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
COL17A1	1308	broad.mit.edu	36	10	105788243	105788243	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:105788243G>A	uc001kxr.1	-	c.2981C>T	c.(2980-2982)CCG>CTG	p.P994L		NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	994	Extracellular (Potential).|Triple-helical region.				cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane				ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)												0.825758	382.259725	395.492023	109	23	GG		KEEP	---	---	---	---	capture		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)	Missense_Mutation	SNP	105788243	105788243	3812	10	G	A	A	39	39	COL17A1	A	1	1
ANKRD30A	91074	broad.mit.edu	36	10	37546716	37546716	+	Silent	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:37546716G>A	uc001iza.1	+	c.3003G>A	c.(3001-3003)GAG>GAA	p.E1001E		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1057	Potential.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)	8														0.448276	82.542717	82.677988	26	32	GG		KEEP	---	---	---	---	capture			Silent	SNP	37546716	37546716	663	10	G	A	A	34	34	ANKRD30A	A	2	2
ADAMTS14	140766	broad.mit.edu	36	10	72165045	72165045	+	Silent	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:72165045C>T	uc001jrg.1	+	c.1476C>T	c.(1474-1476)GGC>GGT	p.G492G	ADAMTS14_uc001jrh.1_Silent_p.G489G|ADAMTS14_uc001jri.1_Silent_p.G12G	NM_139155	NP_631894	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	489	Disintegrin.				collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)	5														0.774194	81.525034	83.687257	24	7	CC		KEEP	---	---	---	---	capture			Silent	SNP	72165045	72165045	260	10	C	T	T	28	28	ADAMTS14	T	2	2
PTEN	5728	broad.mit.edu	36	10	89682973	89682973	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682973G>T	uc001kfb.1	+	c.477G>T	c.(475-477)AGG>AGT	p.R159S		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	159	Phosphatase tensin-type.				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.R159S(4)|p.Y27_N212>Y(2)|p.F56fs*2(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31	p.R159R(NCIH1563-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.648936	187.093165	188.930331	61	33	GG		KEEP	---	---	---	---	capture	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)	Missense_Mutation	SNP	89682973	89682973	13192	10	G	T	T	41	41	PTEN	T	3	3
OR10S1	219873	broad.mit.edu	36	11	123352696	123352696	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123352696G>A	uc001pzm.1	-	c.913C>T	c.(913-915)CGG>TGG	p.R305W		NM_001004474	NP_001004474	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S,	305	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)												0.226744	93.942561	105.727506	39	133	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)	Missense_Mutation	SNP	123352696	123352696	11324	11	G	A	A	38	38	OR10S1	A	1	1
GPR133	283383	broad.mit.edu	36	12	130053762	130053762	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:130053762C>T	uc001uit.2	+	c.1106C>T	c.(1105-1107)ACG>ATG	p.T369M		NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	369	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)													0.264706	85.758229	92.553911	36	100	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)	Missense_Mutation	SNP	130053762	130053762	6917	12	C	T	T	19	19	GPR133	T	1	1
N6AMT2	221143	broad.mit.edu	36	13	20229636	20229636	+	Silent	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:20229636G>A	uc001uno.1	-	c.102C>T	c.(100-102)GGC>GGT	p.G34G	N6AMT2_uc009zzr.1_Silent_p.G34G|N6AMT2_uc001unp.2_Non-coding_Transcript	NM_174928	NP_777588	Q8WVE0	N6MT2_HUMAN	N-6 adenine-specific DNA methyltransferase 2	34							methyltransferase activity|nucleic acid binding				0		all_cancers(29;5.91e-19)|all_epithelial(30;1.42e-15)|all_lung(29;5.9e-14)|Lung SC(185;0.0367)												0.235602	103.37541	115.591307	45	146	GG		KEEP	---	---	---	---	capture		all cancers(112;0.000234)|Epithelial(112;0.000471)|OV - Ovarian serous cystadenocarcinoma(117;0.0111)|Lung(94;0.0161)|LUSC - Lung squamous cell carcinoma(192;0.0431)	Silent	SNP	20229636	20229636	10510	13	G	A	A	38	38	N6AMT2	A	1	1
CHD8	57680	broad.mit.edu	36	14	20946370	20946370	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:20946370C>G	uc001was.1	-	c.1834G>C	c.(1834-1836)GGC>CGC	p.G612R	CHD8_uc001war.1_Missense_Mutation_p.G508R|CHD8_uc001wav.1_Missense_Mutation_p.G54R	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	891	Helicase ATP-binding.				ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|chromatin assembly or disassembly|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	chromatin|MLL1 complex	ATP binding|beta-catenin binding|chromatin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding|transcription activator activity|transcription repressor activity			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)									886				0.254545	106.284208	115.299723	42	123	CC		KEEP	---	---	---	---	capture	Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)	Missense_Mutation	SNP	20946370	20946370	3465	14	C	G	G	21	21	CHD8	G	3	3
DHRS2	10202	broad.mit.edu	36	14	23178863	23178863	+	Silent	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23178863C>T	uc001wkt.2	+	c.339C>T	c.(337-339)GGC>GGT	p.G113G	DHRS2_uc010aku.1_Silent_p.G113G|DHRS2_uc001wku.2_Silent_p.G113G|DHRS2_uc010akv.1_Non-coding_Transcript|DHRS2_uc001wkv.2_Silent_p.G113G	NM_182908	NP_878912	Q13268	DHRS2_HUMAN	dehydrogenase/reductase member 2 isoform 1	91					C21-steroid hormone metabolic process|cellular response to oxidative stress|myeloid dendritic cell differentiation|negative regulation of apoptosis|negative regulation of cell proliferation|oxidation-reduction process|response to toxin	mitochondrion|nuclear envelope	binding|carbonyl reductase (NADPH) activity			large_intestine(1)|ovary(1)	2														0.411111	99.628867	100.227866	37	53	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.00659)	Silent	SNP	23178863	23178863	4669	14	C	T	T	27	27	DHRS2	T	1	1
