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
ARMC3	219681	broad.mit.edu	36	10	23290978	23290978	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:23290978G>A	uc001irm.2	+	c.697G>A	c.(697-699)GGA>AGA	p.G233R		NM_173081	NP_775104	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	233	ARM 6.						binding				0														0.6	101.187717	101.638741	30	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23290978	23290978	970	10	G	A	A	35	35	ARMC3	A	2	2
ZNF248	57209	broad.mit.edu	36	10	38166954	38166954	+	Missense_Mutation	SNP	A	G	G			TCGA-02-0055-01	TCGA-02-0055-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:38166954A>G	uc001izd.1	-	c.107T>C	c.(106-108)GTG>GCG	p.V36A	ZNF248_uc009xmc.1_Missense_Mutation_p.V36A|ZNF248_uc001izb.2_Non-coding_Transcript|ZNF248_uc001izc.2_Missense_Mutation_p.V36A	NM_021045	NP_066383	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	36	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.497512	297.13984	297.141201	100	101	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38166954	38166954	18384	10	A	G	G	6	6	ZNF248	G	4	4
PTEN	5728	broad.mit.edu	36	10	89682887	89682887	+	Missense_Mutation	SNP	A	G	G			TCGA-02-0055-01	TCGA-02-0055-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682887A>G	uc001kfb.1	+	c.391A>G	c.(391-393)ACT>GCT	p.T131A		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	131	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.T131fs*3(3)|p.K128_R130del(2)|p.Y27_N212>Y(2)|p.T131A(1)|p.K128fs*47(1)|p.R130fs*2(1)|p.A121_F145del(1)|p.T131P(1)|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		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.514124	316.835902	316.866869	91	86	AA		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	89682887	89682887	13192	10	A	G	G	2	2	PTEN	G	4	4
OR51D1	390038	broad.mit.edu	36	11	4618163	4618163	+	Silent	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4618163C>T	uc001lzh.1	+	c.567C>T	c.(565-567)CAC>CAT	p.H189H		NM_001004751	NP_001004751	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D,	189	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)												0.22314	129.118369	146.178342	54	188	CC		KEEP	---	---	---	---	capture		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)	Silent	SNP	4618163	4618163	11503	11	C	T	T	20	20	OR51D1	T	2	2
PHRF1	57661	broad.mit.edu	36	11	598380	598380	+	Missense_Mutation	SNP	A	T	T			TCGA-02-0055-01	TCGA-02-0055-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:598380A>T	uc001lqe.1	+	c.2924A>T	c.(2923-2925)GAC>GTC	p.D975V	PHRF1_uc009ybz.1_Missense_Mutation_p.D765V|PHRF1_uc009yca.1_Non-coding_Transcript	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	975							RNA polymerase binding|zinc ion binding				0														0.296296	20.405171	21.39819	8	19	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	598380	598380	12285	11	A	T	T	10	10	PHRF1	T	4	4
TMEM151A	256472	broad.mit.edu	36	11	65818703	65818703	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65818703C>T	uc001ohl.1	+	c.410C>T	c.(409-411)GCG>GTG	p.A137V		NM_153266	NP_694998	Q8N4L1	T151A_HUMAN	transmembrane protein 151A	137						integral to membrane				central_nervous_system(1)	1														0.230769	6.430828	7.285797	3	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65818703	65818703	16602	11	C	T	T	27	27	TMEM151A	T	1	1
PICALM	8301	broad.mit.edu	36	11	85411151	85411151	+	Missense_Mutation	SNP	A	T	T			TCGA-02-0055-01	TCGA-02-0055-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:85411151A>T	uc001pbm.1	-	c.359T>A	c.(358-360)ATG>AAG	p.M120K	PICALM_uc001pbl.1_Missense_Mutation_p.M120K|PICALM_uc001pbn.1_Missense_Mutation_p.M120K	NM_007166	NP_009097	Q13492	PICAL_HUMAN	phosphatidylinositol-binding clathrin assembly	120	ENTH.				clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)								415				0.321429	105.565304	108.73484	36	76	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	85411151	85411151	12304	11	A	T	T	8	8	PICALM	T	4	4
LEPREL2	10536	broad.mit.edu	36	12	6817172	6817172	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6817172G>A	uc001qra.1	+	c.1727G>A	c.(1726-1728)CGC>CAC	p.R576H	LEPREL2_uc001qqz.1_Missense_Mutation_p.R383H|LEPREL2_uc001qrb.1_Missense_Mutation_p.R383H|GNB3_uc001qrc.1_5'Flank|GNB3_uc001qrd.1_5'Flank	NM_014262	NP_055077	Q8IVL6	P3H3_HUMAN	leprecan-like 2	576	Fe2OG dioxygenase.				negative regulation of cell proliferation|oxidation-reduction process	endoplasmic reticulum	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity				0					L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)									0.416667	42.718478	42.936594	15	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6817172	6817172	9055	12	G	A	A	38	38	LEPREL2	A	1	1
