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
PDE3B	5140	broad.mit.edu	36	11	14622263	14622263	+	Silent	SNP	G	C	C			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:14622263G>C	uc001mln.1	+	c.66G>C	c.(64-66)TCG>TCC	p.S22S	PDE3B_uc001mlm.1_Silent_p.S22S|PSMA1_uc001mll.1_5'Flank	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	22					cAMP catabolic process|insulin receptor signaling pathway|negative regulation of cAMP-mediated signaling|negative regulation of cell adhesion mediated by integrin|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0														0.4	11.320772	11.509849	8	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	14622263	14622263	12059	11	G	C	C	38	38	PDE3B	C	3	3
INCENP	3619	broad.mit.edu	36	11	61654639	61654639	+	Splice_Site_SNP	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:61654639G>A	uc001nsw.1	+	c.1063_splice	c.e4+1	p.C355_splice	INCENP_uc009ynv.1_Splice_Site_SNP_p.C355_splice|INCENP_uc009ynw.1_Splice_Site_SNP_p.C355_splice|INCENP_uc001nsx.1_Splice_Site_SNP_p.C355_splice	NM_001040694	NP_001035784			inner centromere protein antigens 135/155kDa						chromosome segregation|cytokinesis|mitotic prometaphase	centromeric heterochromatin|condensed chromosome kinetochore|cytosol|microtubule|spindle	protein binding			lung(1)	1														0.504132	182.065849	182.067549	61	60	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	61654639	61654639	8034	11	G	A	A	48	48	INCENP	A	5	2
RIC3	79608	broad.mit.edu	36	11	8147009	8147009	+	Missense_Mutation	SNP	T	C	C			TCGA-12-0618-01	TCGA-12-0618-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:8147009T>C	uc001mgd.1	-	c.104A>G	c.(103-105)GAG>GGG	p.E35G	RIC3_uc001mgc.1_Missense_Mutation_p.E35G|RIC3_uc009yfm.1_Missense_Mutation_p.E35G|RIC3_uc001mge.1_Missense_Mutation_p.E35G|RIC3_uc009yfn.1_5'UTR|RIC3_uc001mgf.2_Missense_Mutation_p.E35G	NM_024557	NP_078833	Q7Z5B4	RIC3_HUMAN	resistance to inhibitors of cholinesterase 3	35	Lumenal (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				large_intestine(1)|ovary(1)|pancreas(1)	3														0.35	10.353654	10.778919	7	13	TT		KEEP	---	---	---	---	capture		Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)	Missense_Mutation	SNP	8147009	8147009	13829	11	T	C	C	54	54	RIC3	C	4	4
VWF	7450	broad.mit.edu	36	12	5997878	5997878	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5997878G>A	uc001qnn.1	-	c.4967C>T	c.(4966-4968)ACG>ATG	p.T1656M		NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	1656	VWFA 2.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7					Antihemophilic Factor(DB00025)									0.384615	116.886064	118.095966	40	64	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5997878	5997878	17818	12	G	A	A	40	40	VWF	A	1	1
TRIM13	10206	broad.mit.edu	36	13	49485074	49485074	+	Missense_Mutation	SNP	A	T	T			TCGA-12-0618-01	TCGA-12-0618-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:49485074A>T	uc001vdp.1	+	c.1006A>T	c.(1006-1008)ACC>TCC	p.T336S	DLEU2_uc001vdn.1_Intron|DLEU2_uc001vdo.1_Intron|TRIM13_uc001vdq.1_Missense_Mutation_p.T333S|TRIM13_uc001vdr.1_Missense_Mutation_p.T333S|TRIM13_uc001vds.1_Missense_Mutation_p.T333S|TRIM13_uc010adk.1_Missense_Mutation_p.T333S|KCNRG_uc001vdt.1_5'Flank|KCNRG_uc001vdu.1_5'Flank	NM_001007278	NP_998755	O60858	TRI13_HUMAN	ret finger protein 2 isoform 2	333	Helical; (Potential).				anatomical structure morphogenesis|ER-associated protein catabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination	cytoplasm|endoplasmic reticulum membrane|integral to membrane	protein binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)												0.434622	729.854915	731.870381	236	307	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)	Missense_Mutation	SNP	49485074	49485074	17032	13	A	T	T	14	14	TRIM13	T	4	4