LRRC16B	90668	broad.mit.edu	36	14	23594359	23594359	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23594359G>A	uc001wlj.2	+	c.605G>A	c.(604-606)CGA>CAA	p.R202Q		NM_138360	NP_612369	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	202										ovary(2)|breast(2)|pancreas(1)	5														0.126866	27.481756	45.679022	17	117	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.019)	Missense_Mutation	SNP	23594359	23594359	9346	14	G	A	A	39	39	LRRC16B	A	1	1
C15orf2	23742	broad.mit.edu	36	15	22472262	22472262	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:22472262G>A	uc001ywo.1	+	c.155G>A	c.(154-156)CGC>CAC	p.R52H		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	52					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|kidney(1)|central_nervous_system(1)	6		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)								443				0.357143	28.22345	28.69157	10	18	GG		KEEP	---	---	---	---	capture		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)	Missense_Mutation	SNP	22472262	22472262	1834	15	G	A	A	38	38	C15orf2	A	1	1
OTOA	146183	broad.mit.edu	36	16	21606318	21606318	+	Silent	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:21606318C>T	uc002djh.1	+	c.483C>T	c.(481-483)CTC>CTT	p.L161L		NM_144672	NP_653273	Q7RTW8	OTOAN_HUMAN	otoancorin isoform 1	161					sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)	1														0.400943	243.42371	245.245282	85	127	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0414)	Silent	SNP	21606318	21606318	11714	16	C	T	T	29	29	OTOA	T	2	2
SCNN1G	6340	broad.mit.edu	36	16	23133934	23133934	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:23133934C>A	uc002dlm.1	+	c.1593C>A	c.(1591-1593)TTC>TTA	p.F531L		NM_001039	NP_001030	P51170	SCNNG_HUMAN	sodium channel, nonvoltage-gated 1, gamma	531	Helical; (By similarity).				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|large_intestine(1)|pancreas(1)	4					Amiloride(DB00594)|Triamterene(DB00384)									0.606061	124.711925	125.362901	40	26	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0366)	Missense_Mutation	SNP	23133934	23133934	14412	16	C	A	A	31	31	SCNN1G	A	3	3
ITGAD	3681	broad.mit.edu	36	16	31316691	31316691	+	Silent	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31316691G>A	uc010cap.1	+	c.387G>A	c.(385-387)TCG>TCA	p.S129S	ITGAD_uc002ebv.1_Silent_p.S129S|ITGAD_uc002ebw.1_5'UTR	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	129	FG-GAP 2.|Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1														0.405405	39.811779	40.102559	15	22	GG		KEEP	---	---	---	---	capture			Silent	SNP	31316691	31316691	8188	16	G	A	A	38	38	ITGAD	A	1	1
SOLH	6650	broad.mit.edu	36	16	543460	543460	+	Silent	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:543460C>T	uc002chi.1	+	c.3204C>T	c.(3202-3204)ACC>ACT	p.T1068T	SOLH_uc002chj.1_Silent_p.T128T	NM_005632	NP_005623	O75808	CAN15_HUMAN	small optic lobes	1068					proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Hepatocellular(780;0.00335)												0.515789	147.97213	147.992643	49	46	CC		KEEP	---	---	---	---	capture			Silent	SNP	543460	543460	15425	16	C	T	T	22	22	SOLH	T	2	2
NLRC5	84166	broad.mit.edu	36	16	55612212	55612212	+	Silent	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:55612212C>T	uc002ekk.1	+	c.87C>T	c.(85-87)AAC>AAT	p.N29N	NLRC5_uc010ccq.1_Non-coding_Transcript	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27	29					defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|breast(1)|skin(1)	6		all_neural(199;0.225)												0.492063	187.652617	187.659238	62	64	CC		KEEP	---	---	---	---	capture			Silent	SNP	55612212	55612212	10873	16	C	T	T	19	19	NLRC5	T	1	1
KCTD19	146212	broad.mit.edu	36	16	65883158	65883158	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65883158C>T	uc002esu.2	-	c.2302G>A	c.(2302-2304)GTG>ATG	p.V768M	KCTD19_uc002est.2_Missense_Mutation_p.V540M	NM_001100915	NP_001094385	Q17RG1	KCD19_HUMAN	potassium channel tetramerisation domain	768						voltage-gated potassium channel complex	voltage-gated potassium channel activity				0		Ovarian(137;0.192)												0.242718	60.428167	66.641915	25	78	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)	Missense_Mutation	SNP	65883158	65883158	8412	16	C	T	T	19	19	KCTD19	T	1	1
PKD1L2	114780	broad.mit.edu	36	16	79745198	79745198	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:79745198G>C	uc002fgh.1	-	c.4275C>G	c.(4273-4275)CAC>CAG	p.H1425Q	PKD1L2_uc002fgg.1_Non-coding_Transcript	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	1425	Cytoplasmic (Potential).|PLAT.				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.235294	9.791521	10.88126	4	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79745198	79745198	12389	16	G	C	C	44	44	PKD1L2	C	3	3
MYH13	8735	broad.mit.edu	36	17	10153858	10153858	+	Silent	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10153858G>A	uc002gmk.1	-	c.4671C>T	c.(4669-4671)CAC>CAT	p.H1557H		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1557	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.555556	15.575686	15.599848	5	4	GG		KEEP	---	---	---	---	capture			Silent	SNP	10153858	10153858	10427	17	G	A	A	40	40	MYH13	A	1	1
