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
C10orf2	56652	broad.mit.edu	36	10	102738151	102738151	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:102738151G>A	uc001ksf.1	+	c.194G>A	c.(193-195)CGG>CAG	p.R65Q	MRPL43_uc001kry.1_5'Flank|MRPL43_uc001krz.1_5'Flank|MRPL43_uc001ksa.1_5'Flank|MRPL43_uc001ksb.1_5'Flank|MRPL43_uc001ksd.1_5'Flank|MRPL43_uc001ksc.2_5'Flank|MRPL43_uc001kse.1_5'Flank|C10orf2_uc001ksg.1_Missense_Mutation_p.R65Q|C10orf2_uc001ksh.1_Intron|C10orf2_uc001ksi.1_Intron	NM_021830	NP_068602	Q96RR1	PEO1_HUMAN	twinkle	65					cell death|mitochondrial DNA replication|protein hexamerization|protein homooligomerization|transcription from mitochondrial promoter	mitochondrial nucleoid	5'-3' DNA helicase activity|ATP binding|protease binding|single-stranded DNA binding			ovary(1)	1		Colorectal(252;0.122)|all_hematologic(284;0.152)												0.604061	389.889465	391.770601	119	78	GG		KEEP	---	---	---	---	capture		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)|BRCA - Breast invasive adenocarcinoma(275;0.224)	Missense_Mutation	SNP	102738151	102738151	1634	10	G	A	A	39	39	C10orf2	A	1	1
TMEM119	338773	broad.mit.edu	36	12	107510169	107510169	+	Silent	SNP	A	C	C			TCGA-28-5219-01	TCGA-28-5219-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:107510169A>C	uc001tng.1	-	c.120T>G	c.(118-120)GGT>GGG	p.G40G	TMEM119_uc001tnf.1_Non-coding_Transcript|TMEM119_uc009zuz.1_Silent_p.G40G	NM_181724	NP_859075	Q4V9L6	TM119_HUMAN	transmembrane protein 119	40	Extracellular (Potential).					integral to membrane				ovary(1)	1														0.384615	11.484486	11.631325	5	8	AA		KEEP	---	---	---	---	capture			Silent	SNP	107510169	107510169	16563	12	A	C	C	14	14	TMEM119	C	4	4
FOXN4	121643	broad.mit.edu	36	12	108203700	108203700	+	Missense_Mutation	SNP	G	T	T			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:108203700G>T	uc001toe.2	-	c.1189C>A	c.(1189-1191)CAC>AAC	p.H397N	FOXN4_uc009zvf.1_Missense_Mutation_p.H217N|FOXN4_uc009zvg.1_Missense_Mutation_p.H194N|FOXN4_uc001tof.2_Missense_Mutation_p.H217N	NM_213596	NP_998761	Q96NZ1	FOXN4_HUMAN	forkhead box N4	397					axon extension|embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|organ development|pattern specification process|positive regulation of gene-specific transcription|regulation of heart contraction|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(1)|lung(1)	2														0.337662	71.02235	72.818916	26	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	108203700	108203700	6268	12	G	T	T	47	47	FOXN4	T	3	3
HVCN1	84329	broad.mit.edu	36	12	109583418	109583418	+	Silent	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:109583418G>A	uc001trs.1	-	c.240C>T	c.(238-240)CCC>CCT	p.P80P	HVCN1_uc001trq.1_Silent_p.P80P|HVCN1_uc001trt.1_Silent_p.P80P	NM_032369	NP_115745	Q96D96	HVCN1_HUMAN	hydrogen voltage-gated channel 1	80	Cytoplasmic (Potential).				response to pH|response to zinc ion	integral to membrane	voltage-gated proton channel activity				0														0.37037	141.319377	143.31077	50	85	GG		KEEP	---	---	---	---	capture			Silent	SNP	109583418	109583418	7762	12	G	A	A	39	39	HVCN1	A	1	1
ETNK1	55500	broad.mit.edu	36	12	22669484	22669484	+	Silent	SNP	T	C	C			TCGA-28-5219-01	TCGA-28-5219-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:22669484T>C	uc001rft.1	+	c.120T>C	c.(118-120)TCT>TCC	p.S40S	ETNK1_uc001rfs.1_Silent_p.S40S|ETNK1_uc009ziz.1_Silent_p.S40S	NM_018638	NP_061108	Q9HBU6	EKI1_HUMAN	ethanolamine kinase 1 isoform A	40					phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|ethanolamine kinase activity				0						Esophageal Squamous(42;87 913 3224 6226 43339)								0.384615	6.707809	6.911887	5	8	TT		KEEP	---	---	---	---	capture			Silent	SNP	22669484	22669484	5466	12	T	C	C	54	54	ETNK1	C	4	4
KRT18	3875	broad.mit.edu	36	12	51631631	51631631	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51631631C>T	uc001sbe.1	+	c.757C>T	c.(757-759)CGG>TGG	p.R253W	KRT8_uc009zml.1_5'Flank|KRT8_uc009zmm.1_5'Flank|KRT18_uc009zmn.1_Missense_Mutation_p.R253W|KRT18_uc001sbf.1_Missense_Mutation_p.R80W|KRT18_uc001sbg.1_Missense_Mutation_p.R253W|KRT18_uc009zmo.1_Missense_Mutation_p.R253W	NM_199187	NP_954657	P05783	K1C18_HUMAN	keratin 18	253	Interaction with DNAJB6.|Coil 2.|Rod.|Necessary for interaction with PNN.				anatomical structure morphogenesis|cell cycle|Golgi to plasma membrane CFTR protein transport|interspecies interaction between organisms|negative regulation of apoptosis	centriolar satellite|keratin filament|perinuclear region of cytoplasm	protein binding|structural molecule activity				0														0.333333	79.24945	81.387982	29	58	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51631631	51631631	8770	12	C	T	T	23	23	KRT18	T	1	1
