-specific transcription|positive regulation of viral genome replication|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	lipid binding|promoter binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2	Prostate(682;0.19)					Melanoma(179;1138 2773 15678 26136)								0.446215	357.638004	358.272457	112	139	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	198284334	198284334	11041	1	G	C	C	36	36	NR5A2	C	3	3
RYR2	6262	broad.mit.edu	36	1	235686565	235686565	+	Missense_Mutation	SNP	G	A	A	rs16835270	by-cluster,by-frequency,by-hapmap	TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:235686565G>A	uc001hyl.1	+	c.1519G>A	c.(1519-1521)GTC>ATC	p.V507I		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	507	Cytoplasmic (By similarity).				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)												0.423333	373.87125	375.410289	127	173	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		Missense_Mutation	SNP	235686565	235686565	14249	1	G	A	A	40	40	RYR2	A	1	1
OR2T3	343173	broad.mit.edu	36	1	246703854	246703854	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246703854T>C	uc001iel.1	+	c.580T>C	c.(580-582)TGC>CGC	p.C194R		NM_001005495	NP_001005495	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T,	194	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)													0.564356	1198.209182	1200.395048	342	264	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		Missense_Mutation	SNP	246703854	246703854	11429	1	T	C	C	55	55	OR2T3	C	4	4
LRRC41	10489	broad.mit.edu	36	1	46517844	46517844	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:46517844C>G	uc001cpn.1	-	c.2050G>C	c.(2050-2052)GAG>CAG	p.E684Q		NM_006369	NP_006360	Q15345	LRC41_HUMAN	MUF1 protein	684										ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(166;0.155)													0.145215	89.389909	126.084454	44	259	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46517844	46517844	9374	1	C	G	G	29	29	LRRC41	G	3	3
AGRN	375790	broad.mit.edu	36	1	970647	970647	+	Missense_Mutation	SNP	A	C	C			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:970647A>C	uc001ack.1	+	c.2417A>C	c.(2416-2418)GAC>GCC	p.D806A		NM_198576	NP_940978	O00468	AGRIN_HUMAN	agrin	806	Laminin EGF-like 1.				axon guidance|clustering of voltage-gated sodium channels|muscarinic acetylcholine receptor signaling pathway|receptor clustering	basal lamina	laminin binding|structural constituent of cytoskeleton			central_nervous_system(2)|breast(1)	3	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)												0.2	7.101035	8.76724	4	16	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)	Missense_Mutation	SNP	970647	970647	400	1	A	C	C	10	10	AGRN	C	4	4
KRTAP10-9	386676	broad.mit.edu	36	21	44872178	44872178	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44872178C>A	uc002zfp.2	+	c.662C>A	c.(661-663)ACC>AAC	p.T221N	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198690	NP_941963	P60411	KR109_HUMAN	keratin associated protein 10-9	221	22.|25 X 5 AA repeats of C-C-X(3).					keratin filament					0														0.117417	51.842417	125.333275	60	451	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44872178	44872178	8831	21	C	A	A	18	18	KRTAP10-9	A	3	3
MFSD9	84804	broad.mit.edu	36	2	102706685	102706685	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102706685G>C	uc002tcb.1	-	c.543C>G	c.(541-543)ATC>ATG	p.I181M	MFSD9_uc010fja.1_Non-coding_Transcript	NM_032718	NP_116107	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing	181	Helical; (Potential).				response to antibiotic	integral to membrane	tetracycline:hydrogen antiporter activity			ovary(2)|breast(2)	4														0.185446	199.474249	238.982526	79	347	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102706685	102706685	9929	2	G	C	C	33	33	MFSD9	C	3	3
