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
DOCK1	1793	broad.mit.edu	36	10	128725996	128725996	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1092-01	TCGA-12-1092-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:128725996T>C	uc001ljt.1	+	c.1873T>C	c.(1873-1875)TGG>CGG	p.W625R		NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	625	DHR-1.				apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)										0.403846	69.766964	70.186675	21	31	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128725996	128725996	4868	10	T	C	C	51	51	DOCK1	C	4	4
MARCH8	220972	broad.mit.edu	36	10	45273776	45273776	+	Nonsense_Mutation	SNP	C	A	A			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:45273776C>A	uc001jch.2	-	c.1639G>T	c.(1639-1641)GGA>TGA	p.G547*	MARCH8_uc001jcj.1_Nonsense_Mutation_p.G265*|MARCH8_uc001jck.1_Nonsense_Mutation_p.G265*|MARCH8_uc001jcg.1_Nonsense_Mutation_p.G134*|MARCH8_uc001jci.1_Nonsense_Mutation_p.G265*	NM_001002266	NP_659458	Q5T0T0	MARH8_HUMAN	cellular modulator of immune recognition isoform	265						cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0						NSCLC(102;658 1594 2173 16344 34808)								0.257732	62.4174	67.587966	25	72	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	45273776	45273776	9690	10	C	A	A	21	21	MARCH8	A	5	3
SLC22A10	387775	broad.mit.edu	36	11	62814599	62814599	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62814599C>T	uc009yor.1	+	c.386C>T	c.(385-387)TCG>TTG	p.S129L	SLC22A10_uc001nwu.2_Non-coding_Transcript	NM_001039752	NP_001034841	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	129	Extracellular (Potential).				transmembrane transport	integral to membrane	transporter activity			ovary(2)	2														0.127193	44.618978	75.525196	29	199	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62814599	62814599	14937	11	C	T	T	31	31	SLC22A10	T	1	1
SLC38A1	81539	broad.mit.edu	36	12	44886195	44886195	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:44886195C>A	uc009zkj.1	-	c.581G>T	c.(580-582)GGC>GTC	p.G194V	SLC38A1_uc001rpa.1_Missense_Mutation_p.G194V|SLC38A1_uc001rpb.1_Missense_Mutation_p.G194V|SLC38A1_uc001rpc.1_Missense_Mutation_p.G194V|SLC38A1_uc001rpd.1_Missense_Mutation_p.G194V|SLC38A1_uc001rpe.1_Missense_Mutation_p.G194V|SLC38A1_uc009zkk.1_Missense_Mutation_p.G167V	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1	194	Helical; (Potential).				cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|central_nervous_system(1)	3	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)											0.1875	104.136703	127.557359	48	208	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44886195	44886195	15098	12	C	A	A	26	26	SLC38A1	A	3	3
AMDHD1	144193	broad.mit.edu	36	12	94874736	94874736	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:94874736C>T	uc001tel.1	+	c.452C>T	c.(451-453)ACG>ATG	p.T151M	AMDHD1_uc009zth.1_Missense_Mutation_p.T42M	NM_152435	NP_689648	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	151					histidine catabolic process to glutamate and formamide	cytosol	imidazolonepropionase activity|metal ion binding			central_nervous_system(1)	1														0.333333	9.22343	9.444121	3	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94874736	94874736	570	12	C	T	T	19	19	AMDHD1	T	1	1
SERPINA1	5265	broad.mit.edu	36	14	93919025	93919025	+	Silent	SNP	C	A	A			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:93919025C>A	uc001ycx.2	-	c.303G>T	c.(301-303)CTG>CTT	p.L101L	SERPINA1_uc001ycw.2_Non-coding_Transcript|SERPINA1_uc010auw.1_Silent_p.L101L|SERPINA1_uc010aux.1_Silent_p.L101L|SERPINA1_uc001ycy.2_Silent_p.L101L|SERPINA1_uc010auy.1_Silent_p.L101L|SERPINA1_uc001ycz.2_Silent_p.L101L|SERPINA1_uc010auz.1_Silent_p.L101L|SERPINA1_uc010ava.1_Silent_p.L101L|SERPINA1_uc001ydb.2_Silent_p.L101L|SERPINA1_uc010avb.1_Silent_p.L101L|SERPINA1_uc001ydc.2_Silent_p.L101L|SERPINA1_uc001yda.1_Silent_p.L101L	NM_000295	NP_001121179	P01009	A1AT_HUMAN	serine proteinase inhibitor, clade A, member 1	101					acute-phase response|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen|proteinaceous extracellular matrix	protease binding|serine-type endopeptidase inhibitor activity			skin(1)	1		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)	Alpha-1-proteinase inhibitor(DB00058)									0.588652	271.9392	272.905718	83	58	CC		KEEP	---	---	---	---	capture			Silent	SNP	93919025	93919025	14574	14	C	A	A	21	21	SERPINA1	A	3	3