SLITRK6	84189	broad.mit.edu	36	13	85267238	85267238	+	Missense_Mutation	SNP	G	T	T			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:85267238G>T	uc001vll.1	-	c.1407C>A	c.(1405-1407)AAC>AAA	p.N469K	SLITRK6_uc010afe.1_Intron|SLITRK6_uc010aff.1_Missense_Mutation_p.N469K	NM_032229	NP_115605	Q9H5Y7	SLIK6_HUMAN	slit and trk like 6	469	Extracellular (Potential).|LRR 10.			N -> H (in Ref. 1).		integral to membrane				large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_neural(89;0.117)|Medulloblastoma(90;0.163)													0.137778	50.865536	79.426151	31	194	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.0456)	Missense_Mutation	SNP	85267238	85267238	15245	13	G	T	T	44	44	SLITRK6	T	3	3
SLITRK5	26050	broad.mit.edu	36	13	87128053	87128053	+	Missense_Mutation	SNP	G	C	C			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:87128053G>C	uc001vln.1	+	c.2409G>C	c.(2407-2409)CAG>CAC	p.Q803H	SLITRK5_uc010afg.1_Missense_Mutation_p.Q803H	NM_015567	NP_056382	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	803	Cytoplasmic (Potential).					integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5	all_neural(89;0.101)|Medulloblastoma(90;0.163)													0.333333	7.086452	7.386453	4	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87128053	87128053	15244	13	G	C	C	34	34	SLITRK5	C	3	3
SERPINA11	256394	broad.mit.edu	36	14	93982517	93982517	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:93982517G>A	uc001ydd.1	-	c.821C>T	c.(820-822)GCG>GTG	p.A274V		NM_001080451	NP_001073920	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1	274					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			kidney(1)	1														0.451389	379.605727	380.198988	130	158	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(157;0.211)	Missense_Mutation	SNP	93982517	93982517	14576	14	G	A	A	38	38	SERPINA11	A	1	1
NUP88	4927	broad.mit.edu	36	17	5263567	5263567	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:5263567G>A	uc002gbo.1	-	c.128C>T	c.(127-129)GCT>GTT	p.A43V	NUP88_uc010cle.1_Missense_Mutation_p.A43V|RPAIN_uc002gbp.1_5'Flank|RPAIN_uc002gbq.1_5'Flank|RPAIN_uc002gbw.1_5'Flank|RPAIN_uc002gbs.1_5'Flank|RPAIN_uc002gbt.1_5'Flank|RPAIN_uc002gbr.1_5'Flank|RPAIN_uc002gbu.1_5'Flank|RPAIN_uc002gbv.1_5'Flank	NM_002532	NP_002523	Q99567	NUP88_HUMAN	nucleoporin 88kDa	43					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	transporter activity			kidney(1)	1										6				0.938596	696.544225	731.682258	214	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5263567	5263567	11176	17	G	A	A	34	34	NUP88	A	2	2
INTS2	57508	broad.mit.edu	36	17	57301211	57301211	+	Silent	SNP	A	G	G			TCGA-12-0618-01	TCGA-12-0618-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:57301211A>G	uc002izn.1	-	c.3234T>C	c.(3232-3234)CGT>CGC	p.R1078R	INTS2_uc002izm.1_Silent_p.R1070R	NM_020748	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	1078					snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3														0.131148	9.763162	17.829361	8	53	AA		KEEP	---	---	---	---	capture			Silent	SNP	57301211	57301211	8079	17	A	G	G	2	2	INTS2	G	4	4
FADS6	283985	broad.mit.edu	36	17	70401244	70401244	+	Silent	SNP	C	A	A			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:70401244C>A	uc002jmd.1	-	c.45G>T	c.(43-45)CCG>CCT	p.P15P		NM_178128	NP_835229	Q8N9I5	FADS6_HUMAN	fatty acid desaturase domain family, member 6	21					fatty acid biosynthetic process|oxidation-reduction process	integral to membrane	oxidoreductase activity				0	all_lung(278;0.172)|Lung NSC(278;0.207)													0.25	9.491974	10.401421	4	12	CC		KEEP	---	---	---	---	capture			Silent	SNP	70401244	70401244	5565	17	C	A	A	23	23	FADS6	A	3	3