OCA2	4948	broad.mit.edu	36	15	25876456	25876456	+	Missense_Mutation	SNP	C	G	G			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:25876456C>G	uc001zbh.2	-	c.1657G>C	c.(1657-1659)GTC>CTC	p.V553L	OCA2_uc010ayv.1_Missense_Mutation_p.V529L	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	553	Cytoplasmic (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)												0.239583	62.183326	68.12259	23	73	CC		KEEP	---	---	---	---	capture		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)	Missense_Mutation	SNP	25876456	25876456	11220	15	C	G	G	19	19	OCA2	G	3	3
TRPM1	4308	broad.mit.edu	36	15	29130055	29130055	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:29130055G>A	uc001zfm.1	-	c.1220C>T	c.(1219-1221)CCG>CTG	p.P407L	TRPM1_uc010azy.1_Missense_Mutation_p.P314L|TRPM1_uc001zfl.1_Non-coding_Transcript	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	407	Extracellular (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)												0.345588	134.098769	136.954889	47	89	GG		KEEP	---	---	---	---	capture		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)	Missense_Mutation	SNP	29130055	29130055	17136	15	G	A	A	39	39	TRPM1	A	1	1
EXD1	161829	broad.mit.edu	36	15	39271044	39271044	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39271044G>A	uc001znk.1	-	c.578C>T	c.(577-579)ACG>ATG	p.T193M	EXD1_uc001znj.1_5'Flank	NM_152596	NP_689809	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	193					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding			ovary(1)	1														0.317881	128.354573	132.802406	48	103	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39271044	39271044	5490	15	G	A	A	40	40	EXD1	A	1	1
ALDH1A2	8854	broad.mit.edu	36	15	56040309	56040309	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:56040309C>T	uc002aex.1	-	c.1435G>A	c.(1435-1437)GCC>ACC	p.A479T	ALDH1A2_uc002aey.1_Missense_Mutation_p.A441T|ALDH1A2_uc002aew.1_Missense_Mutation_p.A383T	NM_003888	NP_733798	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 1	479					negative regulation of cell proliferation|neural tube development|oxidation-reduction process|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1					NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)									0.188034	42.674545	53.340622	22	95	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	Missense_Mutation	SNP	56040309	56040309	494	15	C	T	T	25	25	ALDH1A2	T	2	2
SCNN1B	6338	broad.mit.edu	36	16	23267539	23267539	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:23267539C>T	uc002dln.1	+	c.118C>T	c.(118-120)CGC>TGC	p.R40C		NM_000336	NP_000327	P51168	SCNNB_HUMAN	sodium channel, nonvoltage-gated 1, beta	40	Cytoplasmic (By similarity).				excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7					Amiloride(DB00594)|Triamterene(DB00384)									0.133333	12.197513	21.988145	10	65	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0465)	Missense_Mutation	SNP	23267539	23267539	14410	16	C	T	T	27	27	SCNN1B	T	1	1
CLDN6	9074	broad.mit.edu	36	16	3005605	3005605	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3005605G>A	uc002csu.2	-	c.419C>T	c.(418-420)GCG>GTG	p.A140V	CLDN6_uc010bsz.1_Missense_Mutation_p.A140V	NM_021195	NP_067018	P56747	CLD6_HUMAN	claudin 6	140	Extracellular (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity				0														0.428571	96.965434	97.307326	33	44	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3005605	3005605	3626	16	G	A	A	38	38	CLDN6	A	1	1
ITGAD	3681	broad.mit.edu	36	16	31330018	31330018	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31330018G>A	uc010cap.1	+	c.1477G>A	c.(1477-1479)GTG>ATG	p.V493M	ITGAD_uc002ebv.1_Missense_Mutation_p.V493M	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	493	Extracellular (Potential).|FG-GAP 5.				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1														0.207547	93.382658	110.194766	44	168	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31330018	31330018	8188	16	G	A	A	40	40	ITGAD	A	1	1