RTF1	23168	broad.mit.edu	36	15	39555980	39555980	+	Silent	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39555980C>T	uc001zny.1	+	c.1152C>T	c.(1150-1152)TAC>TAT	p.Y384Y		NM_015138	NP_055953	Q92541	RTF1_HUMAN	Paf1/RNA polymerase II complex component	509					histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)										0.214286	6.516346	7.572661	3	11	CC		KEEP	---	---	---	---	capture			Silent	SNP	39555980	39555980	14201	15	C	T	T	19	19	RTF1	T	1	1
ARNT2	9915	broad.mit.edu	36	15	78632167	78632167	+	Silent	SNP	C	T	T	rs17853546	unknown	TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:78632167C>T	uc002bfr.1	+	c.1086C>T	c.(1084-1086)CCC>CCT	p.P362P	ARNT2_uc002bfs.1_Silent_p.P351P	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator	362	PAS 2.				central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription regulator activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)											0.175562	250.012764	320.72046	125	587	CC		KEEP	---	---	---	---	capture			Silent	SNP	78632167	78632167	984	15	C	T	T	22	22	ARNT2	T	2	2
PRKCB	5579	broad.mit.edu	36	16	24093346	24093346	+	Silent	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:24093346C>T	uc002dmc.1	+	c.1338C>T	c.(1336-1338)TAC>TAT	p.Y446Y	PRKCB_uc002dmd.1_Silent_p.Y446Y	NM_002738	NP_002729	P05771	KPCB_HUMAN	protein kinase C, beta isoform 2	446	Protein kinase.				apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)					395				0.125	6.324988	12.915202	6	42	CC		KEEP	---	---	---	---	capture			Silent	SNP	24093346	24093346	12951	16	C	T	T	19	19	PRKCB	T	1	1
ANKRD11	29123	broad.mit.edu	36	16	87874489	87874489	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:87874489G>A	uc002fmx.1	-	c.5962C>T	c.(5962-5964)CCC>TCC	p.P1988S	ANKRD11_uc002fmy.1_Missense_Mutation_p.P1988S|ANKRD11_uc002fnc.1_Missense_Mutation_p.P1988S|ANKRD11_uc002fna.1_5'Flank|ANKRD11_uc002fnb.1_Missense_Mutation_p.P1945S	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1988	Pro-rich.					nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)										0.363636	47.390637	48.109338	16	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87874489	87874489	642	16	G	A	A	43	43	ANKRD11	A	2	2
SPG7	6687	broad.mit.edu	36	16	88126536	88126536	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:88126536G>C	uc002fnj.1	+	c.1315G>C	c.(1315-1317)GAA>CAA	p.E439Q	SPG7_uc002fni.1_Missense_Mutation_p.E439Q	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 isoform 1	439	Mitochondrial matrix (Potential).				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)										0.1875	6.514875	7.978653	3	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88126536	88126536	15556	16	G	C	C	33	33	SPG7	C	3	3
AKAP10	11216	broad.mit.edu	36	17	19806764	19806764	+	Silent	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:19806764G>A	uc002gwo.1	-	c.300C>T	c.(298-300)GCC>GCT	p.A100A	AKAP10_uc002gwp.1_Silent_p.A100A|AKAP10_uc010cqw.1_Silent_p.A100A	NM_007202	NP_009133	O43572	AKA10_HUMAN	A-kinase anchor protein 10 precursor	100					blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)													0.433962	72.120201	72.320933	23	30	GG		KEEP	---	---	---	---	capture			Silent	SNP	19806764	19806764	449	17	G	A	A	39	39	AKAP10	A	1	1