TP53	7157	broad.mit.edu	36	17	7518293	7518293	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518293C>T	uc002gim.2	-	c.713G>A	c.(712-714)TGT>TAT	p.C238Y	TP53_uc002gig.1_Missense_Mutation_p.C238Y|TP53_uc002gih.1_Missense_Mutation_p.C238Y|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.C106Y|TP53_uc010cng.1_Missense_Mutation_p.C106Y|TP53_uc002gii.1_Missense_Mutation_p.C106Y|TP53_uc010cnh.1_Missense_Mutation_p.C238Y|TP53_uc010cni.1_Missense_Mutation_p.C238Y|TP53_uc002gij.2_Missense_Mutation_p.C238Y|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.C145Y|TP53_uc002gio.2_Missense_Mutation_p.C106Y	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	238	|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).	Zinc.	C -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> F (in sporadic cancers; somatic mutation).|C -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> Y (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> R (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.C238Y(46)|p.C238F(28)|p.C238S(6)|p.0?(6)|p.C238fs*21(1)|p.M237_N239delMCN(1)|p.Y236_M243delYMCNSSCM(1)|p.C238del(1)|p.H233fs*6(1)|p.V225fs*23(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)|p.M237fs*1(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.C238S(LN18-Tumor)|p.C238Y(MC116-Tumor)|p.C238S(MOLM16-Tumor)|p.C238S(SNU626-Tumor)|p.C238fs(SW1417-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.923077	272.163483	288.830023	84	7	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7518293	7518293	16923	17	C	T	T	17	17	TP53	T	2	2
ZCCHC2	54877	broad.mit.edu	36	18	58394774	58394774	+	Silent	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:58394774G>A	uc002lip.2	+	c.3519G>A	c.(3517-3519)ACG>ACA	p.T1173T	ZCCHC2_uc002lio.2_Non-coding_Transcript|ZCCHC2_uc002liq.1_Silent_p.T643T	NM_017742	NP_060212	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	1173					cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding				0														0.42623	77.259747	77.54433	26	35	GG		KEEP	---	---	---	---	capture			Silent	SNP	58394774	58394774	18175	18	G	A	A	40	40	ZCCHC2	A	1	1
ZNF492	57615	broad.mit.edu	36	19	22638494	22638494	+	Missense_Mutation	SNP	T	A	A			TCGA-12-0618-01	TCGA-12-0618-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:22638494T>A	uc002nqw.2	+	c.183T>A	c.(181-183)AAT>AAA	p.N61K		NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492	61					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)												0.551724	54.003393	54.070997	16	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22638494	22638494	18537	19	T	A	A	52	52	ZNF492	A	4	4
MAG	4099	broad.mit.edu	36	19	40492853	40492853	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40492853G>A	uc002nyy.1	+	c.1468G>A	c.(1468-1470)GCG>ACG	p.A490T	MAG_uc002nyz.1_Missense_Mutation_p.A490T|MAG_uc002nyx.1_Missense_Mutation_p.A490T|MAG_uc010eds.1_Missense_Mutation_p.A465T	NM_002361	NP_002352	P20916	MAG_HUMAN	myelin associated glycoprotein isoform a	490	Ig-like C2-type 4.|Extracellular (Potential).				blood coagulation|cell adhesion|leukocyte migration|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane	sugar binding			central_nervous_system(1)	1	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)												0.452991	157.559092	157.784433	53	64	GG		KEEP	---	---	---	---	capture	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		Missense_Mutation	SNP	40492853	40492853	9539	19	G	A	A	38	38	MAG	A	1	1
SARS2	54938	broad.mit.edu	36	19	44100586	44100586	+	Missense_Mutation	SNP	T	G	G			TCGA-12-0618-01	TCGA-12-0618-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:44100586T>G	uc002oka.1	-	c.950A>C	c.(949-951)GAC>GCC	p.D317A	SARS2_uc002ojz.1_Missense_Mutation_p.D127A|SARS2_uc002okb.1_Missense_Mutation_p.D317A	NM_017827	NP_060297	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2	317					seryl-tRNA aminoacylation	mitochondrial matrix	ATP binding|protein binding|serine-tRNA ligase activity			ovary(1)|pancreas(1)	2	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)													0.2	6.616615	7.872187	3	12	TT		KEEP	---	---	---	---	capture	Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)		Missense_Mutation	SNP	44100586	44100586	14326	19	T	G	G	58	58	SARS2	G	4	4