FIGN	55137	broad.mit.edu	36	2	164174907	164174907	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:164174907C>T	uc002uck.1	-	c.1681G>A	c.(1681-1683)GGA>AGA	p.G561R		NM_018086	NP_060556	Q5HY92	FIGN_HUMAN	fidgetin	561						nuclear matrix	ATP binding|nucleoside-triphosphatase activity			large_intestine(2)|ovary(1)	3														0.176136	69.517798	86.916498	31	145	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	164174907	164174907	6129	2	C	T	T	24	24	FIGN	T	2	2
CPO	130749	broad.mit.edu	36	2	207535406	207535406	+	Missense_Mutation	SNP	A	T	T			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:207535406A>T	uc002vby.1	+	c.600A>T	c.(598-600)CAA>CAT	p.Q200H		NM_173077	NP_775100	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	200					proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			large_intestine(1)|ovary(1)	2														0.798479	685.780742	707.55759	210	53	AA		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)	Missense_Mutation	SNP	207535406	207535406	3958	2	A	T	T	3	3	CPO	T	4	4
NRXN1	9378	broad.mit.edu	36	2	50619206	50619206	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:50619206T>A	uc002rxe.2	-	c.1832A>T	c.(1831-1833)GAT>GTT	p.D611V	NRXN1_uc010fbq.1_Missense_Mutation_p.D298V|NRXN1_uc002rxb.2_Missense_Mutation_p.D283V|NRXN1_uc002rxc.1_Non-coding_Transcript	NM_004801	NP_004792	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha1 precursor	215	Extracellular (Potential).|Laminin G-like.				neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)												0.761111	434.148567	445.357442	137	43	TT		KEEP	---	---	---	---	capture	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)		Missense_Mutation	SNP	50619206	50619206	11070	2	T	A	A	50	50	NRXN1	A	4	4
ARHGAP25	9938	broad.mit.edu	36	2	68899931	68899931	+	Silent	SNP	T	C	C			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:68899931T>C	uc010fdg.1	+	c.1176T>C	c.(1174-1176)TCT>TCC	p.S392S	ARHGAP25_uc002seu.1_Silent_p.S391S|ARHGAP25_uc002sev.2_Silent_p.S385S|ARHGAP25_uc002sew.1_Silent_p.S384S|ARHGAP25_uc002sex.1_Silent_p.S385S|ARHGAP25_uc002sey.1_Silent_p.S118S	NM_001007231	NP_001007232	P42331	RHG25_HUMAN	Rho GTPase activating protein 25 isoform a	391					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4														0.202703	126.869634	145.074996	45	177	TT		KEEP	---	---	---	---	capture			Silent	SNP	68899931	68899931	886	2	T	C	C	53	53	ARHGAP25	C	4	4
DRD3	1814	broad.mit.edu	36	3	115330449	115330449	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:115330449C>T	uc003ebd.2	-	c.1007G>A	c.(1006-1008)GGG>GAG	p.G336E	DRD3_uc003ebb.1_Missense_Mutation_p.G303E|DRD3_uc003ebc.1_Missense_Mutation_p.G336E|DRD3_uc010hqn.1_Missense_Mutation_p.G336E	NM_000796	NP_000787	P35462	DRD3_HUMAN	dopamine receptor D3 isoform a	336	Helical; Name=6.				activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|dopamine metabolic process|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|regulation of dopamine uptake|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)									0.507692	312.525641	312.535731	99	96	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115330449	115330449	4942	3	C	T	T	22	22	DRD3	T	2	2
PCYT1A	5130	broad.mit.edu	36	3	197453876	197453876	+	Nonsense_Mutation	SNP	A	C	C			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:197453876A>C	uc003fwg.1	-	c.519T>G	c.(517-519)TAT>TAG	p.Y173*	PCYT1A_uc003fwh.1_Nonsense_Mutation_p.Y173*	NM_005017	NP_005008	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline,	173	Catalytic (Potential).					cytosol|soluble fraction	choline-phosphate cytidylyltransferase activity				0	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)				Choline(DB00122)									0.190184	84.133996	98.75619	31	132	AA		KEEP	---	---	---	---	capture	Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Nonsense_Mutation	SNP	197453876	197453876	12031	3	A	C	C	4	4	PCYT1A	C	5	4