ERBB2	2064	broad.mit.edu	36	17	35137087	35137087	+	Missense_Mutation	SNP	A	C	C			TCGA-12-1092-01	TCGA-12-1092-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:35137087A>C	uc002hso.1	+	c.3173A>C	c.(3172-3174)GAC>GCC	p.D1058A	ERBB2_uc002hsm.1_Missense_Mutation_p.D1028A|ERBB2_uc002hsp.1_Missense_Mutation_p.D861A|ERBB2_uc010cwb.1_Intron	NM_004448	NP_001005862	P04626	ERBB2_HUMAN	erbB-2 isoform a	1058	Cytoplasmic (Potential).				cell proliferation|heart development|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell adhesion|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|protein autophosphorylation|regulation of angiogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|wound healing	integral to membrane|nucleus|perinuclear region of cytoplasm|receptor complex	ATP binding|DNA binding|epidermal growth factor receptor activity|ErbB-3 class receptor binding|identical protein binding|protein C-terminus binding|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(71)|central_nervous_system(16)|ovary(13)|stomach(12)|breast(5)|upper_aerodigestive_tract(4)|large_intestine(3)|liver(3)|endometrium(2)|pancreas(1)	130	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	Lapatinib(DB01259)|Letrozole(DB01006)|Trastuzumab(DB00072)			1		271	TCGA GBM(5;<1E-8)			0.333333	6.52234	6.743577	3	6	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35137087	35137087	5399	17	A	C	C	10	10	ERBB2	C	4	4
TP53	7157	broad.mit.edu	36	17	7518263	7518263	+	Missense_Mutation	SNP	C	T	T	rs11540652	by-hapmap	TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518263C>T	uc002gim.2	-	c.743G>A	c.(742-744)CGG>CAG	p.R248Q	TP53_uc002gig.1_Missense_Mutation_p.R248Q|TP53_uc002gih.1_Missense_Mutation_p.R248Q|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R116Q|TP53_uc010cng.1_Missense_Mutation_p.R116Q|TP53_uc002gii.1_Missense_Mutation_p.R116Q|TP53_uc010cnh.1_Missense_Mutation_p.R248Q|TP53_uc010cni.1_Missense_Mutation_p.R248Q|TP53_uc002gij.2_Missense_Mutation_p.R248Q|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.R155Q|TP53_uc002gio.2_Missense_Mutation_p.R116Q	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	248	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|NR -> IP (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.R248Q(503)|p.R248L(63)|p.R248P(11)|p.0?(6)|p.N247_R248delNR(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)	R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIN87_STOMACH)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NIHOVCAR3_OVARY)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(HCC70_BREAST)|R248Q(KYSE150_OESOPHAGUS)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PC14_LUNG)	111	p.R248L(NCIH211-Tumor)|p.R248L(NB4-Tumor)|p.R248L(PC14-Tumor)|p.R248L(KYO1-Tumor)|p.R248L(PCM6-Tumor)|p.R248L(NUDHL1-Tumor)|p.R248L(BL41-Tumor)|p.R248Q(FADU-Tumor)|p.R248L(CI1-Tumor)|p.R248L(SW1463-Tumor)|p.R248L(COLO699-Tumor)|p.R248L(HS683-Tumor)|p.R248*(DB-Tumor)|p.R248L(HCC1143-Tumor)|p.R248L(NCIN87-Tumor)|p.R248A(SF126-Tumor)|p.R248L(PANC02.03-Tumor)|p.R248L(HEC1B-Tumor)|p.R248L(PECAPJ15-Tumor)|p.R248L(LNCAPCLONEFGC-Tumor)|p.R248L(NIHOVCAR3-Tumor)|p.R248L(NUDUL1-Tumor)|p.R248L(ONCODG1-Tumor)|p.R248L(RT112-Tumor)|p.R248L(SF295-Tumor)|p.R248L(P12ICHIKAWA-Tumor)|p.R248L(DND41-Tumor)|p.R248Q(SBC5-Tumor)|p.R248L(KOPN8-Tumor)|p.R248L(KASUMI1-Tumor)|p.R248L(EM2-Tumor)|p.R248L(SKUT1-Tumor)|p.R248L(NCCSTCK140-Tumor)|p.R248L(TE6-Tumor)|p.R248L(MOLM6-Tumor)|p.R248L(SEM-Tumor)|p.R248L(NAMALWA-Tumor)|p.R248L(CA46-Tumor)|p.R248L(639V-Tumor)|p.R248L(SKM1-Tumor)|p.R248Q(NCIH1573-Tumor)|p.R248Q(NCIH1618-Tumor)|p.R248L(HCC70-Tumor)|p.R248L(WSUDLCL2-Tumor)|p.R248L(HEC1A-Tumor)|p.R248L(KYSE150-Tumor)|p.R248L(HSC4-Tumor)|p.R248L(CL40-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.35503	559.700148	569.070525	180	327	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7518263	7518263	16923	17	C	T	T	23	23	TP53	T	1	1
LASS1	10715	broad.mit.edu	36	19	18865289	18865289	+	Nonsense_Mutation	SNP	G	T	T			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18865289G>T	uc002nkj.1	-	c.345C>A	c.(343-345)TAC>TAA	p.Y115*	GDF1_uc002nki.1_5'UTR|LASS1_uc010ebx.1_Nonsense_Mutation_p.Y17*	NM_198207	NP_937850	P27544	LASS1_HUMAN	longevity assurance gene 1 isoform 2	115	TLC.|Helical; (Potential).				ceramide biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|microsome	sphingosine N-acyltransferase activity				0														0.230769	14.835727	16.563359	6	20	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	18865289	18865289	8961	19	G	T	T	48	48	LASS1	T	5	3