ZNF524	147807	broad.mit.edu	36	19	60805534	60805534	+	Missense_Mutation	SNP	A	G	G			TCGA-12-0618-01	TCGA-12-0618-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60805534A>G	uc002qlk.1	+	c.244A>G	c.(244-246)AGC>GGC	p.S82G	FIZ1_uc002qli.2_5'Flank|FIZ1_uc002qlj.2_5'Flank|ZNF524_uc010eta.1_Missense_Mutation_p.S82G	NM_153219	NP_694951	Q96C55	ZN524_HUMAN	zinc finger protein 524	82					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.285714	7.187778	7.769457	4	10	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)	Missense_Mutation	SNP	60805534	60805534	18560	19	A	G	G	11	11	ZNF524	G	4	4
ARHGEF18	23370	broad.mit.edu	36	19	7437967	7437967	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7437967G>A	uc002mgi.1	+	c.2408G>A	c.(2407-2409)CGG>CAG	p.R803Q	ARHGEF18_uc002mgg.1_Missense_Mutation_p.R645Q|ARHGEF18_uc002mgh.1_Missense_Mutation_p.R645Q|ARHGEF18_uc002mgj.1_Missense_Mutation_p.R446Q	NM_015318	NP_056133	Q6ZSZ5	ARHGI_HUMAN	Rho-specific guanine nucleotide exchange factor	803	Potential.				actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)												0.47541	270.622402	270.717772	87	96	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7437967	7437967	915	19	G	A	A	39	39	ARHGEF18	A	1	1
FLG2	388698	broad.mit.edu	36	1	150590839	150590839	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150590839G>A	uc001ezw.2	-	c.6047C>T	c.(6046-6048)ACA>ATA	p.T2016I		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	2016	Filaggrin 9.						calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.451937	883.171181	884.581306	315	382	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150590839	150590839	6161	1	G	A	A	48	48	FLG2	A	2	2
SPTA1	6708	broad.mit.edu	36	1	156851661	156851661	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156851661G>A	uc001fst.1	-	c.6757C>T	c.(6757-6759)CAA>TAA	p.Q2253*		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2253	Spectrin 21.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.497619	599.050506	599.052481	209	211	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	156851661	156851661	15630	1	G	A	A	46	46	SPTA1	A	5	2
IGFN1	91156	broad.mit.edu	36	1	199458575	199458575	+	Missense_Mutation	SNP	T	G	G			TCGA-12-0618-01	TCGA-12-0618-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199458575T>G	uc001gwc.1	+	c.1767T>G	c.(1765-1767)TTT>TTG	p.F589L	IGFN1_uc001gwb.1_Non-coding_Transcript	NM_178275	NP_840059			immunoglobulin-like and fibronectin type III											ovary(2)|pancreas(1)	3												OREG0014073	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.427184	152.792248	153.266662	44	59	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	199458575	199458575	7891	1	T	G	G	63	63	IGFN1	G	4	4
LIN9	286826	broad.mit.edu	36	1	224487519	224487519	+	Splice_Site_SNP	SNP	T	C	C			TCGA-12-0618-01	TCGA-12-0618-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:224487519T>C	uc001hqa.1	-	c.1474_splice	c.e14-1	p.C492_splice	LIN9_uc001hqb.1_Splice_Site_SNP_p.C457_splice|LIN9_uc001hqc.1_Splice_Site_SNP_p.C424_splice|LIN9_uc009xel.1_Intron	NM_173083	NP_775106			lin-9 homolog						cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)					Ovarian(197;1696 2974 11248 14117)								0.49	364.460977	364.477898	98	102	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(131;0.131)	Splice_Site_SNP	SNP	224487519	224487519	9140	1	T	C	C	53	53	LIN9	C	5	4
DLGAP3	58512	broad.mit.edu	36	1	35104386	35104386	+	Missense_Mutation	SNP	T	C	C			TCGA-12-0618-01	TCGA-12-0618-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:35104386T>C	uc001byc.1	-	c.2825A>G	c.(2824-2826)GAA>GGA	p.E942G		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	942					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)												0.428571	8.856473	8.934349	6	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35104386	35104386	4741	1	T	C	C	62	62	DLGAP3	C	4	4