C3orf38	285237	broad.mit.edu	36	3	88288004	88288004	+	Nonsense_Mutation	SNP	G	A	A			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:88288004G>A	uc003dqw.1	+	c.513G>A	c.(511-513)TGG>TGA	p.W171*		NM_173824	NP_776185	Q5JPI3	CC038_HUMAN	hypothetical protein LOC285237	173					apoptosis						0		Lung NSC(201;0.17)												0.651163	450.247404	454.577345	140	75	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)	Nonsense_Mutation	SNP	88288004	88288004	2321	3	G	A	A	42	42	C3orf38	A	5	2
MLF1IP	79682	broad.mit.edu	36	4	185868261	185868261	+	Silent	SNP	A	G	G			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:185868261A>G	uc003iwq.1	-	c.756T>C	c.(754-756)AAT>AAC	p.N252N	MLF1IP_uc003iwp.1_Non-coding_Transcript|MLF1IP_uc003iwr.1_Silent_p.N252N	NM_024629	NP_078905	Q71F23	CENPU_HUMAN	MLF1 interacting protein	252					CenH3-containing nucleosome assembly at centromere|interspecies interaction between organisms|mitotic prometaphase|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|condensed chromosome kinetochore|cytosol|nucleoplasm					0		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)												0.4	138.587474	139.459717	40	60	AA		KEEP	---	---	---	---	capture		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)	Silent	SNP	185868261	185868261	10005	4	A	G	G	16	16	MLF1IP	G	4	4
MFSD10	10227	broad.mit.edu	36	4	2904721	2904721	+	Silent	SNP	C	G	G			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:2904721C>G	uc003gfw.1	-	c.282G>C	c.(280-282)TCG>TCC	p.S94S	MFSD10_uc003gfv.1_5'Flank|MFSD10_uc003gfx.1_Intron|MFSD10_uc003gfy.1_Non-coding_Transcript|MFSD10_uc003gfz.1_Silent_p.S94S|MFSD10_uc003gga.1_Silent_p.S94S|MFSD10_uc003ggb.1_Silent_p.S94S|MFSD10_uc003ggc.1_Silent_p.S94S|C4orf10_uc003ggd.1_5'Flank|C4orf10_uc003gge.1_5'Flank|C4orf10_uc003ggg.1_5'Flank|C4orf10_uc003ggh.2_5'Flank	NM_001120	NP_001111	Q14728	MFS10_HUMAN	major facilitator superfamily domain containing	94	Helical; (Potential).				apoptosis	integral to membrane	tetracycline transporter activity				0														0.285714	8.484067	9.069368	4	10	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Silent	SNP	2904721	2904721	9918	4	C	G	G	23	23	MFSD10	G	3	3
RAB24	53917	broad.mit.edu	36	5	176661785	176661785	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176661785T>C	uc003mfv.1	-	c.434A>G	c.(433-435)AAT>AGT	p.N145S	RAB24_uc003mfu.1_Missense_Mutation_p.N116S|RAB24_uc003mfw.1_Missense_Mutation_p.N145S|PRELID1_uc003mfx.1_5'Flank|PRELID1_uc003mfy.1_5'Flank	NM_130781	NP_570137	Q969Q5	RAB24_HUMAN	RAB24 gene product	145					autophagy|protein transport|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|protein binding				0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)												0.42	212.203651	213.040267	63	87	TT		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Missense_Mutation	SNP	176661785	176661785	13370	5	T	C	C	50	50	RAB24	C	4	4
MTRR	4552	broad.mit.edu	36	5	7928377	7928377	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:7928377G>A	uc003jed.1	+	c.371G>A	c.(370-372)GGT>GAT	p.G124D	MTRR_uc010itn.1_Non-coding_Transcript|MTRR_uc003jee.2_Missense_Mutation_p.G97D|MTRR_uc003jef.2_Non-coding_Transcript|MTRR_uc003jeg.2_Non-coding_Transcript|MTRR_uc010ito.1_Non-coding_Transcript	NM_024010	NP_076915	Q9UBK8	MTRR_HUMAN	methionine synthase reductase isoform 2	124	FMN (By similarity).|Flavodoxin-like.				methionine biosynthetic process|oxidation-reduction process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)									0.166667	80.035782	106.550204	42	210	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7928377	7928377	10354	5	G	A	A	44	44	MTRR	A	2	2
SYNE1	23345	broad.mit.edu	36	6	152821625	152821625	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:152821625C>G	uc010kiw.1	-	c.2528G>C	c.(2527-2529)CGT>CCT	p.R843P	SYNE1_uc003qot.2_Missense_Mutation_p.R850P|SYNE1_uc003qou.2_Missense_Mutation_p.R843P|SYNE1_uc010kjb.1_Missense_Mutation_p.R826P|SYNE1_uc003qox.1_Missense_Mutation_p.R359P|SYNE1_uc003qoz.2_Missense_Mutation_p.R275P|SYNE1_uc003qoy.2_Missense_Mutation_p.R410P|SYNE1_uc003qow.2_Missense_Mutation_p.R138P	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	843	Cytoplasmic (Potential).|Potential.				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|ovary(8)|large_intestine(5)|pancreas(2)	30		Ovarian(120;0.0955)												0.132075	42.36946	63.271294	21	138	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	Missense_Mutation	SNP	152821625	152821625	15966	6	C	G	G	19	19	SYNE1	G	3	3