TP53	7157	broad.mit.edu	36	17	7518928	7518928	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518928C>T	uc002gim.2	-	c.646G>A	c.(646-648)GTG>ATG	p.V216M	TP53_uc002gig.1_Missense_Mutation_p.V216M|TP53_uc002gih.1_Missense_Mutation_p.V216M|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.V84M|TP53_uc010cng.1_Missense_Mutation_p.V84M|TP53_uc002gii.1_Missense_Mutation_p.V84M|TP53_uc010cnh.1_Missense_Mutation_p.V216M|TP53_uc010cni.1_Missense_Mutation_p.V216M|TP53_uc002gij.2_Missense_Mutation_p.V216M|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.V123M|TP53_uc002gio.2_Missense_Mutation_p.V84M	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	216	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		V -> A (in sporadic cancers; somatic mutation).|V -> E (in sporadic cancers; somatic mutation).|V -> W (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|V -> M (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> G (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.V216M(46)|p.V216del(8)|p.V216L(7)|p.0?(6)|p.H214fs*5(2)|p.V216fs*6(2)|p.D208fs*1(1)|p.S215_V216insX(1)|p.S215fs*31(1)|p.S215_V218>R(1)|p.T211fs*28(1)|p.V216fs*5(1)|p.V216fs*32(1)|p.D207_V216del10(1)|p.S215fs*27(1)|p.V216fs*33(1)|p.V216_Y220delVVVPY(1)|p.S215fs*29(1)|p.D208_V216delDRNTFRHSV(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.V216M(ECC12-Tumor)|p.V216L(LCLC103H-Tumor)|p.V216M(HT-Tumor)|p.V216M(SNU216-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.610169	110.20754	110.833574	36	23	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7518928	7518928	16923	17	C	T	T	17	17	TP53	T	2	2
LMNB2	84823	broad.mit.edu	36	19	2384987	2384987	+	Missense_Mutation	SNP	T	C	C			TCGA-02-0055-01	TCGA-02-0055-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2384987T>C	uc002lwa.1	-	c.1319A>G	c.(1318-1320)GAG>GGG	p.E440G	LMNB2_uc002lvy.1_Missense_Mutation_p.E420G	NM_032737	NP_116126	Q03252	LMNB2_HUMAN	lamin B2	420	Nuclear localization signal (Potential).|Tail.			LEVEEPLGSGPSVLGTGTGGSGGFHLAQQASASGSVS -> WRWRSPWQRPKRPGHGHGWQRWLPPGPAGLGLGQRH (in Ref. 5; AAA80979).		nuclear inner membrane	structural molecule activity			large_intestine(1)|ovary(1)	2		Hepatocellular(1079;0.137)								1275				0.243902	9.428448	11.989294	10	31	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	2384987	2384987	9179	19	T	C	C	54	54	LMNB2	C	4	4
NUDT19	390916	broad.mit.edu	36	19	37874940	37874940	+	Silent	SNP	C	G	G			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:37874940C>G	uc010edf.1	+	c.234C>G	c.(232-234)GGC>GGG	p.G78G		NM_001105570	NP_001099040	A8MXV4	NUD19_HUMAN	nudix (nucleoside diphosphate linked moiety	78	Nudix hydrolase.					mitochondrion|peroxisome	hydrolase activity|metal ion binding				0	Esophageal squamous(110;0.137)													0.5	8.360423	8.360423	4	4	CC		KEEP	---	---	---	---	capture			Silent	SNP	37874940	37874940	11141	19	C	G	G	26	26	NUDT19	G	3	3
PAPL	390928	broad.mit.edu	36	19	44289481	44289481	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:44289481G>A	uc002oki.1	+	c.1168G>A	c.(1168-1170)GTG>ATG	p.V390M	PAPL_uc010egl.1_Intron	NM_001004318	NP_001004318	Q6ZNF0	PAPL_HUMAN	FLJ16165 protein	390						extracellular region	acid phosphatase activity|metal ion binding				0														0.144578	16.844904	26.938448	12	71	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44289481	44289481	11844	19	G	A	A	40	40	PAPL	A	1	1
NKPD1	284353	broad.mit.edu	36	19	50347987	50347987	+	Nonsense_Mutation	SNP	G	T	T			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50347987G>T	uc002pau.1	-	c.882C>A	c.(880-882)TAC>TAA	p.Y294*		NM_198478	NP_940880			NTPase, KAP family P-loop domain containing 1												0		Ovarian(192;0.0728)|all_neural(266;0.112)												0.25	8.938108	9.817353	4	12	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)	Nonsense_Mutation	SNP	50347987	50347987	10847	19	G	T	T	44	44	NKPD1	T	5	3
COL5A3	50509	broad.mit.edu	36	19	9938022	9938022	+	Missense_Mutation	SNP	T	G	G			TCGA-02-0055-01	TCGA-02-0055-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:9938022T>G	uc002mmq.1	-	c.4750A>C	c.(4750-4752)ACC>CCC	p.T1584P		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	1584	Fibrillar collagen NC1.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)	9														0.272727	6.92096	7.43271	3	8	TT		KEEP	---	---	---	---	capture	Epithelial(33;7.11e-05)		Missense_Mutation	SNP	9938022	9938022	3836	19	T	G	G	58	58	COL5A3	G	4	4