EIF2C3	192669	broad.mit.edu	36	1	36247218	36247218	+	Missense_Mutation	SNP	T	C	C			TCGA-12-0618-01	TCGA-12-0618-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36247218T>C	uc001bzp.1	+	c.1015T>C	c.(1015-1017)TAC>CAC	p.Y339H	EIF2C3_uc001bzq.1_Missense_Mutation_p.Y105H	NM_024852	NP_803171	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3	339	PAZ.				mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				Colon(144;60 2363 31043 40539)								0.222222	7.115853	11.384045	12	42	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36247218	36247218	5196	1	T	C	C	53	53	EIF2C3	C	4	4
KLF17	128209	broad.mit.edu	36	1	44367723	44367723	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:44367723G>A	uc001clp.1	+	c.193G>A	c.(193-195)GCA>ACA	p.A65T	KLF17_uc009vxf.1_Missense_Mutation_p.A28T	NM_173484	NP_775755	Q5JT82	KLF17_HUMAN	zinc finger protein 393	65					regulation of transcription from RNA polymerase II promoter	nucleus	promoter binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)													0.444444	142.791169	143.080453	48	60	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44367723	44367723	8657	1	G	A	A	38	38	KLF17	A	1	1
RPN2	6185	broad.mit.edu	36	20	35298482	35298482	+	Silent	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:35298482G>A	uc002xgp.1	+	c.1839G>A	c.(1837-1839)ACG>ACA	p.T613T	RPN2_uc002xgq.1_Silent_p.T581T	NM_002951	NP_002942	P04844	RPN2_HUMAN	ribophorin II isoform 1 precursor	613	Helical; (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|nucleus|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)												0.463415	165.701363	165.839212	57	66	GG		KEEP	---	---	---	---	capture			Silent	SNP	35298482	35298482	14087	20	G	A	A	40	40	RPN2	A	1	1
TSHZ2	128553	broad.mit.edu	36	20	51304068	51304068	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:51304068G>A	uc002xwo.2	+	c.664G>A	c.(664-666)GCG>ACG	p.A222T		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	222	C2H2-type 1.				multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4														0.376471	87.072683	88.213111	32	53	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(23;0.1)		Missense_Mutation	SNP	51304068	51304068	17175	20	G	A	A	38	38	TSHZ2	A	1	1
INPP5J	27124	broad.mit.edu	36	22	29854557	29854557	+	Nonsense_Mutation	SNP	C	T	T			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:29854557C>T	uc003aju.2	+	c.2110C>T	c.(2110-2112)CAG>TAG	p.Q704*	INPP5J_uc003ajw.2_Nonsense_Mutation_p.Q140*|INPP5J_uc003ajv.2_Nonsense_Mutation_p.Q337*|INPP5J_uc003ajs.2_Nonsense_Mutation_p.Q337*|INPP5J_uc010gwg.1_Nonsense_Mutation_p.Q269*|INPP5J_uc003ajt.2_Nonsense_Mutation_p.Q336*|INPP5J_uc003ajx.1_Nonsense_Mutation_p.Q69*|INPP5J_uc003ajy.1_Nonsense_Mutation_p.Q69*|INPP5J_uc003ajz.1_Nonsense_Mutation_p.Q144*	NM_001002837	NP_001002837	Q15735	PI5PA_HUMAN	phosphatidylinositol (4,5) bisphosphate	704	Catalytic (Potential).					cytoplasm|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|SH3 domain binding			skin(1)	1														0.446667	215.606878	215.978575	67	83	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	29854557	29854557	8060	22	C	T	T	21	21	INPP5J	T	5	2
PHF5A	84844	broad.mit.edu	36	22	40193471	40193471	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:40193471C>T	uc003bab.1	-	c.170G>A	c.(169-171)CGC>CAC	p.R57H	ACO2_uc003bac.1_5'Flank|ACO2_uc003bad.1_5'Flank	NM_032758	NP_116147	Q7RTV0	PHF5A_HUMAN	PHD-finger 5A	57					nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent	nuclear speck|U12-type spliceosomal complex|U2 snRNP	DNA binding|sequence-specific DNA binding transcription factor activity				0						Ovarian(15;130 571 1826 2981 46141)								0.427481	163.777594	164.378537	56	75	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40193471	40193471	12260	22	C	T	T	27	27	PHF5A	T	1	1