SERPINB1	1992	broad.mit.edu	36	6	2778978	2778978	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:2778978C>G	uc003mub.1	-	c.1003G>C	c.(1003-1005)GCT>CCT	p.A335P	SERPINB1_uc003muc.1_Missense_Mutation_p.A184P	NM_030666	NP_109591	P30740	ILEU_HUMAN	serine (or cysteine) proteinase inhibitor, clade	335					regulation of proteolysis	cytoplasm|extracellular space	serine-type endopeptidase inhibitor activity			breast(4)|ovary(1)	5	Ovarian(93;0.0412)									73				0.190476	6.386986	8.270312	4	17	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(45;0.0717)	Missense_Mutation	SNP	2778978	2778978	14584	6	C	G	G	28	28	SERPINB1	G	3	3
HLA-A	3105	broad.mit.edu	36	6	30019178	30019178	+	Silent	SNP	C	T	T	rs41559615	unknown	TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30019178C>T	uc003non.1	+	c.498C>T	c.(496-498)ATC>ATT	p.I166I	HLA-H_uc010jrp.1_Intron|HCG4P6_uc003nog.1_Non-coding_Transcript|HLA-A_uc003nok.1_Silent_p.I45I|HLA-A_uc003nom.1_Silent_p.I45I|HLA-A_uc003noo.1_Silent_p.I166I|HLA-A_uc010jrr.1_Silent_p.I166I|HLA-A_uc003nol.1_Silent_p.I166I	NM_002116	NP_002107	P04439	1A03_HUMAN	major histocompatibility complex, class I, A	166	Extracellular (Potential).|Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity|protein binding			ovary(1)	1											Multiple Myeloma(9;0.094)			0.25	6.818861	7.500982	3	9	CC		KEEP	---	---	---	---	capture			Silent	SNP	30019178	30019178	7486	6	C	T	T	29	29	HLA-A	T	2	2
TTBK1	84630	broad.mit.edu	36	6	43358476	43358476	+	Missense_Mutation	SNP	G	T	T			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43358476G>T	uc003ouq.1	+	c.2020G>T	c.(2020-2022)GGC>TGC	p.G674C		NM_032538	NP_115927	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	674					protein phosphorylation	cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9										85				0.326848	219.912751	226.801108	84	173	GG		KEEP	---	---	---	---	capture	Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)		Missense_Mutation	SNP	43358476	43358476	17230	6	G	T	T	47	47	TTBK1	T	3	3
GIMAP5	55340	broad.mit.edu	36	7	150071044	150071044	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150071044T>A	uc003whr.1	+	c.884T>A	c.(883-885)CTT>CAT	p.L295H	GIMAP5_uc010lpu.1_Missense_Mutation_p.L153H	NM_018384	NP_060854	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	295	Helical; Anchor for type IV membrane protein; (Potential).					integral to membrane|mitochondrial outer membrane	GTP binding			ovary(1)|central_nervous_system(1)	2														0.310526	159.547445	165.627412	59	131	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	150071044	150071044	6650	7	T	A	A	56	56	GIMAP5	A	4	4
XKR5	389610	broad.mit.edu	36	8	6668504	6668504	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0871-01	TCGA-14-0871-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:6668504T>A	uc003wqp.1	-	c.586A>T	c.(586-588)AGT>TGT	p.S196C	XKR5_uc003wqq.1_Missense_Mutation_p.S33C|XKR5_uc003wqr.1_Non-coding_Transcript	NM_207411	NP_997294	Q6UX68	XKR5_HUMAN	XK-related protein 5a	196						integral to membrane					0														0.208333	11.161378	13.052473	5	19	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(24;0.0984)	READ - Rectum adenocarcinoma(644;0.137)|COAD - Colon adenocarcinoma(149;0.166)	Missense_Mutation	SNP	6668504	6668504	18015	8	T	A	A	54	54	XKR5	A	4	4