KRT27	342574	broad.mit.edu	36	17	36189616	36189616	+	Silent	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36189616C>T	uc002hvg.1	-	c.708G>A	c.(706-708)GCG>GCA	p.A236A		NM_181537	NP_853515	Q7Z3Y8	K1C27_HUMAN	keratin 27	236	Rod.|Linker 12.					cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.000812)												0.359375	68.011609	69.124045	23	41	CC		KEEP	---	---	---	---	capture			Silent	SNP	36189616	36189616	8779	17	C	T	T	23	23	KRT27	T	1	1
SEPT4	5414	broad.mit.edu	36	17	53954395	53954395	+	Silent	SNP	C	A	A			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53954395C>A	uc002iwm.1	-	c.729G>T	c.(727-729)CTG>CTT	p.L243L	SEPT4_uc002iwk.1_Silent_p.L96L|SEPT4_uc002iwl.1_Silent_p.L96L|SEPT4_uc002iwn.1_Silent_p.L144L|SEPT4_uc002iwo.1_Silent_p.L224L|SEPT4_uc002iwp.1_Silent_p.L224L|SEPT4_uc010dcy.1_Silent_p.L125L	NM_004574	NP_004565	O43236	SEPT4_HUMAN	septin 4 isoform 1	243					apoptosis|cell cycle|cytokinesis|regulation of apoptosis	cytoskeleton|mitochondrion|nucleus	GTP binding|GTPase activity|protein binding|structural molecule activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.12	12.819611	30.592429	15	110	CC		KEEP	---	---	---	---	capture			Silent	SNP	53954395	53954395	14552	17	C	A	A	29	29	SEPT4	A	3	3
C17orf71	55181	broad.mit.edu	36	17	54645022	54645022	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2559-01	TCGA-06-2559-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:54645022A>G	uc002ixi.1	+	c.2056A>G	c.(2056-2058)ACC>GCC	p.T686A		NM_018149	NP_060619	Q8ND04	SMG8_HUMAN	hypothetical protein LOC55181	686					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of protein kinase activity		protein binding			ovary(3)	3	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)													0.481884	455.768805	455.847024	133	143	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54645022	54645022	1935	17	A	G	G	2	2	C17orf71	G	4	4
TP53	7157	broad.mit.edu	36	17	7519005	7519005	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519005G>A	uc002gim.2	-	c.569C>T	c.(568-570)CCT>CTT	p.P190L	TP53_uc002gig.1_Missense_Mutation_p.P190L|TP53_uc002gih.1_Missense_Mutation_p.P190L|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.P58L|TP53_uc010cng.1_Missense_Mutation_p.P58L|TP53_uc002gii.1_Missense_Mutation_p.P58L|TP53_uc010cnh.1_Missense_Mutation_p.P190L|TP53_uc010cni.1_Missense_Mutation_p.P190L|TP53_uc002gij.2_Missense_Mutation_p.P190L|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.P97L|TP53_uc002gio.2_Missense_Mutation_p.P58L	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	190	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		P -> R (in sporadic cancers; somatic mutation).|P -> H (in a sporadic cancer; somatic mutation).|P -> S (in sporadic cancers; somatic mutation).|P -> A (in sporadic cancers; somatic mutation).|P -> T (in sporadic cancers; somatic mutation).|P -> L (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.P190L(21)|p.0?(6)|p.P190del(5)|p.A189_V197delAPPQHLIRV(4)|p.P190fs*57(3)|p.?(2)|p.P190R(2)|p.G187fs*16(2)|p.D186_P191delDGLAPP(1)|p.P190H(1)|p.P191fs*18(1)|p.A189_Q192>E(1)|p.L188_P191del(1)|p.A189_P190>X(1)|p.A189fs*53(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.PPQH190del(JHH5-Tumor)|p.P190L(SNU1033-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.455696	114.388824	114.524168	36	43	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7519005	7519005	16923	17	G	A	A	35	35	TP53	A	2	2
TP53	7157	broad.mit.edu	36	17	7519191	7519191	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519191G>T	uc002gim.2	-	c.464C>A	c.(463-465)ACC>AAC	p.T155N	TP53_uc002gig.1_Missense_Mutation_p.T155N|TP53_uc002gih.1_Missense_Mutation_p.T155N|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.T23N|TP53_uc010cng.1_Missense_Mutation_p.T23N|TP53_uc002gii.1_Missense_Mutation_p.T23N|TP53_uc010cnh.1_Missense_Mutation_p.T155N|TP53_uc010cni.1_Missense_Mutation_p.T155N|TP53_uc002gij.2_Missense_Mutation_p.T155N|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.T62N|TP53_uc002gio.2_Missense_Mutation_p.T23N	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	155	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		T -> N (in LFS; germline mutation and in sporadic cancers; somatic mutation).|T -> S (in sporadic cancers; somatic mutation).|T -> P (in sporadic cancers; somatic mutation).|T -> A (in sporadic cancers; somatic mutation).|T -> I (in sporadic cancers; somatic mutation).|T -> M (in a sporadic cancer; 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.T155N(19)|p.T155I(10)|p.0?(6)|p.P152fs*14(3)|p.P153fs*22(2)|p.T155fs*23(2)|p.G154fs*14(2)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*25(1)|p.T155_R156delTR(1)|p.P151_V173del23(1)|p.T155fs*25(1)|p.D148fs*23(1)|p.S149fs*72(1)|p.G154_R156delGTR(1)|p.T155S(1)|p.D148_T155delDSTPPPGT(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.P152fs(RH41-Tumor)|p.T155N(NCIH524-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.411111	106.655214	107.276785	37	53	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7519191	7519191	16923	17	G	T	T	44	44	TP53	T	3	3
ODF4	146852	broad.mit.edu	36	17	8184275	8184275	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:8184275C>T	uc002gle.1	+	c.181C>T	c.(181-183)CGC>TGC	p.R61C		NM_153007	NP_694552	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	61					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(1)	1														0.466667	63.975513	64.018468	21	24	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8184275	8184275	11238	17	C	T	T	27	27	ODF4	T	1	1