LRP2	4036	broad.mit.edu	36	2	169730783	169730783	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:169730783C>T	uc002ues.1	-	c.11663G>A	c.(11662-11664)CGT>CAT	p.R3888H		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	3888	LDL-receptor class A 35.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	23					Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)				p.R3888H(LN18-Tumor)	2055				0.458716	306.391351	306.712749	100	118	CC		KEEP	---	---	---	---	capture		STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Missense_Mutation	SNP	169730783	169730783	9329	2	C	T	T	19	19	LRP2	T	1	1
AOX1	316	broad.mit.edu	36	2	201232143	201232143	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:201232143G>A	uc002uvx.1	+	c.3182G>A	c.(3181-3183)CGT>CAT	p.R1061H	AOX1_uc010fsu.1_Missense_Mutation_p.R427H	NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1	1061					inflammatory response|oxidation-reduction process|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)	5					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)									0.435185	144.113164	144.507837	47	61	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	201232143	201232143	739	2	G	A	A	40	40	AOX1	A	1	1
NEU2	4759	broad.mit.edu	36	2	233607808	233607808	+	Nonsense_Mutation	SNP	C	T	T			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:233607808C>T	uc002vtu.1	+	c.940C>T	c.(940-942)CGA>TGA	p.R314*		NM_005383	NP_005374	Q9Y3R4	NEUR2_HUMAN	neuraminidase 2	314							exo-alpha-sialidase activity				0		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)												0.460465	281.194319	281.486957	99	116	CC		KEEP	---	---	---	---	capture		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Nonsense_Mutation	SNP	233607808	233607808	10741	2	C	T	T	27	27	NEU2	T	5	1
COL6A3	1293	broad.mit.edu	36	2	237945508	237945508	+	Silent	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237945508G>A	uc002vwl.2	-	c.3891C>T	c.(3889-3891)AAC>AAT	p.N1297N	COL6A3_uc002vwk.2_Silent_p.N1297N|COL6A3_uc002vwm.2_Silent_p.N1096N|COL6A3_uc002vwn.2_Silent_p.N1097N|COL6A3_uc002vwo.2_Silent_p.N1091N|COL6A3_uc002vwq.2_Silent_p.N1091N|COL6A3_uc002vwr.2_Silent_p.N890N	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1297	VWFA 7.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity	p.N1297N(1)		ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)												0.395973	163.378844	164.792929	59	90	GG		KEEP	---	---	---	---	capture		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)	Silent	SNP	237945508	237945508	3839	2	G	A	A	40	40	COL6A3	A	1	1
NEU4	129807	broad.mit.edu	36	2	242406957	242406957	+	Missense_Mutation	SNP	C	G	G			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:242406957C>G	uc002wcn.1	+	c.1401C>G	c.(1399-1401)TTC>TTG	p.F467L	NEU4_uc002wcl.1_Non-coding_Transcript|NEU4_uc010fzr.1_Missense_Mutation_p.F455L|NEU4_uc002wcm.1_Missense_Mutation_p.F455L|NEU4_uc002wco.1_Missense_Mutation_p.F455L|NEU4_uc002wcp.1_Missense_Mutation_p.F467L	NM_080741	NP_542779	Q8WWR8	NEUR4_HUMAN	sialidase 4	455						lysosomal lumen|organelle inner membrane	exo-alpha-sialidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)												0.425926	73.916207	74.174672	23	31	CC		KEEP	---	---	---	---	capture		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)	Missense_Mutation	SNP	242406957	242406957	10743	2	C	G	G	32	32	NEU4	G	3	3
IFT172	26160	broad.mit.edu	36	2	27536096	27536096	+	Missense_Mutation	SNP	G	T	T			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:27536096G>T	uc002rku.1	-	c.2626C>A	c.(2626-2628)CAC>AAC	p.H876N		NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog	876	TPR 4.				cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)													0.467433	725.60992	726.095501	244	278	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27536096	27536096	7858	2	G	T	T	45	45	IFT172	T	3	3