C12orf12	196477	broad.mit.edu	36	12	89871659	89871659	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:89871659C>G	uc001tbj.1	-	c.992G>C	c.(991-993)GGA>GCA	p.G331A		NM_152638	NP_689851	Q8TC90	CL012_HUMAN	hypothetical protein LOC196477	331	Potential.|Glu-rich.									central_nervous_system(1)|pancreas(1)	2														0.43	148.912942	149.339647	43	57	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89871659	89871659	1720	12	C	G	G	30	30	C12orf12	G	3	3
C13orf27	93081	broad.mit.edu	36	13	102216859	102216859	+	Missense_Mutation	SNP	A	G	G			TCGA-28-5219-01	TCGA-28-5219-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:102216859A>G	uc001vpn.1	-	c.454T>C	c.(454-456)TCC>CCC	p.S152P	C13orf27_uc001vpo.1_Missense_Mutation_p.S152P|C13orf27_uc001vpp.1_Missense_Mutation_p.S152P	NM_138779	NP_620134	Q5JUR7	CM027_HUMAN	hypothetical protein LOC93081	193							hydrolase activity				0	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)													0.62766	221.650377	222.996682	59	35	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102216859	102216859	1770	13	A	G	G	9	9	C13orf27	G	4	4
MGA	23269	broad.mit.edu	36	15	39828154	39828154	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39828154C>A	uc001zoh.1	+	c.5387C>A	c.(5386-5388)ACT>AAT	p.T1796N	MGA_uc001zoi.2_5'UTR	NM_001080541	NP_001074010	Q8IWI9	MGAP_HUMAN	MAX gene associated	1747					regulation of transcription, DNA-dependent	MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|skin(1)	11		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)								606				0.2	6.985155	8.664238	4	16	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Missense_Mutation	SNP	39828154	39828154	9930	15	C	A	A	20	20	MGA	A	3	3
GTF3C1	2975	broad.mit.edu	36	16	27407214	27407214	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27407214C>G	uc002dov.1	-	c.3535G>C	c.(3535-3537)GGG>CGG	p.G1179R	GTF3C1_uc002dou.2_Missense_Mutation_p.G1179R	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	1179					5S class rRNA transcription from RNA polymerase III type 1 promoter|tRNA transcription from RNA polymerase III promoter	transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|breast(1)|pancreas(1)	4														0.292929	261.402114	272.805919	87	210	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27407214	27407214	7152	16	C	G	G	22	22	GTF3C1	G	3	3
MYH13	8735	broad.mit.edu	36	17	10206486	10206486	+	Silent	SNP	G	A	A	rs61745307	unknown	TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10206486G>A	uc002gmk.1	-	c.264C>T	c.(262-264)ATC>ATT	p.I88I		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	88	Myosin head-like.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.722045	734.263547	748.142406	226	87	GG		KEEP	---	---	---	---	capture			Silent	SNP	10206486	10206486	10427	17	G	A	A	37	37	MYH13	A	1	1
TP53	7157	broad.mit.edu	36	17	7520424	7520424	+	Splice_Site_SNP	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7520424C>T	uc002gim.2	-	c.96_splice	c.e3+1	p.L32_splice	TP53_uc002gig.1_Splice_Site_SNP_p.L32_splice|TP53_uc002gih.1_Splice_Site_SNP_p.L32_splice|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Splice_Site_SNP_p.L32_splice|TP53_uc010cni.1_Splice_Site_SNP_p.L32_splice|TP53_uc002gij.2_Splice_Site_SNP_p.L32_splice|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Splice_Site_SNP_p.L32_splice|TP53_uc002gio.2_Intron|TP53_uc010cnk.1_Splice_Site_SNP_p.L47_splice	NM_001126112	NP_001119584			tumor protein p53 isoform a						activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.0?(6)|p.?(2)|p.S33fs*10(1)|p.P13fs*18(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		690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.688172	205.824571	208.754199	64	29	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Splice_Site_SNP	SNP	7520424	7520424	16923	17	C	T	T	18	18	TP53	T	5	2