PSG5	5673	broad.mit.edu	36	19	48371446	48371446	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48371446G>A	uc002ovv.1	-	c.1004C>T	c.(1003-1005)CCC>CTC	p.P335L	PSG5_uc010eir.1_Missense_Mutation_p.P117L|PSG5_uc002ovu.1_Missense_Mutation_p.P242L|PSG5_uc002ovw.1_Intron|PSG5_uc002ovx.1_Missense_Mutation_p.P242L	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	242	Ig-like C2-type 2.				female pregnancy	extracellular region					0		Prostate(69;0.00899)												0.422222	295.474516	296.664482	95	130	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48371446	48371446	13111	19	G	A	A	43	43	PSG5	A	2	2
EML2	24139	broad.mit.edu	36	19	50829560	50829560	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50829560G>T	uc002pcq.1	-	c.792C>A	c.(790-792)TAC>TAA	p.Y264*	EML2_uc002pcn.1_Nonsense_Mutation_p.Y63*|EML2_uc002pco.1_Non-coding_Transcript|EML2_uc002pcp.1_Intron|EML2_uc010ekj.1_Nonsense_Mutation_p.Y63*|EML2_uc010ekk.1_5'Flank	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like	63					sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)												0.333333	6.58172	6.88419	4	8	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)	Nonsense_Mutation	SNP	50829560	50829560	5289	19	G	T	T	44	44	EML2	T	5	3
PTPRS	5802	broad.mit.edu	36	19	5172107	5172107	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2559-01	TCGA-06-2559-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5172107T>C	uc002mbv.1	-	c.3359A>G	c.(3358-3360)AAC>AGC	p.N1120S	PTPRS_uc002mbu.1_Missense_Mutation_p.N689S|PTPRS_uc002mbw.1_Missense_Mutation_p.N1098S|PTPRS_uc002mbx.1_Missense_Mutation_p.N693S|PTPRS_uc002mby.1_Missense_Mutation_p.N689S	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	1120	Extracellular (Potential).				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4														0.4	175.60738	176.791611	54	81	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Missense_Mutation	SNP	5172107	5172107	13269	19	T	C	C	60	60	PTPRS	C	4	4
KIR2DL4	3805	broad.mit.edu	36	19	60008098	60008098	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60008098G>A	uc002qhc.1	+	c.109G>A	c.(109-111)GCT>ACT	p.A37T	KIR2DS4_uc010erv.1_Intron|KIR2DS4_uc010erx.1_Intron|KIR2DS4_uc010esa.1_Intron|KIR3DL1_uc002qhd.2_Intron|KIR3DL1_uc010esb.1_Intron|KIR2DL4_uc010esc.1_Missense_Mutation_p.A39T|KIR2DL4_uc002qhi.1_Missense_Mutation_p.A39T|KIR2DL4_uc002qhh.1_Intron|KIR2DL4_uc002qhj.1_Missense_Mutation_p.A39T|KIR2DL4_uc010esd.1_Missense_Mutation_p.A39T|KIR2DL4_uc002qhf.1_Intron|KIR2DL4_uc002qhg.1_Missense_Mutation_p.A39T|KIR2DL4_uc010ese.1_5'Flank	NM_002255	NP_002246	Q99706	KI2L4_HUMAN	killer cell immunoglobulin-like receptor, two	39	Extracellular (Potential).				cellular defense response|regulation of immune response	integral to plasma membrane	protein binding|transmembrane receptor activity			ovary(1)	1														0.242991	61.608156	68.045471	26	81	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0192)	Missense_Mutation	SNP	60008098	60008098	8630	19	G	A	A	38	38	KIR2DL4	A	1	1
NLRP4	147945	broad.mit.edu	36	19	61061334	61061334	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61061334C>T	uc002qmd.2	+	c.763C>T	c.(763-765)CGG>TGG	p.R255W	NLRP4_uc002qme.1_Missense_Mutation_p.R255W|NLRP4_uc002qmf.1_Missense_Mutation_p.R180W|NLRP4_uc010etf.1_Missense_Mutation_p.R86W	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	255	NACHT.						ATP binding			ovary(5)|lung(3)|kidney(1)|pancreas(1)	10		Colorectal(82;0.0002)|Ovarian(87;0.221)												0.41958	176.874356	177.681508	60	83	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0606)	Missense_Mutation	SNP	61061334	61061334	10882	19	C	T	T	19	19	NLRP4	T	1	1
SPTA1	6708	broad.mit.edu	36	1	156921590	156921590	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156921590C>T	uc001fst.1	-	c.196G>A	c.(196-198)GGG>AGG	p.G66R		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	66	Spectrin 2.				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)													0.486957	180.642566	180.657346	56	59	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156921590	156921590	15630	1	C	T	T	22	22	SPTA1	T	2	2
KIAA1751	85452	broad.mit.edu	36	1	1908302	1908302	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2559-01	TCGA-06-2559-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1908302T>C	uc009vkz.1	-	c.329A>G	c.(328-330)GAC>GGC	p.D110G	KIAA1751_uc001aim.1_Missense_Mutation_p.D110G|KIAA1751_uc001ain.1_Missense_Mutation_p.D110G	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	110										pancreas(1)	1	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;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)												0.157143	7.182929	14.951808	11	59	TT		KEEP	---	---	---	---	capture		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)	Missense_Mutation	SNP	1908302	1908302	8567	1	T	C	C	58	58	KIAA1751	C	4	4
LRRC40	55631	broad.mit.edu	36	1	70414105	70414105	+	Missense_Mutation	SNP	T	G	G			TCGA-06-2559-01	TCGA-06-2559-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:70414105T>G	uc001der.1	-	c.953A>C	c.(952-954)GAC>GCC	p.D318A		NM_017768	NP_060238	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	318	LRR 11.									ovary(1)	1														0.397727	118.108101	118.912766	35	53	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70414105	70414105	9373	1	T	G	G	58	58	LRRC40	G	4	4
NEXN	91624	broad.mit.edu	36	1	78164759	78164759	+	Missense_Mutation	SNP	A	T	T			TCGA-06-2559-01	TCGA-06-2559-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:78164759A>T	uc001dic.2	+	c.562A>T	c.(562-564)AAT>TAT	p.N188Y	NEXN_uc001dia.2_Missense_Mutation_p.N174Y|NEXN_uc001dib.2_Missense_Mutation_p.N124Y|NEXN_uc009wcb.1_Missense_Mutation_p.N110Y|NEXN_uc001did.1_Missense_Mutation_p.N98Y|NEXN_uc001dif.1_Missense_Mutation_p.N80Y	NM_144573	NP_653174	Q0ZGT2	NEXN_HUMAN	nexilin (F actin binding protein)	188	Glu-rich.				regulation of cell migration|regulation of cytoskeleton organization	cytoskeleton|Z disc	actin filament binding|structural constituent of muscle			ovary(2)	2														0.144144	21.933875	35.463425	16	95	AA		KEEP	---	---	---	---	capture		Colorectal(170;0.114)	Missense_Mutation	SNP	78164759	78164759	10755	1	A	T	T	9	9	NEXN	T	4	4