RETNLB	84666	broad.mit.edu	36	3	109957334	109957334	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:109957334C>T	uc003dxh.2	-	c.317G>A	c.(316-318)CGC>CAC	p.R106H		NM_032579	NP_115968	Q9BQ08	RETNB_HUMAN	resistin like beta precursor	106					cell proliferation	extracellular region	hormone activity				0														0.385714	229.554726	231.947972	81	129	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109957334	109957334	13707	3	C	T	T	27	27	RETNLB	T	1	1
SEC62	7095	broad.mit.edu	36	3	171177503	171177503	+	Missense_Mutation	SNP	C	A	A			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:171177503C>A	uc003fgg.2	+	c.221C>A	c.(220-222)ACC>AAC	p.T74N	SEC62_uc003fgh.1_Missense_Mutation_p.T74N	NM_003262	NP_003253	Q99442	SEC62_HUMAN	translocation protein 1	74	Cytoplasmic (Potential).				cotranslational protein targeting to membrane|transmembrane transport	aggresome|endoplasmic reticulum membrane|integral to membrane|intermediate filament cytoskeleton|rough endoplasmic reticulum	protein transporter activity|receptor activity			ovary(1)	1														0.435644	133.482282	133.847348	44	57	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	171177503	171177503	14490	3	C	A	A	18	18	SEC62	A	3	3
DKK2	27123	broad.mit.edu	36	4	108066443	108066443	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:108066443C>T	uc003hyi.1	-	c.335G>A	c.(334-336)CGA>CAA	p.R112Q	DKK2_uc003hyj.1_Missense_Mutation_p.R112Q|DKK2_uc010ilw.1_Non-coding_Transcript	NM_014421	NP_055236	Q9UBU2	DKK2_HUMAN	dickkopf homolog 2 precursor	112	DKK-type Cys-1.				multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)												0.471042	367.579803	367.763017	122	137	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)	Missense_Mutation	SNP	108066443	108066443	4725	4	C	T	T	31	31	DKK2	T	1	1
SH3RF2	153769	broad.mit.edu	36	5	145373710	145373710	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:145373710C>T	uc003lnt.1	+	c.952C>T	c.(952-954)CGC>TGC	p.R318C		NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	318							ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)	1														0.457995	478.443076	479.005868	169	200	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Missense_Mutation	SNP	145373710	145373710	14751	5	C	T	T	27	27	SH3RF2	T	1	1
PRELID1	27166	broad.mit.edu	36	5	176666174	176666174	+	Silent	SNP	G	T	T			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176666174G>T	uc003mfx.1	+	c.657G>T	c.(655-657)GTG>GTT	p.V219V	RAB24_uc003mfu.1_5'Flank|RAB24_uc003mfv.1_5'Flank|RAB24_uc003mfw.1_5'Flank|PRELID1_uc003mfy.1_Silent_p.V217V|MXD3_uc010jkk.1_3'UTR	NM_013237	NP_037369	Q9Y255	PRLD1_HUMAN	PRELI domain containing 1	219					immune response|multicellular organismal development	mitochondrion|nucleus					0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)												0.333333	7.479983	7.783264	4	8	GG		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Silent	SNP	176666174	176666174	12914	5	G	T	T	48	48	PRELID1	T	3	3
CRISP3	10321	broad.mit.edu	36	6	49804513	49804513	+	Silent	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:49804513G>A	uc003ozs.1	-	c.627C>T	c.(625-627)TAC>TAT	p.Y209Y	CRISP3_uc003ozt.2_Silent_p.Y209Y	NM_006061	NP_006052	P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	209					innate immune response	proteinaceous extracellular matrix|specific granule				skin(1)	1	Lung NSC(77;0.0161)													0.354839	93.245968	94.974056	33	60	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)		Silent	SNP	49804513	49804513	4020	6	G	A	A	40	40	CRISP3	A	1	1
ORAI2	80228	broad.mit.edu	36	7	101873980	101873980	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:101873980G>A	uc010lhz.1	+	c.241G>A	c.(241-243)GTG>ATG	p.V81M	ORAI2_uc003uzj.2_Missense_Mutation_p.V81M|ORAI2_uc003uzk.2_Missense_Mutation_p.V81M	NM_001126340	NP_001119812	Q96SN7	ORAI2_HUMAN	ORAI calcium release-activated calcium modulator	81	Helical; (Potential).					integral to membrane	protein binding			ovary(1)|kidney(1)	2														0.304348	74.670452	77.809899	28	64	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101873980	101873980	11669	7	G	A	A	44	44	ORAI2	A	2	2