NOTCH3	4854	broad.mit.edu	36	19	15141951	15141951	+	Silent	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15141951C>T	uc002nan.1	-	c.5145G>A	c.(5143-5145)GGG>GGA	p.G1715G		NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3	1715	Cytoplasmic (Potential).				Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			ovary(5)|lung(2)|central_nervous_system(1)	8										417				0.307692	21.890228	22.747408	8	18	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)		Silent	SNP	15141951	15141951	10953	19	C	T	T	22	22	NOTCH3	T	2	2
MBD3	53615	broad.mit.edu	36	19	1529435	1529435	+	Silent	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1529435C>T	uc002ltl.1	-	c.780G>A	c.(778-780)GCG>GCA	p.A260A	MBD3_uc002ltj.2_Silent_p.A260A|MBD3_uc002ltk.2_Silent_p.A228A	NM_003926	NP_003917	O95983	MBD3_HUMAN	methyl-CpG binding domain protein 3	260					transcription, DNA-dependent	NuRD complex	DNA binding|protein binding			ovary(1)|pancreas(1)	2		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)												0.392157	103.712331	104.738354	40	62	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.179)|STAD - Stomach adenocarcinoma(1328;0.18)	Silent	SNP	1529435	1529435	9728	19	C	T	T	27	27	MBD3	T	1	1
FKBP8	23770	broad.mit.edu	36	19	18509452	18509452	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18509452G>A	uc002njj.1	-	c.904C>T	c.(904-906)CAC>TAC	p.H302Y	FKBP8_uc002nji.1_Missense_Mutation_p.H139Y|FKBP8_uc002njk.1_Missense_Mutation_p.H301Y|FKBP8_uc002njl.1_Missense_Mutation_p.H302Y|FKBP8_uc002njm.1_Missense_Mutation_p.H301Y|FKBP8_uc010ebr.1_Missense_Mutation_p.H140Y|FKBP8_uc002njn.1_Non-coding_Transcript	NM_012181	NP_036313	Q14318	FKBP8_HUMAN	FK506-binding protein 8	301	TPR 2.				apoptosis|interspecies interaction between organisms|intracellular signal transduction|protein folding	integral to endoplasmic reticulum membrane|mitochondrial membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1														0.411765	90.526126	91.098029	35	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18509452	18509452	6152	19	G	A	A	46	46	FKBP8	A	2	2
ZNF257	113835	broad.mit.edu	36	19	22063137	22063137	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:22063137G>A	uc010ecx.1	+	c.745G>A	c.(745-747)GTA>ATA	p.V249I	ZNF257_uc010ecy.1_Missense_Mutation_p.V217I	NM_033468	NP_258429	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	249	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.0961)|Lung NSC(12;0.103)												0.322222	80.28549	82.789465	29	61	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22063137	22063137	18391	19	G	A	A	44	44	ZNF257	A	2	2
NFKBIB	4793	broad.mit.edu	36	19	44090040	44090040	+	Silent	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:44090040C>T	uc002ojw.1	+	c.870C>T	c.(868-870)GCC>GCT	p.A290A	NFKBIB_uc002ojx.1_Silent_p.A258A|NFKBIB_uc002ojy.1_Silent_p.A290A	NM_002503	NP_002494	Q15653	IKBB_HUMAN	nuclear factor of kappa light polypeptide gene	290	ANK 6.				innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription, DNA-dependent	cytosol|nucleus	protein binding|signal transducer activity|transcription coactivator activity			kidney(1)	1	all_cancers(60;4.39e-06)|Ovarian(47;0.0454)					Pancreas(165;1492 2005 6979 7739 34483)								0.320988	69.904824	72.219791	26	55	CC		KEEP	---	---	---	---	capture	Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)		Silent	SNP	44090040	44090040	10778	19	C	T	T	22	22	NFKBIB	T	2	2
CEACAM16	388551	broad.mit.edu	36	19	49898711	49898711	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49898711G>C	uc002ozq.1	+	c.467G>C	c.(466-468)GGC>GCC	p.G156A		NM_001039213	NP_001034302	A7LI12	A7LI12_HUMAN	carcinoembryonic antigen-related cell adhesion	97										ovary(1)	1	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)												0.25	7.509402	8.408258	4	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49898711	49898711	3321	19	G	C	C	42	42	CEACAM16	C	3	3
GABRD	2563	broad.mit.edu	36	1	1946946	1946946	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1946946G>A	uc001aip.2	+	c.379G>A	c.(379-381)GTG>ATG	p.V127M		NM_000815	NP_000806	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	127	Extracellular (Probable).					cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)												0.320442	149.783765	154.969656	58	123	GG		KEEP	---	---	---	---	capture		Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)	Missense_Mutation	SNP	1946946	1946946	6420	1	G	A	A	40	40	GABRD	A	1	1