GPI	2821	broad.mit.edu	36	19	39560255	39560255	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:39560255G>A	uc002nvf.1	+	c.410G>A	c.(409-411)CGG>CAG	p.R137Q	GPI_uc002nvg.1_Missense_Mutation_p.R137Q|GPI_uc010edl.1_Missense_Mutation_p.R137Q	NM_000175	NP_000166	P06744	G6PI_HUMAN	glucose phosphate isomerase	137					angiogenesis|gluconeogenesis|glycolysis|hemostasis|humoral immune response	cytosol|extracellular space|nucleus|plasma membrane	cytokine activity|glucose-6-phosphate isomerase activity|growth factor activity			ovary(1)|kidney(1)	2	Esophageal squamous(110;0.162)													0.25	72.182832	78.312052	27	81	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39560255	39560255	6885	19	G	A	A	39	39	GPI	A	1	1
ZNF460	10794	broad.mit.edu	36	19	62493952	62493952	+	Silent	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:62493952G>A	uc002qog.2	+	c.231G>A	c.(229-231)CAG>CAA	p.Q77Q		NM_006635	NP_006626	Q14592	ZN460_HUMAN	zinc finger protein 460	77	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)										0.22963	79.054952	88.103443	31	104	GG		KEEP	---	---	---	---	capture			Silent	SNP	62493952	62493952	18517	19	G	A	A	35	35	ZNF460	A	2	2
NOTCH2	4853	broad.mit.edu	36	1	120269450	120269450	+	Splice_Site_SNP	SNP	C	A	A			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:120269450C>A	uc001eik.1	-	c.e25_splice_site				NM_024408	NP_077719			notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(7)|ovary(4)|lung(3)|central_nervous_system(2)|kidney(2)|breast(1)	19	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)						581				0.295533	488.67003	510.438112	172	410	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	120269450	120269450	10951	1	C	A	A	20	20	NOTCH2	A	5	3
LMX1A	4009	broad.mit.edu	36	1	163443975	163443975	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:163443975G>A	uc001gcy.1	-	c.766C>T	c.(766-768)CGA>TGA	p.R256*	LMX1A_uc001gcz.1_Nonsense_Mutation_p.R256*|LMX1A_uc001gcw.1_5'UTR|LMX1A_uc001gcx.1_Nonsense_Mutation_p.R7*	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	256	Gln-rich.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			central_nervous_system(3)|pancreas(1)	4	all_hematologic(923;0.248)													0.245902	80.098717	87.264852	30	92	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	163443975	163443975	9190	1	G	A	A	38	38	LMX1A	A	5	1
CNTN2	6900	broad.mit.edu	36	1	203302317	203302317	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:203302317C>G	uc001hbr.1	+	c.1942C>G	c.(1942-1944)CCA>GCA	p.P648A	CNTN2_uc001hbq.1_Missense_Mutation_p.P539A|CNTN2_uc001hbs.1_Missense_Mutation_p.P436A	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor	648	Fibronectin type-III 1.				axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			Melanoma(183;2548 2817 37099 41192)								0.927419	431.681377	454.259987	115	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	203302317	203302317	3779	1	C	G	G	30	30	CNTN2	G	3	3
RYR2	6262	broad.mit.edu	36	1	235843981	235843981	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1092-01	TCGA-12-1092-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:235843981T>G	uc001hyl.1	+	c.4930T>G	c.(4930-4932)TTG>GTG	p.L1644V		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1644	Cytoplasmic (By similarity).|4 X approximate repeats.				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)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.186747	74.40151	89.706448	31	135	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	235843981	235843981	14249	1	T	G	G	60	60	RYR2	G	4	4