ABCB4	5244	broad.mit.edu	36	7	86917293	86917293	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86917293C>T	uc003uiv.1	-	c.760G>A	c.(760-762)GCC>ACC	p.A254T	ABCB4_uc003uiw.1_Missense_Mutation_p.A254T|ABCB4_uc003uix.1_Missense_Mutation_p.A254T	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	254	ABC transmembrane type-1 1.|Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|pancreas(1)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)													0.311111	295.4604	306.904502	112	248	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86917293	86917293	44	7	C	T	T	27	27	ABCB4	T	1	1
EYA1	2138	broad.mit.edu	36	8	72319450	72319450	+	Missense_Mutation	SNP	C	A	A			TCGA-12-0618-01	TCGA-12-0618-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:72319450C>A	uc003xys.2	-	c.1082G>T	c.(1081-1083)CGA>CTA	p.R361L	EYA1_uc003xyt.2_Missense_Mutation_p.R328L|EYA1_uc003xyr.2_Intron|EYA1_uc010lzf.1_Missense_Mutation_p.R288L|EYA1_uc003xyu.1_Missense_Mutation_p.R361L|EYA1_uc003xyv.1_Missense_Mutation_p.R239L	NM_172058	NP_742055	Q99502	EYA1_HUMAN	eyes absent 1 isoform b	361					double-strand break repair|histone dephosphorylation|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|sensory perception of sound|transcription, DNA-dependent	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity	p.R361L(1)		ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	5	Breast(64;0.046)													0.466667	68.772564	68.815969	21	24	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.0837)|all cancers(69;0.247)		Missense_Mutation	SNP	72319450	72319450	5522	8	C	A	A	31	31	EYA1	A	3	3
PRDM12	59335	broad.mit.edu	36	9	132533492	132533492	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0618-01	TCGA-12-0618-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:132533492G>A	uc004bzt.1	+	c.541G>A	c.(541-543)GGC>AGC	p.G181S		NM_021619	NP_067632	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	181	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)												0.268116	199.232366	212.62642	74	202	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;0.000344)	Missense_Mutation	SNP	132533492	132533492	12895	9	G	A	A	39	39	PRDM12	A	1	1
PTEN	5728	broad.mit.edu	36	10	89643759	89643760	+	Splice_Site_Ins	INS	-	AGAT	AGAT			TCGA-12-0618-01	TCGA-12-0618-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:89643759_89643760insAGAT	uc001kfb.1	+	c.e3_splice_site				NM_000314	NP_000305			phosphatase and tensin homolog						apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.0?(12)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)				31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.80			49	12				---	---	---	---	capture_indel			Splice_Site_Ins	INS	89643759	89643760	13192	10	-	AGAT	AGAT	29	29	PTEN	AGAT	5	5
EZH2	2146	broad.mit.edu	36	7	148145939	148145942	+	Frame_Shift_Del	DEL	TTCT	-	-			TCGA-12-0618-01	TCGA-12-0618-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:148145939_148145942delTTCT	uc003wfb.1	-	c.1200_1203delAGAA	c.(1198-1203)AAAGAAfs	p.K400fs	EZH2_uc003wfc.1_Frame_Shift_Del_p.K356fs|EZH2_uc003wfd.1_Frame_Shift_Del_p.K395fs	NM_004456	NP_004447	Q15910	EZH2_HUMAN	enhancer of zeste 2 isoform a	395_396					negative regulation of retinoic acid receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding|transcription repressor activity	p.E401fs*22(1)		haematopoietic_and_lymphoid_tissue(169)|skin(2)|large_intestine(1)	172	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)											0.31			158	352				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	148145939	148145942	5528	7	TTCT	-	-	56	56	EZH2	-	5	5