NAV1	89796	broad.mit.edu	36	1	200048909	200048909	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:200048909C>T	uc001gwu.2	+	c.5231C>T	c.(5230-5232)TCG>TTG	p.S1744L	NAV1_uc001gwx.2_Missense_Mutation_p.S1353L	NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1747					cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(2)|ovary(1)	3														0.397351	172.46218	173.856017	60	91	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	200048909	200048909	10579	1	C	T	T	31	31	NAV1	T	1	1
SH2D5	400745	broad.mit.edu	36	1	20926628	20926628	+	Missense_Mutation	SNP	A	C	C			TCGA-28-5219-01	TCGA-28-5219-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:20926628A>C	uc009vpy.1	-	c.143T>G	c.(142-144)GTG>GGG	p.V48G	SH2D5_uc001bdt.1_5'UTR|SH2D5_uc001bdu.1_Intron	NM_001103161	NP_001096631	Q6ZV89	SH2D5_HUMAN	SH2 domain containing 5 isoform 1	Error:Variant_position_missing_in_Q6ZV89_after_alignment											0		Colorectal(325;3.46e-05)|all_lung(284;5.32e-05)|Lung NSC(340;5.51e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)												0.25	6.373883	7.301588	4	12	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|GBM - Glioblastoma multiforme(114;0.000465)|Kidney(64;0.000476)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(64;0.00634)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)	Missense_Mutation	SNP	20926628	20926628	14728	1	A	C	C	6	6	SH2D5	C	4	4
RYR2	6262	broad.mit.edu	36	1	236003506	236003506	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:236003506C>T	uc001hyl.1	+	c.11710C>T	c.(11710-11712)CGG>TGG	p.R3904W		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3904					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)												0.293478	71.687851	75.200746	27	65	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		Missense_Mutation	SNP	236003506	236003506	14249	1	C	T	T	19	19	RYR2	T	1	1
RERE	473	broad.mit.edu	36	1	8606966	8606966	+	Missense_Mutation	SNP	T	G	G			TCGA-28-5219-01	TCGA-28-5219-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:8606966T>G	uc001ape.1	-	c.386A>C	c.(385-387)GAC>GCC	p.D129A	RERE_uc001apf.1_Missense_Mutation_p.D129A|RERE_uc001aph.1_Missense_Mutation_p.D129A	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	129	BAH.				multicellular organismal development|NLS-bearing substrate import into nucleus|regulation of transcription, DNA-dependent	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)												0.373913	294.202542	297.409788	86	144	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)	Missense_Mutation	SNP	8606966	8606966	13700	1	T	G	G	58	58	RERE	G	4	4
C20orf85	128602	broad.mit.edu	36	20	56162070	56162070	+	Missense_Mutation	SNP	A	T	T			TCGA-28-5219-01	TCGA-28-5219-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:56162070A>T	uc002xyv.1	+	c.133A>T	c.(133-135)ACA>TCA	p.T45S		NM_178456	NP_848551	Q9H1P6	CT085_HUMAN	hypothetical protein LOC128602	45										ovary(1)	1	all_epithelial(3;5.99e-14)|Lung NSC(12;0.000152)|all_lung(29;0.000518)|Melanoma(10;0.118)													0.336879	272.144442	278.77853	95	187	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(13;5.53e-12)|Epithelial(14;7.42e-08)|all cancers(14;7.19e-07)		Missense_Mutation	SNP	56162070	56162070	2200	20	A	T	T	2	2	C20orf85	T	4	4
TMPRSS15	5651	broad.mit.edu	36	21	18635636	18635636	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:18635636G>C	uc002ykw.1	-	c.1529C>G	c.(1528-1530)CCA>CGA	p.P510R		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	510	Extracellular (Potential).				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|breast(1)	6														0.658228	374.553399	378.052827	104	54	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18635636	18635636	16787	21	G	C	C	47	47	TMPRSS15	C	3	3
RIPK4	54101	broad.mit.edu	36	21	42034529	42034529	+	Silent	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42034529G>A	uc002yzn.1	-	c.1893C>T	c.(1891-1893)AAC>AAT	p.N631N		NM_020639	NP_065690	Q9H4D1	Q9H4D1_HUMAN	ankyrin repeat domain 3	631					protein phosphorylation	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7										268				0.714286	307.022025	312.782207	100	40	GG		KEEP	---	---	---	---	capture			Silent	SNP	42034529	42034529	13860	21	G	A	A	40	40	RIPK4	A	1	1