MYH7B	57644	broad.mit.edu	36	20	33050291	33050291	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33050291C>G	uc002xbi.1	+	c.4228C>G	c.(4228-4230)CTG>GTG	p.L1410V		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	1368	Potential.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2														0.307692	8.49399	8.923349	4	9	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(18;0.00691)		Missense_Mutation	SNP	33050291	33050291	10435	20	C	G	G	28	28	MYH7B	G	3	3
MAPK1	5594	broad.mit.edu	36	22	20472672	20472672	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:20472672G>A	uc002zvn.1	-	c.730C>T	c.(730-732)CTT>TTT	p.L244F	MAPK1_uc002zvo.1_Missense_Mutation_p.L244F|MAPK1_uc010gtk.1_Intron	NM_002745	NP_620407	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	244	Protein kinase.				activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|epidermal growth factor receptor signaling pathway|ERK1 and ERK2 cascade|induction of apoptosis|innate immune response|insulin receptor signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|synaptic transmission|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|nucleoplasm	ATP binding|DNA binding|MAP kinase activity|phosphatase binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(1)	1	Colorectal(54;0.105)	all_lung(157;3.89e-05)			Arsenic trioxide(DB01169)					164				0.45	229.18051	229.529146	72	88	GG		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(21;0.0689)	Missense_Mutation	SNP	20472672	20472672	9654	22	G	A	A	33	33	MAPK1	A	2	2
IL2RB	3560	broad.mit.edu	36	22	35854442	35854442	+	Silent	SNP	G	T	T			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:35854442G>T	uc003aqv.1	-	c.1296C>A	c.(1294-1296)CCC>CCA	p.P432P		NM_000878	NP_000869	P14784	IL2RB_HUMAN	interleukin 2 receptor beta precursor	432	Cytoplasmic (Potential).				interspecies interaction between organisms|positive regulation of survival gene product expression|protein complex assembly	external side of plasma membrane|integral to plasma membrane	interleukin-2 receptor activity				0					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)									0.157895	14.831969	21.204497	9	48	GG		KEEP	---	---	---	---	capture			Silent	SNP	35854442	35854442	7988	22	G	T	T	47	47	IL2RB	T	3	3
IL18RAP	8807	broad.mit.edu	36	2	102424270	102424270	+	Splice_Site_SNP	SNP	G	T	T			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102424270G>T	uc002tbx.1	+	c.796_splice	c.e7+1	p.G266_splice	IL18RAP_uc010fiz.1_Splice_Site_SNP_p.G124_splice	NM_003853	NP_003844			interleukin 18 receptor accessory protein						cell surface receptor linked signaling pathway|inflammatory response|innate immune response	integral to membrane	transmembrane receptor activity			ovary(2)	2														0.518987	133.273769	133.298331	41	38	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	102424270	102424270	7949	2	G	T	T	44	44	IL18RAP	T	5	3
LRP2	4036	broad.mit.edu	36	2	169717627	169717627	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2559-01	TCGA-06-2559-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:169717627A>G	uc002ues.1	-	c.12389T>C	c.(12388-12390)CTT>CCT	p.L4130P		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	4130	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.L4130P(LNCAPCLONEFGC-Tumor)	2055				0.475703	651.43972	651.639696	186	205	AA		KEEP	---	---	---	---	capture		STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Missense_Mutation	SNP	169717627	169717627	9329	2	A	G	G	3	3	LRP2	G	4	4
LRP2	4036	broad.mit.edu	36	2	169809666	169809666	+	Silent	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:169809666C>T	uc002ues.1	-	c.3213G>A	c.(3211-3213)GCG>GCA	p.A1071A		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	1071	LDL-receptor class A 9.|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)					2055				0.095477	10.705253	43.356205	19	180	CC		KEEP	---	---	---	---	capture		STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Silent	SNP	169809666	169809666	9329	2	C	T	T	19	19	LRP2	T	1	1
AOX1	316	broad.mit.edu	36	2	201186843	201186843	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:201186843C>T	uc002uvx.1	+	c.1520C>T	c.(1519-1521)GCG>GTG	p.A507V	AOX1_uc010fsu.1_5'UTR	NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1	507					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)									0.442105	122.747266	123.022464	42	53	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	201186843	201186843	739	2	C	T	T	27	27	AOX1	T	1	1
LTBP1	4052	broad.mit.edu	36	2	33189321	33189321	+	Silent	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:33189321G>A	uc002ros.1	+	c.1032G>A	c.(1030-1032)CAG>CAA	p.Q344Q		NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	344					negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|lung(1)|central_nervous_system(1)	7	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)												0.43871	201.47561	201.983444	68	87	GG		KEEP	---	---	---	---	capture			Silent	SNP	33189321	33189321	9449	2	G	A	A	34	34	LTBP1	A	2	2