CSMD2	114784	broad.mit.edu	36	1	34030644	34030644	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:34030644C>T	uc001bxm.1	-	c.1517G>A	c.(1516-1518)GGT>GAT	p.G506D	CSMD2_uc001bxn.1_Missense_Mutation_p.G466D	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	466	CUB 3.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(5)|pancreas(1)	6		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)												0.225806	48.824665	55.247935	21	72	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34030644	34030644	4086	1	C	T	T	18	18	CSMD2	T	2	2
RIMKLA	284716	broad.mit.edu	36	1	42637763	42637763	+	Nonsense_Mutation	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:42637763C>T	uc001chi.2	+	c.142C>T	c.(142-144)CGA>TGA	p.R48*		NM_173642	NP_775913	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family	89					protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0														0.261905	29.505884	31.660168	11	31	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	42637763	42637763	13842	1	C	T	T	27	27	RIMKLA	T	5	1
CCBL2	56267	broad.mit.edu	36	1	89207032	89207032	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:89207032C>T	uc001dmp.1	-	c.212G>A	c.(211-213)GGC>GAC	p.G71D	CCBL2_uc001dmq.1_Missense_Mutation_p.G37D|CCBL2_uc001dmr.1_5'UTR	NM_001008661	NP_001008662	Q6YP21	KAT3_HUMAN	kynurenine aminotransferase III isoform 1	71		Substrate; via amide nitrogen (By similarity).			biosynthetic process|kynurenine metabolic process|tryptophan catabolic process		cysteine-S-conjugate beta-lyase activity|kynurenine-glyoxylate transaminase activity|kynurenine-oxoglutarate transaminase activity|pyridoxal phosphate binding			ovary(1)	1		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)									0.363636	45.985694	46.706458	16	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89207032	89207032	2853	1	C	T	T	26	26	CCBL2	T	2	2
ERG	2078	broad.mit.edu	36	21	38717211	38717211	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:38717211C>T	uc010gnw.1	-	c.400G>A	c.(400-402)GTG>ATG	p.V134M	ERG_uc002ywz.1_Missense_Mutation_p.V134M|ERG_uc010gnv.1_Missense_Mutation_p.V35M|ERG_uc010gnx.1_Missense_Mutation_p.V134M|ERG_uc002yxb.1_Missense_Mutation_p.V134M|ERG_uc002yxc.2_Missense_Mutation_p.V134M|ERG_uc002yxa.1_Missense_Mutation_p.V127M	NM_182918	NP_891548	P11308	ERG_HUMAN	ets-related isoform 1	134	PNT.				cell proliferation|multicellular organismal development|protein phosphorylation|regulation of transcription, DNA-dependent	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2058)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2058)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|ovary(1)	2386		Prostate(19;3.6e-06)				Esophageal Squamous(130;336 1700 3010 3083 40589)				177				0.329843	178.859104	183.761347	63	128	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38717211	38717211	5415	21	C	T	T	19	19	ERG	T	1	1
ASPHD2	57168	broad.mit.edu	36	22	25160128	25160128	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:25160128G>A	uc003acg.1	+	c.469G>A	c.(469-471)GCA>ACA	p.A157T		NM_020437	NP_065170	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	183	Lumenal (Potential).				oxidation-reduction process|peptidyl-amino acid modification	integral to endoplasmic reticulum membrane	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity			ovary(1)	1														0.4	19.148175	19.278993	6	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25160128	25160128	1074	22	G	A	A	38	38	ASPHD2	A	1	1
ASCC2	84164	broad.mit.edu	36	22	28530640	28530640	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:28530640G>A	uc003agr.1	-	c.1340C>T	c.(1339-1341)TCG>TTG	p.S447L	ASCC2_uc003ags.1_Non-coding_Transcript|ASCC2_uc003agt.1_Missense_Mutation_p.S447L	NM_032204	NP_115580	Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit	447					regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)											0.270531	304.632368	324.287549	112	302	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28530640	28530640	1050	22	G	A	A	37	37	ASCC2	A	1	1