PRAME	23532	broad.mit.edu	36	22	21222481	21222481	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:21222481C>T	uc002zwf.1	-	c.620G>A	c.(619-621)CGC>CAC	p.R207H	PRAME_uc010gtr.1_Missense_Mutation_p.R207H|PRAME_uc002zwg.1_Missense_Mutation_p.R207H|PRAME_uc002zwh.1_Missense_Mutation_p.R207H|PRAME_uc002zwi.1_Missense_Mutation_p.R207H|PRAME_uc002zwj.1_Missense_Mutation_p.R207H|PRAME_uc002zwk.1_Missense_Mutation_p.R207H	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	207					apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|positive regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding|transcription repressor activity			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)				Melanoma(73;1707 1838 15168 27201)				1184				0.348624	197.718626	202.13385	76	142	CC		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(21;0.0649)	Missense_Mutation	SNP	21222481	21222481	12860	22	C	T	T	27	27	PRAME	T	1	1
PLXNB2	23654	broad.mit.edu	36	22	49063290	49063290	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49063290G>C	uc003bkv.2	-	c.2964C>G	c.(2962-2964)TTC>TTG	p.F988L	PLXNB2_uc003bkt.1_5'Flank|PLXNB2_uc003bku.1_5'Flank	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2	988	IPT/TIG 3.|Extracellular (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)	5		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.277778	10.96731	11.767356	5	13	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49063290	49063290	12550	22	G	C	C	37	37	PLXNB2	C	3	3
TTN	7273	broad.mit.edu	36	2	179147197	179147197	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179147197G>A	uc002umr.1	-	c.64204C>T	c.(64204-64206)CGG>TGG	p.R21402W	TTN_uc002ums.1_Missense_Mutation_p.R15097W|TTN_uc010frc.1_Missense_Mutation_p.R15030W|TTN_uc010frd.1_Missense_Mutation_p.R14905W	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	22329								p.R21402C(1)		ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.265487	71.295761	76.914505	30	83	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179147197	179147197	17290	2	G	A	A	40	40	TTN	A	1	1
TTN	7273	broad.mit.edu	36	2	179174710	179174710	+	Missense_Mutation	SNP	C	A	A			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179174710C>A	uc002umr.1	-	c.47648G>T	c.(47647-47649)CGA>CTA	p.R15883L	TTN_uc002ums.1_Missense_Mutation_p.R9578L|TTN_uc010frc.1_Missense_Mutation_p.R9511L|TTN_uc010frd.1_Missense_Mutation_p.R9386L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16810										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.319149	168.436519	173.899347	60	128	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179174710	179174710	17290	2	C	A	A	31	31	TTN	A	3	3
DNAH7	56171	broad.mit.edu	36	2	196533854	196533854	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:196533854G>A	uc002utj.2	-	c.2266C>T	c.(2266-2268)CGT>TGT	p.R756C		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	756	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(2)	2														0.337838	201.559003	206.720653	75	147	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	196533854	196533854	4789	2	G	A	A	40	40	DNAH7	A	1	1
ABCG8	64241	broad.mit.edu	36	2	43933063	43933063	+	Missense_Mutation	SNP	G	A	A	rs9282574	by-cluster,by-frequency,by-hapmap	TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:43933063G>A	uc002rtq.1	+	c.628G>A	c.(628-630)GTG>ATG	p.V210M		NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8	210	ABC transporter.|Cytoplasmic (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|intestinal cholesterol absorption|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)												0.364583	95.398863	96.94725	35	61	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43933063	43933063	73	2	G	A	A	40	40	ABCG8	A	1	1
TMEM14E	645843	broad.mit.edu	36	3	153541222	153541222	+	Silent	SNP	A	G	G			TCGA-28-5219-01	TCGA-28-5219-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:153541222A>G	uc010hvo.1	-	c.162T>C	c.(160-162)TCT>TCC	p.S54S	MBNL1_uc003ezh.1_Intron|MBNL1_uc003ezi.1_Intron|MBNL1_uc003ezj.1_Intron|MBNL1_uc003ezm.1_Intron|MBNL1_uc003ezl.1_Intron|MBNL1_uc003ezp.1_Intron|MBNL1_uc003ezn.1_Intron|MBNL1_uc003ezo.1_Intron	NM_001123228	NP_001116700	Q6UXP3	TM14E_HUMAN	transmembrane protein 14E	54						integral to membrane					0														0.274336	94.27873	99.46009	31	82	AA		KEEP	---	---	---	---	capture			Silent	SNP	153541222	153541222	16598	3	A	G	G	11	11	TMEM14E	G	4	4