PTPRD	5789	broad.mit.edu	36	9	8379318	8379318	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0871-01	TCGA-14-0871-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:8379318C>T	uc003zkk.1	-	c.4300G>A	c.(4300-4302)GAA>AAA	p.E1434K	PTPRD_uc003zkp.1_Missense_Mutation_p.E1028K|PTPRD_uc003zkq.1_Missense_Mutation_p.E1027K|PTPRD_uc003zkr.1_Missense_Mutation_p.E1018K|PTPRD_uc003zks.1_Missense_Mutation_p.E1027K|PTPRD_uc003zkl.1_Missense_Mutation_p.E1425K|PTPRD_uc003zkm.1_Missense_Mutation_p.E1421K|PTPRD_uc003zko.1_Missense_Mutation_p.E1024K|PTPRD_uc003zkn.1_Missense_Mutation_p.E1023K	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1434	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.				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)								1253	TSP Lung(15;0.13)			0.280702	83.851032	88.779781	32	82	CC		KEEP	---	---	---	---	capture		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)	Missense_Mutation	SNP	8379318	8379318	13256	9	C	T	T	31	31	PTPRD	T	1	1
SLC28A3	64078	broad.mit.edu	36	9	86114447	86114447	+	Missense_Mutation	SNP	A	T	T			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:86114447A>T	uc010mpz.1	-	c.159T>A	c.(157-159)GAT>GAA	p.D53E	SLC28A3_uc004anu.1_Missense_Mutation_p.D53E|SLC28A3_uc010mqb.1_5'UTR	NM_022127	NP_071410	Q9HAS3	S28A3_HUMAN	concentrative Na+-nucleoside cotransporter	53	Cytoplasmic (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|plasma membrane	nucleoside binding			ovary(1)|pancreas(1)	2						Ovarian(106;425 1539 34835 42413 43572)								0.247191	122.821032	133.16782	44	134	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86114447	86114447	15030	9	A	T	T	8	8	SLC28A3	T	4	4
NUP62CL	54830	broad.mit.edu	36	X	106284016	106284016	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0871-01	TCGA-14-0871-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:106284016G>C	uc004ena.1	-	c.311C>G	c.(310-312)GCT>GGT	p.A104G	NUP62CL_uc004enb.1_Intron	NM_017681	NP_060151	Q9H1M0	N62CL_HUMAN	nucleoporin 62kDa C-terminal like	104					protein transport	nuclear pore	structural constituent of nuclear pore				0														0.210227	95.006216	108.770952	37	139	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106284016	106284016	11174	23	G	C	C	34	34	NUP62CL	C	3	3
UBE2NL	389898	broad.mit.edu	36	X	142795152	142795153	+	Missense	DNP	AG	TA	TA			TCGA-14-0871-01	TCGA-14-0871-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:142795152A>T	uc004fca.1	+	c.284A>T	c.(283-285)AAG>ATG	p.K95M		NM_001012989	NP_001013007	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like	95					post-translational protein modification		acid-amino acid ligase activity				0	Acute lymphoblastic leukemia(192;6.56e-05)													0.95302	476.379224	492.661845	142	7	AA		KEEP	---	---	---	---	capture			Missense	DNP	142795152	142795153	17424	23	AG	TA	TA	3	3	UBE2NL	TA	4	4
TP53	7157	broad.mit.edu	36	17	7517760	7517761	+	Frame_Shift_Ins	INS	-	G	G			TCGA-14-0871-01	TCGA-14-0871-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7517760_7517761insG	uc002gim.2	-	c.902_903insC	c.(901-903)CCAfs	p.P301fs	TP53_uc002gig.1_Intron|TP53_uc002gih.1_Frame_Shift_Ins_p.P301fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Ins_p.P169fs|TP53_uc010cng.1_Frame_Shift_Ins_p.P169fs|TP53_uc002gii.1_Frame_Shift_Ins_p.P169fs|TP53_uc010cnh.1_Frame_Shift_Ins_p.P301fs|TP53_uc010cni.1_Frame_Shift_Ins_p.P301fs|TP53_uc002gij.2_Frame_Shift_Ins_p.P301fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	301	Interaction with HIPK1 (By similarity).|Interaction with CARM1.		P -> T (in a sporadic cancer; somatic mutation).|P -> A (in sporadic cancers; somatic mutation).|P -> Q (in sporadic cancers; somatic mutation).|P -> L (in sporadic cancers; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.0?(6)|p.G302fs*4(3)|p.?(2)|p.P301fs*44(2)|p.P301_S303delPGS(1)|p.L299fs*2(1)|p.P301fs*5(1)|p.L265_K305del41(1)|p.P301Q(1)|p.P301P(1)|p.G293fs*1(1)|p.P301L(1)|p.E298_P301delELPP(1)|p.H296_S303delHHELPPGS(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.P301fs(KCL22-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.84			108	21				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	7517760	7517761	16923	17	-	G	G	55	55	TP53	G	5	5