DYSF	8291	broad.mit.edu	36	2	71759698	71759698	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:71759698C>T	uc010fen.1	+	c.5888C>T	c.(5887-5889)TCC>TTC	p.S1963F	DYSF_uc002sie.1_Missense_Mutation_p.S1924F|DYSF_uc002sig.2_Missense_Mutation_p.S1910F|DYSF_uc010fee.1_Missense_Mutation_p.S1945F|DYSF_uc010fef.1_Missense_Mutation_p.S1962F|DYSF_uc010feg.1_Missense_Mutation_p.S1955F|DYSF_uc010feh.1_Missense_Mutation_p.S1931F|DYSF_uc010fei.1_Missense_Mutation_p.S1941F|DYSF_uc010fej.1_Missense_Mutation_p.S1932F|DYSF_uc002sif.1_Missense_Mutation_p.S1925F|DYSF_uc010fek.1_Missense_Mutation_p.S1942F|DYSF_uc010fel.1_Missense_Mutation_p.S1911F|DYSF_uc010fem.1_Missense_Mutation_p.S1946F|DYSF_uc010feo.1_Missense_Mutation_p.S1956F	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	1924	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)	6														0.225225	57.612981	65.316841	25	86	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71759698	71759698	5045	2	C	T	T	30	30	DYSF	T	2	2
CTNNA2	1496	broad.mit.edu	36	2	80636378	80636378	+	Silent	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:80636378G>A	uc002soi.1	+	c.1593G>A	c.(1591-1593)GAG>GAA	p.E531E	CTNNA2_uc002sog.1_Silent_p.E531E|CTNNA2_uc002soh.1_Silent_p.E530E	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2	530					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)	8										489				0.229508	72.639565	80.821679	28	94	GG		KEEP	---	---	---	---	capture			Silent	SNP	80636378	80636378	4172	2	G	A	A	35	35	CTNNA2	A	2	2
CHL1	10752	broad.mit.edu	36	3	411477	411477	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1092-01	TCGA-12-1092-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:411477A>G	uc003bot.1	+	c.3016A>G	c.(3016-3018)AAA>GAA	p.K1006E	CHL1_uc003bou.1_Missense_Mutation_p.K990E|CHL1_uc003bow.1_Missense_Mutation_p.K990E	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	990	Fibronectin type-III 4.|Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				central_nervous_system(4)|large_intestine(2)|ovary(1)	7		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)						659				0.333333	163.171733	167.229973	55	110	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	411477	411477	3483	3	A	G	G	5	5	CHL1	G	4	4
LRIG1	26018	broad.mit.edu	36	3	66548101	66548101	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:66548101G>A	uc003dmx.1	-	c.580C>T	c.(580-582)CGC>TGC	p.R194C	LRIG1_uc010hnz.1_5'UTR|LRIG1_uc010hoa.1_Missense_Mutation_p.R194C	NM_015541	NP_056356	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like	194	Extracellular (Potential).|LRR 6.					integral to membrane				ovary(2)|skin(1)	3		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)										0.276316	53.443002	56.866236	21	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66548101	66548101	9317	3	G	A	A	37	37	LRIG1	A	1	1
ADAD1	132612	broad.mit.edu	36	4	123534196	123534196	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:123534196C>G	uc003ieo.1	+	c.532C>G	c.(532-534)CCT>GCT	p.P178A	ADAD1_uc003iep.1_Missense_Mutation_p.P178A|ADAD1_uc003ieq.1_Missense_Mutation_p.P160A	NM_139243	NP_640336	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1	178					multicellular organismal development|RNA processing	nucleus	adenosine deaminase activity|double-stranded RNA binding				0														0.0875	6.362021	20.132397	7	73	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123534196	123534196	232	4	C	G	G	30	30	ADAD1	G	3	3
ADAM29	11086	broad.mit.edu	36	4	176134089	176134089	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:176134089C>T	uc003iuc.1	+	c.838C>T	c.(838-840)CGG>TGG	p.R280W	ADAM29_uc003iud.1_Missense_Mutation_p.R280W|ADAM29_uc003iue.1_Missense_Mutation_p.R280W|ADAM29_uc010irr.1_Missense_Mutation_p.R280W	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	280	Peptidase M12B.|Extracellular (Potential).				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(1)	10		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		Ovarian(140;1727 1835 21805 25838 41440)				106				0.167568	129.434953	168.169822	62	308	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	176134089	176134089	248	4	C	T	T	23	23	ADAM29	T	1	1