TMPPE	643853	broad.mit.edu	36	3	33109394	33109394	+	Missense_Mutation	SNP	C	A	A			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:33109394C>A	uc003cfk.1	-	c.1298G>T	c.(1297-1299)GGG>GTG	p.G433V	GLB1_uc003cfh.1_Intron|GLB1_uc003cfi.1_Intron|GLB1_uc003cfj.1_Intron|TMPPE_uc010hfy.1_Missense_Mutation_p.G433V	NM_001039770	NP_001034859	Q6ZT21	TMPPE_HUMAN	hypothetical protein LOC643853 isoform 1	433						integral to membrane	metal ion binding				0														0.393443	70.386884	70.993193	24	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33109394	33109394	16778	3	C	A	A	22	22	TMPPE	A	3	3
NEUROG2	63973	broad.mit.edu	36	4	113655706	113655706	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:113655706C>T	uc003ias.1	-	c.375G>A	c.(373-375)ATG>ATA	p.M125I	NEUROG2_uc010imp.1_Missense_Mutation_p.M125I	NM_024019	NP_076924	Q9H2A3	NGN2_HUMAN	neurogenin 2	125	Helix-loop-helix motif.|Basic motif.				transcription, DNA-dependent	nucleus	transcription regulator activity			central_nervous_system(1)	1		Ovarian(17;0.156)												0.368421	90.391389	91.83999	35	60	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;0.00168)	Missense_Mutation	SNP	113655706	113655706	10753	4	C	T	T	25	25	NEUROG2	T	2	2
RGS12	6002	broad.mit.edu	36	4	3402436	3402436	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:3402436C>T	uc003ggw.1	+	c.4070C>T	c.(4069-4071)CCG>CTG	p.P1357L	RGS12_uc003ggz.1_Missense_Mutation_p.P709L|RGS12_uc003gha.1_Missense_Mutation_p.P699L|RGS12_uc010icv.1_Missense_Mutation_p.P556L|RGS12_uc003ggv.1_Missense_Mutation_p.P1357L|RGS12_uc003ggy.1_3'UTR	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	1357						condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1														0.340426	46.191267	47.246396	16	31	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (64;0.168)	Missense_Mutation	SNP	3402436	3402436	13769	4	C	T	T	23	23	RGS12	T	1	1
PDGFRA	5156	broad.mit.edu	36	4	54828658	54828658	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:54828658G>A	uc003han.2	+	c.1114G>A	c.(1114-1116)GAA>AAA	p.E372K	PDGFRA_uc003haa.1_Intron|PDGFRA_uc010igq.1_Missense_Mutation_p.E266K|PDGFRA_uc003ham.2_Non-coding_Transcript	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	372	Ig-like C2-type 4.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)				Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.236402	558.870046	619.603619	226	730	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Missense_Mutation	SNP	54828658	54828658	12082	4	G	A	A	41	41	PDGFRA	A	2	2
PDGFRA	5156	broad.mit.edu	36	4	54838893	54838893	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:54838893G>C	uc003han.2	+	c.1965G>C	c.(1963-1965)TTG>TTC	p.L655F	PDGFRA_uc003haa.1_Missense_Mutation_p.L415F|PDGFRA_uc010igq.1_Missense_Mutation_p.L549F|PDGFRA_uc003ham.2_Non-coding_Transcript|PDGFRA_uc003hao.1_Missense_Mutation_p.L34F	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	655	Protein kinase.|Cytoplasmic (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)				Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.137555	254.414914	370.814993	126	790	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Missense_Mutation	SNP	54838893	54838893	12082	4	G	C	C	45	45	PDGFRA	C	3	3
GAK	2580	broad.mit.edu	36	4	852325	852325	+	Splice_Site_SNP	SNP	A	C	C			TCGA-06-2559-01	TCGA-06-2559-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:852325A>C	uc003gbm.2	-	c.2395_splice	c.e20+1	p.E799_splice	GAK_uc010ibi.1_5'Flank|GAK_uc010ibj.1_Splice_Site_SNP|GAK_uc003gbl.2_Splice_Site_SNP_p.E663_splice|GAK_uc003gbn.2_Splice_Site_SNP_p.E720_splice|GAK_uc010ibk.1_Splice_Site_SNP_p.E693_splice	NM_005255	NP_005246			cyclin G associated kinase						cell cycle|protein phosphorylation	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)	3										679				0.363636	9.795786	9.976177	4	7	AA		KEEP	---	---	---	---	capture		Colorectal(103;0.219)	Splice_Site_SNP	SNP	852325	852325	6459	4	A	C	C	14	14	GAK	C	5	4
FBN2	2201	broad.mit.edu	36	5	127756740	127756740	+	Silent	SNP	G	T	T			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:127756740G>T	uc003kuu.1	-	c.1452C>A	c.(1450-1452)ATC>ATA	p.I484I		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	484					bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|kidney(1)|pancreas(1)	14		all_cancers(142;0.0216)|Prostate(80;0.0551)								1552				0.394872	221.230969	223.117689	77	118	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)	Silent	SNP	127756740	127756740	5939	5	G	T	T	45	45	FBN2	T	3	3
PCDHGB4	8641	broad.mit.edu	36	5	140749153	140749153	+	Silent	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140749153C>T	uc003lkc.1	+	c.1518C>T	c.(1516-1518)AGC>AGT	p.S506S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGA8_uc003lkd.1_5'Flank|PCDHGB4_uc010jfy.1_Silent_p.S506S|PCDHGA8_uc003lkb.2_5'Flank	NM_003736	NP_003727	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4 isoform 1	506	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.414414	134.538787	135.245866	46	65	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140749153	140749153	11985	5	C	T	T	27	27	PCDHGB4	T	1	1
PRDM9	56979	broad.mit.edu	36	5	23562714	23562714	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:23562714G>A	uc003jgo.1	+	c.1760G>A	c.(1759-1761)CGG>CAG	p.R587Q		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	587	C2H2-type 4.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6														0.387597	144.202241	145.634912	50	79	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23562714	23562714	12906	5	G	A	A	39	39	PRDM9	A	1	1
MAP3K1	4214	broad.mit.edu	36	5	56204263	56204263	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2559-01	TCGA-06-2559-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:56204263T>C	uc003jqw.2	+	c.1462T>C	c.(1462-1464)TGT>CGT	p.C488R		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	488	RING-type.				cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)								201				0.412162	190.95024	191.946984	61	87	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)	Missense_Mutation	SNP	56204263	56204263	9626	5	T	C	C	51	51	MAP3K1	C	4	4