SUSD5	26032	broad.mit.edu	36	3	33169590	33169590	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:33169590G>A	uc003cfo.1	-	c.1538C>T	c.(1537-1539)ACG>ATG	p.T513M		NM_015551	NP_056366	O60279	SUSD5_HUMAN	sushi domain containing 5	513	Extracellular (Potential).				cell adhesion	integral to membrane	hyaluronic acid binding			ovary(1)|central_nervous_system(1)	2														0.5	93.099922	93.099922	32	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33169590	33169590	15931	3	G	A	A	40	40	SUSD5	A	1	1
STAB1	23166	broad.mit.edu	36	3	52526149	52526149	+	Silent	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52526149C>T	uc003dej.1	+	c.4473C>T	c.(4471-4473)GAC>GAT	p.D1491D	STAB1_uc003dek.1_5'Flank	NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	1491	Extracellular (Potential).|EGF-like 11.				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	7														0.45283	139.085662	139.291038	48	58	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)	Silent	SNP	52526149	52526149	15755	3	C	T	T	19	19	STAB1	T	1	1
HS3ST1	9957	broad.mit.edu	36	4	11010364	11010364	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:11010364C>T	uc003gmq.1	-	c.364G>A	c.(364-366)GCG>ACG	p.A122T	HS3ST1_uc010ido.1_Missense_Mutation_p.A122T	NM_005114	NP_005105	O14792	HS3S1_HUMAN	heparan sulfate D-glucosaminyl	122						Golgi lumen|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity				0														0.189189	53.260376	66.603711	28	120	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11010364	11010364	7657	4	C	T	T	27	27	HS3ST1	T	1	1
PDE6B	5158	broad.mit.edu	36	4	609881	609881	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:609881G>A	uc003gap.1	+	c.466G>A	c.(466-468)GAG>AAG	p.E156K	PDE6B_uc003gao.2_Missense_Mutation_p.E156K	NM_000283	NP_000274	P35913	PDE6B_HUMAN	rod cGMP-phosphodiesterase beta-subunit isoform	156	GAF 1.				cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0						GBM(71;463 1194 9848 25922 46834)								0.444444	12.298741	12.322966	4	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	609881	609881	12067	4	G	A	A	37	37	PDE6B	A	1	1
UGT2A1	10941	broad.mit.edu	36	4	70489865	70489865	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70489865C>T	uc010ihs.1	-	c.1401G>A	c.(1399-1401)ATG>ATA	p.M467I	UGT2A1_uc003hem.2_Missense_Mutation_p.M466I|UGT2A1_uc010iht.1_Missense_Mutation_p.M422I|UGT2A1_uc010ihu.1_Missense_Mutation_p.M466I	NM_001105677	NP_001099147	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family,	466	Extracellular (Potential).				detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1														0.248148	149.472141	165.070453	67	203	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70489865	70489865	17511	4	C	T	T	25	25	UGT2A1	T	2	2
ODAM	54959	broad.mit.edu	36	4	71097008	71097008	+	Missense_Mutation	SNP	A	T	T			TCGA-28-5219-01	TCGA-28-5219-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71097008A>T	uc003hfc.1	+	c.62A>T	c.(61-63)CAG>CTG	p.Q21L		NM_017855	NP_060325	A1E959	ODAM_HUMAN	odontogenic ameloblast-associated protein	21					biomineral tissue development|odontogenesis of dentine-containing tooth	fibril				ovary(3)|large_intestine(1)	4														0.295455	74.416122	77.709389	26	62	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71097008	71097008	11229	4	A	T	T	7	7	ODAM	T	4	4
PCDHA1	56147	broad.mit.edu	36	5	140148076	140148076	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140148076G>A	uc003lhb.1	+	c.2017G>A	c.(2017-2019)GGC>AGC	p.G673S	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lgz.1_Missense_Mutation_p.G673S	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	673	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding				0														0.412587	173.900678	174.854068	59	84	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140148076	140148076	11939	5	G	A	A	39	39	PCDHA1	A	1	1
MAST4	375449	broad.mit.edu	36	5	66120322	66120322	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:66120322G>A	uc003jur.2	+	c.586G>A	c.(586-588)GTG>ATG	p.V196M	MAST4_uc010iwz.1_Missense_Mutation_p.V196M	NM_198828	NP_942123	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	196					protein phosphorylation	cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)								805				0.25	29.548998	32.504471	13	39	GG		KEEP	---	---	---	---	capture		Lung(70;0.011)	Missense_Mutation	SNP	66120322	66120322	9711	5	G	A	A	40	40	MAST4	A	1	1