SMR3B	10879	broad.mit.edu	36	4	71290119	71290119	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71290119C>A	uc003hfh.1	+	c.205C>A	c.(205-207)CCA>ACA	p.P69T		NM_006685	NP_006676	P02814	SMR3B_HUMAN	submaxillary gland androgen regulated protein 3	69	Pro-rich.					extracellular space				skin(1)	1		all_hematologic(202;0.196)												0.210084	52.601398	61.86568	25	94	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71290119	71290119	15312	4	C	A	A	30	30	SMR3B	A	3	3
AFP	174	broad.mit.edu	36	4	74537158	74537158	+	Silent	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:74537158G>A	uc003hha.1	+	c.1605G>A	c.(1603-1605)AAG>AAA	p.K535K	AFP_uc003hgz.1_Silent_p.K535K	NM_001134	NP_001125	P02771	FETA_HUMAN	alpha-fetoprotein precursor	535	Albumin 3.				transport		metal ion binding			ovary(1)	1	Breast(15;0.00102)		Epithelial(6;2.42e-05)|all cancers(17;0.000268)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)											0.154116	179.226968	244.533164	88	483	GG		KEEP	---	---	---	---	capture			Silent	SNP	74537158	74537158	364	4	G	A	A	35	35	AFP	A	2	2
DNAH5	1767	broad.mit.edu	36	5	13845240	13845240	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:13845240G>A	uc003jfd.2	-	c.8311C>T	c.(8311-8313)CGC>TGC	p.R2771C		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2771	AAA 3 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|breast(1)|central_nervous_system(1)|pancreas(1)	17	Lung NSC(4;0.00476)													0.227273	59.303384	66.828668	25	85	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13845240	13845240	4787	5	G	A	A	40	40	DNAH5	A	1	1
EPB41L2	2037	broad.mit.edu	36	6	131248103	131248103	+	Splice_Site_SNP	SNP	T	C	C			TCGA-12-1092-01	TCGA-12-1092-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:131248103T>C	uc003qch.1	-	c.e12_splice_site			EPB41L2_uc003qce.1_5'Flank|EPB41L2_uc003qcf.1_5'Flank|EPB41L2_uc003qcg.1_Splice_Site_SNP|EPB41L2_uc010kfk.1_Splice_Site_SNP|EPB41L2_uc003qci.1_Splice_Site_SNP|EPB41L2_uc010kfl.1_Splice_Site_SNP	NM_001431	NP_001422			erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)								OREG0017660	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.091463	12.709123	40.275595	15	149	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	131248103	131248103	5346	6	T	C	C	53	53	EPB41L2	C	5	4
DNAH8	1769	broad.mit.edu	36	6	38985352	38985352	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:38985352G>A	uc003ooe.1	+	c.8943G>A	c.(8941-8943)TGG>TGA	p.W2981*		NM_001371	NP_001362	Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy polypeptide 8	2981	AAA 4 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(5)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	17										2979				0.28433	480.924478	506.784942	176	443	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	38985352	38985352	4790	6	G	A	A	42	42	DNAH8	A	5	2
TAS2R40	259286	broad.mit.edu	36	7	142629903	142629903	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142629903G>A	uc003wch.1	+	c.610G>A	c.(610-612)GTT>ATT	p.V204I		NM_176882	NP_795363	P59535	T2R40_HUMAN	taste receptor, type 2, member 40	204	Helical; Name=5; (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(1)	1	Melanoma(164;0.059)													0.304094	152.944846	158.795464	52	119	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142629903	142629903	16100	7	G	A	A	40	40	TAS2R40	A	1	1
GNAT3	346562	broad.mit.edu	36	7	79926075	79926075	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1092-01	TCGA-12-1092-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:79926075T>C	uc010leb.1	-	c.913A>G	c.(913-915)AAC>GAC	p.N305D	CD36_uc003uhc.1_Intron	NM_001102386	NP_001095856	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha	305					detection of chemical stimulus involved in sensory perception of bitter taste|G-protein signaling, coupled to cAMP nucleotide second messenger|rhodopsin mediated phototransduction|sensory perception of sweet taste|sensory perception of umami taste	cytoplasm|heterotrimeric G-protein complex|photoreceptor inner segment|photoreceptor outer segment	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1														0.202186	92.880512	107.951782	37	146	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79926075	79926075	6782	7	T	C	C	62	62	GNAT3	C	4	4