GPR98	84059	broad.mit.edu	36	5	90025482	90025482	+	Silent	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:90025482C>T	uc003kju.1	+	c.7153C>T	c.(7153-7155)CTG>TTG	p.L2385L	GPR98_uc003kjt.1_Silent_p.L91L|GPR98_uc003kjv.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	2385	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)												0.411765	39.940019	40.172071	14	20	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)	Silent	SNP	90025482	90025482	6997	5	C	T	T	28	28	GPR98	T	2	2
UHRF1BP1	54887	broad.mit.edu	36	6	34935243	34935243	+	Silent	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:34935243G>A	uc003oju.2	+	c.3132G>A	c.(3130-3132)GTG>GTA	p.V1044V	UHRF1BP1_uc010jvm.1_Non-coding_Transcript|UHRF1BP1_uc010jvn.1_Non-coding_Transcript|UHRF1BP1_uc010jvo.1_Non-coding_Transcript	NM_017754	NP_060224	Q6BDS2	URFB1_HUMAN	ICBP90 binding protein 1	1044										ovary(3)	3														0.376744	217.902064	220.775619	81	134	GG		KEEP	---	---	---	---	capture			Silent	SNP	34935243	34935243	17526	6	G	A	A	48	48	UHRF1BP1	A	2	2
MOCS1	4337	broad.mit.edu	36	6	40001541	40001541	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:40001541C>T	uc003opb.2	-	c.277G>A	c.(277-279)GTC>ATC	p.V93I	MOCS1_uc003opa.2_Missense_Mutation_p.V93I|MOCS1_uc003opc.2_Missense_Mutation_p.V93I|MOCS1_uc003opd.2_Missense_Mutation_p.V93I|MOCS1_uc003ope.2_Missense_Mutation_p.V6I	NM_005942	NP_005933	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis-step 1 protein	93	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding			ovary(1)|liver(1)|central_nervous_system(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)								0.35	35.923012	36.723521	14	26	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40001541	40001541	10081	6	C	T	T	18	18	MOCS1	T	2	2
GRM8	2918	broad.mit.edu	36	7	125960642	125960642	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2559-01	TCGA-06-2559-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:125960642A>G	uc003vlr.2	-	c.2030T>C	c.(2029-2031)TTT>TCT	p.F677S	GRM8_uc003vls.2_3'UTR|GRM8_uc003vlt.2_Missense_Mutation_p.F677S|GRM8_uc010lkz.1_Non-coding_Transcript	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a	677	Cytoplasmic (Potential).				negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				ovary(5)|pancreas(1)	6		Prostate(267;0.186)			L-Glutamic Acid(DB00142)									0.304636	147.296166	152.435906	46	105	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125960642	125960642	7082	7	A	G	G	1	1	GRM8	G	4	4
TAF6	6878	broad.mit.edu	36	7	99543985	99543985	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99543985G>A	uc003uth.1	-	c.1570C>T	c.(1570-1572)CGG>TGG	p.R524W	AP4M1_uc003utd.2_Intron|TAF6_uc003utg.1_Missense_Mutation_p.R389W|TAF6_uc003uti.1_Missense_Mutation_p.R467W|TAF6_uc003utk.1_Missense_Mutation_p.R467W|TAF6_uc003utj.1_Missense_Mutation_p.R457W|TAF6_uc003utm.1_Missense_Mutation_p.R467W|TAF6_uc003utl.1_Missense_Mutation_p.R467W	NM_139315	NP_647476	P49848	TAF6_HUMAN	TBP-associated factor 6 isoform alpha	467					negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|general RNA polymerase II transcription factor activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription initiation factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.260274	145.058452	156.474012	57	162	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99543985	99543985	16051	7	G	A	A	37	37	TAF6	A	1	1
FLJ43860	389690	broad.mit.edu	36	8	142546758	142546758	+	Missense_Mutation	SNP	T	G	G			TCGA-06-2559-01	TCGA-06-2559-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:142546758T>G	uc003ywi.2	-	c.2245A>C	c.(2245-2247)ACC>CCC	p.T749P	FLJ43860_uc010meu.1_Non-coding_Transcript	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690	749							binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)													0.241379	7.840519	9.687247	7	22	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.0493)		Missense_Mutation	SNP	142546758	142546758	6170	8	T	G	G	59	59	FLJ43860	G	4	4
TAF1L	138474	broad.mit.edu	36	9	32620579	32620579	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:32620579C>T	uc003zrg.1	-	c.4999G>A	c.(4999-5001)GAT>AAT	p.D1667N		NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1667					male meiosis|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding|transcription activator activity			lung(8)|large_intestine(3)|central_nervous_system(3)|skin(2)|ovary(2)|breast(1)|pancreas(1)	20										234				0.396325	434.826481	438.41548	151	230	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)	Missense_Mutation	SNP	32620579	32620579	16044	9	C	T	T	29	29	TAF1L	T	2	2
ZNF658	26149	broad.mit.edu	36	9	40762401	40762401	+	Missense_Mutation	SNP	T	A	A			TCGA-06-2559-01	TCGA-06-2559-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:40762401T>A	uc004abs.2	-	c.2874A>T	c.(2872-2874)AGA>AGT	p.R958S	ZNF658_uc010mmm.1_Intron|ZNF658_uc010mmn.1_Missense_Mutation_p.R958S	NM_033160	NP_149350	Q5TYW1	ZN658_HUMAN	zinc finger protein 658	958	C2H2-type 21.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.515873	383.339972	383.394638	130	122	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)	Missense_Mutation	SNP	40762401	40762401	18664	9	T	A	A	62	62	ZNF658	A	4	4