SLC44A4	80736	broad.mit.edu	36	6	31946571	31946571	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:31946571C>T	uc010jti.1	-	c.934G>A	c.(934-936)GCC>ACC	p.A312T		NM_025257	NP_079533	Q53GD3	CTL4_HUMAN	choline transporter-like protein 4	312	Helical; (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4					Choline(DB00122)									0.308511	64.62316	67.705753	29	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31946571	31946571	15135	6	C	T	T	27	27	SLC44A4	T	1	1
FBXO9	26268	broad.mit.edu	36	6	53049247	53049247	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:53049247G>C	uc003pbo.1	+	c.284G>C	c.(283-285)CGA>CCA	p.R95P	FBXO9_uc003pbk.1_Missense_Mutation_p.R51P|FBXO9_uc003pbl.1_Missense_Mutation_p.R85P|FBXO9_uc003pbm.1_5'UTR|FBXO9_uc003pbn.1_5'UTR	NM_012347	NP_036479	Q9UK97	FBX9_HUMAN	F-box only protein 9 isoform 1	95	TPR.					ubiquitin ligase complex	ubiquitin-protein ligase activity			pancreas(1)	1	Lung NSC(77;0.103)													0.5	8.424657	8.424657	3	3	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53049247	53049247	5999	6	G	C	C	37	37	FBXO9	C	3	3
COL19A1	1310	broad.mit.edu	36	6	70694588	70694588	+	Silent	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:70694588C>T	uc003pfc.1	+	c.333C>T	c.(331-333)AAC>AAT	p.N111N	COL19A1_uc010kam.1_Silent_p.N7N	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	111	TSP N-terminal.			FRVRRNAKKERWFL -> ETTVPFWRFFVLET (in Ref. 6; AAA36358).	cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4														0.305019	203.418928	212.208471	79	180	CC		KEEP	---	---	---	---	capture			Silent	SNP	70694588	70694588	3814	6	C	T	T	19	19	COL19A1	T	1	1
MLL3	58508	broad.mit.edu	36	7	151535392	151535392	+	Missense_Mutation	SNP	G	C	C			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:151535392G>C	uc003wla.1	-	c.3767C>G	c.(3766-3768)GCT>GGT	p.A1256G	MLL3_uc003wkz.1_Missense_Mutation_p.A317G	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	1256					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			pancreas(12)|ovary(7)|large_intestine(6)|central_nervous_system(4)|urinary_tract(1)|skin(1)	31	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)				Colon(68;14 1149 1884 27689 34759)				1780				0.181818	183.341803	223.099981	76	342	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)	Missense_Mutation	SNP	151535392	151535392	10012	7	G	C	C	34	34	MLL3	C	3	3
AHR	196	broad.mit.edu	36	7	17345173	17345173	+	Missense_Mutation	SNP	C	T	T			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:17345173C>T	uc003stu.1	+	c.1199C>T	c.(1198-1200)ACG>ATG	p.T400M	AHR_uc003stt.2_Non-coding_Transcript	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor	400					apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|promoter binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulator activity			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)													0.210084	162.229958	189.997708	75	282	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17345173	17345173	419	7	C	T	T	19	19	AHR	T	1	1
PCLO	27445	broad.mit.edu	36	7	82622586	82622586	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82622586G>A	uc003uhx.2	-	c.1307C>T	c.(1306-1308)CCT>CTT	p.P436L	PCLO_uc003uhv.2_Missense_Mutation_p.P436L	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	388	Gln-rich.|Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.133621	100.315897	160.765067	62	402	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82622586	82622586	12003	7	G	A	A	35	35	PCLO	A	2	2
ZNF706	51123	broad.mit.edu	36	8	102283137	102283137	+	Silent	SNP	A	G	G			TCGA-28-5219-01	TCGA-28-5219-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:102283137A>G	uc003yka.1	-	c.9T>C	c.(7-9)CGT>CGC	p.R3R	ZNF706_uc003ykb.1_Silent_p.R3R	NM_001042510	NP_057180	Q9Y5V0	ZN706_HUMAN	HSPC038 protein	3						intracellular	zinc ion binding			ovary(2)	2	all_cancers(14;3.3e-07)|all_epithelial(15;3.47e-09)|Lung NSC(17;3.44e-05)|all_lung(17;0.000117)													0.149425	7.817683	18.309012	13	74	AA		KEEP	---	---	---	---	capture	Epithelial(11;8.57e-11)|all cancers(13;1.43e-08)|OV - Ovarian serous cystadenocarcinoma(57;1.43e-05)		Silent	SNP	102283137	102283137	18706	8	A	G	G	6	6	ZNF706	G	4	4