NPTX2	4885	broad.mit.edu	36	7	98095732	98095732	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98095732G>A	uc003upl.1	+	c.1151G>A	c.(1150-1152)CGC>CAC	p.R384H		NM_002523	NP_002514	P47972	NPTX2_HUMAN	neuronal pentraxin II	384	Pentaxin.				synaptic transmission	extracellular region	metal ion binding|sugar binding			central_nervous_system(2)	2	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)											0.147059	15.611727	23.746724	10	58	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	98095732	98095732	11008	7	G	A	A	38	38	NPTX2	A	1	1
MTERFD1	51001	broad.mit.edu	36	8	97338444	97338444	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1092-01	TCGA-12-1092-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:97338444G>A	uc003yhs.1	-	c.409C>T	c.(409-411)CCT>TCT	p.P137S	MTERFD1_uc003yhr.1_Missense_Mutation_p.P16S|MTERFD1_uc010mbd.1_Missense_Mutation_p.P137S	NM_015942	NP_057026	Q96E29	MTER1_HUMAN	MTERF domain containing 1	137					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion	promoter binding			ovary(1)	1	Breast(36;5.16e-05)													0.293839	170.665948	178.693467	62	149	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97338444	97338444	10312	8	G	A	A	43	43	MTERFD1	A	2	2
GABRE	2564	broad.mit.edu	36	X	150889327	150889327	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1092-01	TCGA-12-1092-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:150889327C>T	uc004ffi.1	-	c.260G>A	c.(259-261)CGC>CAC	p.R87H	GABRE_uc004ffg.1_5'UTR|GABRE_uc004fff.1_5'UTR|GABRE_uc004ffh.1_5'UTR	NM_004961	NP_068830	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor,	87	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	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(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.565217	245.151332	245.661072	78	60	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150889327	150889327	6421	23	C	T	T	27	27	GABRE	T	1	1
PJA1	64219	broad.mit.edu	36	X	68298062	68298063	+	Missense_Mutation	DNP	AC	TT	TT			TCGA-12-1092-01	TCGA-12-1092-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:68298062_68298063AC>TT	uc004dxh.1	-	c.1744_1745GT>AA	c.(1744-1746)GTC>AAC	p.V582N	PJA1_uc004dxg.1_Missense_Mutation_p.V394N|PJA1_uc004dxi.1_Missense_Mutation_p.V527N|PJA1_uc004dxf.2_Missense_Mutation_p.V582N	NM_145119	NP_001027568	Q8NG27	PJA1_HUMAN	praja 1 isoform a	582							zinc ion binding				0														0.216867	32.601314	38.744909	18	65	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	68298062	68298063	12385	23	AC	TT	TT	10	10	PJA1	TT	4	4
CELSR3	1951	broad.mit.edu	36	3	48657926	48657927	+	Frame_Shift_Ins	INS	-	C	C			TCGA-12-1092-01	TCGA-12-1092-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:48657926_48657927insC	uc003cuf.1	-	c.7960_7961insG	c.(7960-7962)GTGfs	p.V2654fs	CELSR3_uc010hkf.1_5'Flank|CELSR3_uc010hkg.1_Frame_Shift_Ins_p.V567fs|CELSR3_uc003cul.1_Frame_Shift_Ins_p.V2584fs	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	2584	Helical; Name=2; (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	48657926	48657927	3356	3	-	C	C	6	6	CELSR3	C	5	5
NFKBIL2	4796	broad.mit.edu	36	8	145632973	145632974	+	Frame_Shift_Ins	INS	-	C	C			TCGA-12-1092-01	TCGA-12-1092-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145632973_145632974insC	uc003zcu.2	-	c.1387_1388insG	c.(1387-1389)GCGfs	p.A463fs		NM_013432	NP_038460	Q96HA7	TONSL_HUMAN	NF-kappa-B inhibitor-like protein 2	622	ANK 3.				cytoplasmic sequestering of transcription factor|double-strand break repair via homologous recombination|replication fork processing	cytoplasm|nuclear replication fork	histone binding|transcription corepressor activity				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)											0.36			4	7				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	145632973	145632974	10782	8	-	C	C	38	38	NFKBIL2	C	5	5