COL4A6	1288	broad.mit.edu	36	X	107567869	107567869	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:107567869G>C	uc004enw.2	-	c.25C>G	c.(25-27)CTC>GTC	p.L9V	COL4A6_uc004env.2_Missense_Mutation_p.L8V|COL4A6_uc010npk.1_Missense_Mutation_p.L8V|COL4A6_uc004enx.2_Non-coding_Transcript|COL4A6_uc004eny.2_Non-coding_Transcript|COL4A5_uc004enz.1_5'Flank|COL4A5_uc010npl.1_5'Flank|COL4A5_uc010npm.1_5'Flank|COL4A5_uc010npn.1_5'Flank	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	9					cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						Melanoma(87;1895 1945 2589 7165)								0.266667	7.488675	8.230605	4	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107567869	107567869	3833	23	G	C	C	34	34	COL4A6	C	3	3
DDX53	168400	broad.mit.edu	36	X	22928192	22928192	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2559-01	TCGA-06-2559-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:22928192A>G	uc004daj.1	+	c.97A>G	c.(97-99)AGT>GGT	p.S33G		NM_182699	NP_874358	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	33						nucleus	ATP binding|ATP-dependent helicase activity|RNA binding			large_intestine(1)|kidney(1)	2														0.416667	8.056573	8.154612	5	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22928192	22928192	4542	23	A	G	G	11	11	DDX53	G	4	4
TAF1	6872	broad.mit.edu	36	X	70597337	70597337	+	Silent	SNP	C	T	T			TCGA-06-2559-01	TCGA-06-2559-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70597337C>T	uc004dzt.2	+	c.5418C>T	c.(5416-5418)GAC>GAT	p.D1806D	TAF1_uc004dzu.2_Silent_p.D1785D|TAF1_uc010nle.1_Silent_p.D210D|TAF1_uc010nlf.1_Silent_p.D210D|TAF1_uc004dzx.2_Non-coding_Transcript|TAF1_uc004dzy.2_Non-coding_Transcript|TAF1_uc004dzw.1_Non-coding_Transcript|TAF1_uc010nlg.1_Non-coding_Transcript|TAF1_uc004dzv.2_Silent_p.D993D	NM_004606	NP_004597	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 1	1785	Asp/Glu-rich (acidic tail).|Protein kinase 2.				G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|response to DNA damage stimulus|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(5)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	15	Renal(35;0.156)	all_lung(315;0.000321)							p.D1806D(JHUEM1-Tumor)|p.D1806D(SKUT1-Tumor)	472				0.777778	23.529879	24.169104	7	2	CC		KEEP	---	---	---	---	capture			Silent	SNP	70597337	70597337	16034	23	C	T	T	19	19	TAF1	T	1	1
PCDH11X	27328	broad.mit.edu	36	X	91019448	91019448	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2559-01	TCGA-06-2559-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:91019448G>A	uc004efk.1	+	c.1553G>A	c.(1552-1554)CGT>CAT	p.R518H	PCDH11X_uc004efl.1_Missense_Mutation_p.R518H|PCDH11X_uc004efn.1_Missense_Mutation_p.R518H|PCDH11X_uc004efo.1_Missense_Mutation_p.R518H|PCDH11X_uc010nmv.1_Missense_Mutation_p.R518H|PCDH11X_uc004efm.1_Missense_Mutation_p.R518H|PCDH11X_uc004efh.1_Missense_Mutation_p.R518H|PCDH11X_uc004efj.1_Missense_Mutation_p.R518H	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	518	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.859155	204.707203	213.542141	61	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	91019448	91019448	11928	23	G	A	A	40	40	PCDH11X	A	1	1
RASGRP2	10235	broad.mit.edu	36	11	64254176	64254176	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-2559-01	TCGA-06-2559-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64254176_64254176delC	uc009ypu.1	-	c.1479_1479delG	c.(1477-1479)GGGfs	p.G493fs	RASGRP2_uc001oat.1_Frame_Shift_Del_p.G395fs|RASGRP2_uc001oau.1_Frame_Shift_Del_p.G348fs|RASGRP2_uc009ypv.1_Frame_Shift_Del_p.G493fs|RASGRP2_uc009ypw.1_Frame_Shift_Del_p.G493fs	NM_001098671	NP_722541	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2	493					platelet activation|Ras protein signal transduction|regulation of cell growth|regulation of small GTPase mediated signal transduction	cell junction|cytosol|ruffle membrane|synapse|synaptosome	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity				0														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	64254176	64254176	13536	11	C	-	-	26	26	RASGRP2	-	5	5
CASKIN2	57513	broad.mit.edu	36	17	71009655	71009657	+	In_Frame_Del	DEL	GGA	-	-			TCGA-06-2559-01	TCGA-06-2559-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:71009655_71009657delGGA	uc002joc.1	-	c.3093_3095delTCC	c.(3091-3096)CCTCCA>CCA	p.1031_1032PP>P		NM_020753	NP_065804	Q8WXE0	CSKI2_HUMAN	cask-interacting protein 2 isoform a	1031_1032	Pro-rich.					cytoplasm				pancreas(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)											0.37			32	55				---	---	---	---	capture_indel			In_Frame_Del	DEL	71009655	71009657	2786	17	GGA	-	-	47	47	CASKIN2	-	5	5
UBR3	130507	broad.mit.edu	36	2	170638184	170638186	+	In_Frame_Del	DEL	GAA	-	-			TCGA-06-2559-01	TCGA-06-2559-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:170638184_170638186delGAA	uc002uft.2	+	c.1591_1593delGAA	c.(1591-1593)GAAdel	p.E534del	UBR3_uc002ufs.2_In_Frame_Del_p.E530del|UBR3_uc002ufr.2_Non-coding_Transcript|UBR3_uc010fqa.1_In_Frame_Del_p.E498del|UBR3_uc002ufu.2_In_Frame_Del_p.E183del	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3	1677					sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0														0.32			84	180				---	---	---	---	capture_indel			In_Frame_Del	DEL	170638184	170638186	17461	2	GAA	-	-	41	41	UBR3	-	5	5
TG	7038	broad.mit.edu	36	8	134111272	134111272	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-2559-01	TCGA-06-2559-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:134111272_134111272delG	uc003ytw.1	+	c.7061_7061delG	c.(7060-7062)TGGfs	p.W2354fs	TG_uc010mdw.1_Frame_Shift_Del_p.W1113fs	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin	2354					hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)						1778				0.47			43	48				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	134111272	134111272	16341	8	G	-	-	47	47	TG	-	5	5