DNM1	1759	broad.mit.edu	36	9	130049500	130049500	+	Missense_Mutation	SNP	C	G	G			TCGA-28-5219-01	TCGA-28-5219-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:130049500C>G	uc010mxv.1	+	c.1807C>G	c.(1807-1809)CTG>GTG	p.L603V	DNM1_uc010mxs.1_Missense_Mutation_p.L603V|DNM1_uc010mxt.1_3'UTR|DNM1_uc010mxu.1_3'UTR|DNM1_uc004bub.1_5'UTR|DNM1_uc004buc.1_Missense_Mutation_p.L70V|DNM1_uc004bud.2_Non-coding_Transcript|MIR199B_hsa-mir-199b|MI0000282_5'Flank	NM_004408	NP_004399	Q05193	DYN1_HUMAN	dynamin 1 isoform 1	603	PH.				receptor-mediated endocytosis	microtubule	GTP binding|GTPase activity|motor activity			ovary(2)	2						GBM(113;146 1575 2722 28670 29921)								0.294118	7.310471	7.996262	5	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130049500	130049500	4853	9	C	G	G	28	28	DNM1	G	3	3
PNPLA7	375775	broad.mit.edu	36	9	139509371	139509371	+	Missense_Mutation	SNP	G	A	A			TCGA-28-5219-01	TCGA-28-5219-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139509371G>A	uc010ncj.1	-	c.2062C>T	c.(2062-2064)CGG>TGG	p.R688W	PNPLA7_uc004cnf.2_Missense_Mutation_p.R663W	NM_001098537	NP_001092007	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	663	cNMP 3.				lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity				0	all_cancers(76;0.126)													0.343511	116.934305	119.768354	45	86	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)	Missense_Mutation	SNP	139509371	139509371	12597	9	G	A	A	37	37	PNPLA7	A	1	1
CNTNAP3	79937	broad.mit.edu	36	9	39130559	39130559	+	Silent	SNP	T	A	A			TCGA-28-5219-01	TCGA-28-5219-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:39130559T>A	uc004abi.1	-	c.1833A>T	c.(1831-1833)GGA>GGT	p.G611G	CNTNAP3_uc004abj.1_Silent_p.G611G|CNTNAP3_uc004abk.1_Silent_p.G611G|CNTNAP3_uc010mmf.1_Non-coding_Transcript|CNTNAP3_uc004abl.1_Silent_p.G430G	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3	611	Fibrinogen C-terminal.|Extracellular (Potential).				cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1														0.337349	143.639928	147.528395	56	110	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)	Silent	SNP	39130559	39130559	3786	9	T	A	A	62	62	CNTNAP3	A	4	4
ZCCHC13	389874	broad.mit.edu	36	X	73441123	73441123	+	Missense_Mutation	SNP	T	A	A			TCGA-28-5219-01	TCGA-28-5219-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:73441123T>A	uc004ebs.2	+	c.297T>A	c.(295-297)CAT>CAA	p.H99Q		NM_203303	NP_976048	Q8WW36	ZCH13_HUMAN	zinc finger, CCHC domain containing 13	99	CCHC-type 4.						nucleic acid binding|zinc ion binding				0														0.168224	34.995169	46.142029	18	89	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73441123	73441123	18170	23	T	A	A	50	50	ZCCHC13	A	4	4
JAK1	3716	broad.mit.edu	36	1	65074447	65074448	+	Frame_Shift_Ins	INS	-	AT	AT			TCGA-28-5219-01	TCGA-28-5219-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:65074447_65074448insAT	uc001dbu.1	-	c.3179_3180insAT	c.(3178-3180)ATTfs	p.I1060fs	JAK1_uc009wam.1_Frame_Shift_Ins_p.I1060fs|JAK1_uc009wal.1_Frame_Shift_Ins_p.I237fs	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1	1060	Protein kinase 2.				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(30)|prostate(7)|soft_tissue(6)|lung(4)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|breast(1)|ovary(1)	55				BRCA - Breast invasive adenocarcinoma(111;0.0485)						1025				0.38			35	56				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	65074447	65074448	8241	1	-	AT	AT	5	5	JAK1	AT	5	5
GLI2	2736	broad.mit.edu	36	2	121460566	121460566	+	Frame_Shift_Del	DEL	G	-	-			TCGA-28-5219-01	TCGA-28-5219-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:121460566_121460566delG	uc010flp.1	+	c.2199_2199delG	c.(2197-2199)AAGfs	p.K733fs	GLI2_uc002tmq.1_Frame_Shift_Del_p.K405fs|GLI2_uc002tmr.1_Frame_Shift_Del_p.K388fs|GLI2_uc002tmt.2_Frame_Shift_Del_p.K405fs|GLI2_uc002tmu.2_Frame_Shift_Del_p.K388fs|GLI2_uc002tmw.1_Frame_Shift_Del_p.K716fs	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	733					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(7)|central_nervous_system(1)	8	Renal(3;0.0496)	Prostate(154;0.0623)								376				0.33			39	80				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	121460566	121460566	6706	2	G	-	-	33	33	GLI2	-	5	5