COL11A1	1301	broad.mit.edu	36	1	103225800	103225800	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:103225800G>A	uc001dum.1	-	c.2515C>T	c.(2515-2517)CCT>TCT	p.P839S	COL11A1_uc001duk.1_Silent_p.V17V|COL11A1_uc001dul.1_Missense_Mutation_p.P827S|COL11A1_uc001dun.1_Missense_Mutation_p.P788S|COL11A1_uc009weh.1_Missense_Mutation_p.P711S	NM_080629	NP_542196	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform B	827	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging	p.P839S(1)		ovary(6)|breast(3)|central_nervous_system(1)|pancreas(1)	11		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)												0.426471	170.52676	171.167772	58	78	GG		KEEP	---	---	---	---	capture		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)	Missense_Mutation	SNP	103225800	103225800	3805	1	G	A	A	41	41	COL11A1	A	2	2
PYHIN1	149628	broad.mit.edu	36	1	157178747	157178747	+	Silent	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:157178747G>A	uc001ftb.1	+	c.936G>A	c.(934-936)CCG>CCA	p.P312P	PYHIN1_uc001ftc.1_Silent_p.P303P|PYHIN1_uc001ftd.1_Silent_p.P312P|PYHIN1_uc001fte.1_Silent_p.P303P	NM_152501	NP_689714	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1 alpha 1	312	HIN-200.				cell cycle	nuclear speck				ovary(3)|pancreas(1)	4	all_hematologic(112;0.0378)													0.401961	121.557566	122.413853	41	61	GG		KEEP	---	---	---	---	capture			Silent	SNP	157178747	157178747	13323	1	G	A	A	37	37	PYHIN1	A	1	1
DUSP27	92235	broad.mit.edu	36	1	165330814	165330814	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:165330814C>T	uc001geb.1	+	c.104C>T	c.(103-105)CCT>CTT	p.P35L		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	35					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3														0.296296	9.72595	10.774725	8	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	165330814	165330814	5009	1	C	T	T	24	24	DUSP27	T	2	2
CENPF	1063	broad.mit.edu	36	1	212853776	212853776	+	Missense_Mutation	SNP	A	G	G			TCGA-02-0055-01	TCGA-02-0055-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:212853776A>G	uc001hkm.1	+	c.56A>G	c.(55-57)AAA>AGA	p.K19R		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	19	Interaction with SNAP25 and required for localization to the cytoplasm (By similarity).|Potential.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding	p.K19R(1)		ovary(6)|central_nervous_system(4)|large_intestine(2)	12						Colon(80;575 1284 11000 14801 43496)								0.353333	170.941649	173.781803	53	97	AA		KEEP	---	---	---	---	capture		all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)	Missense_Mutation	SNP	212853776	212853776	3364	1	A	G	G	1	1	CENPF	G	4	4
OBSCN	84033	broad.mit.edu	36	1	226571083	226571083	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226571083G>A	uc009xez.1	+	c.13336G>A	c.(13336-13338)GGC>AGC	p.G4446S	OBSCN_uc001hsn.1_Missense_Mutation_p.G4446S	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	4446	Ig-like 46.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.352941	33.924098	34.557213	12	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	226571083	226571083	11217	1	G	A	A	39	39	OBSCN	A	1	1
OR2L13	284521	broad.mit.edu	36	1	246329657	246329657	+	Silent	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246329657C>T	uc001ids.1	+	c.357C>T	c.(355-357)TAC>TAT	p.Y119Y	OR2L13_uc009xha.1_Silent_p.Y119Y	NM_175911	NP_787107	Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L,	119	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)									85				0.29484	301.901442	317.197635	120	287	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0132)		Silent	SNP	246329657	246329657	11412	1	C	T	T	19	19	OR2L13	T	1	1
GJB3	2707	broad.mit.edu	36	1	35023429	35023429	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:35023429G>A	uc001bxx.1	+	c.479G>A	c.(478-480)CGC>CAC	p.R160H	GJB3_uc001bxy.1_Missense_Mutation_p.R160H|GJB3_uc001bxz.2_Missense_Mutation_p.R160H	NM_024009	NP_076872	O75712	CXB3_HUMAN	connexin 31	160	Extracellular (Potential).				cell communication	connexon complex|integral to membrane	gap junction channel activity				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)												0.346369	157.312892	161.034544	62	117	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35023429	35023429	6677	1	G	A	A	38	38	GJB3	A	1	1
C8B	732	broad.mit.edu	36	1	57167765	57167765	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:57167765C>T	uc001cyp.1	-	c.1676G>A	c.(1675-1677)GGA>GAA	p.G559E		NM_000066	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	559	TSP type-1 2.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	membrane attack complex				central_nervous_system(2)|large_intestine(1)|ovary(1)	4														0.296774	120.149601	125.90241	46	109	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57167765	57167765	2526	1	C	T	T	30	30	C8B	T	2	2
HOOK1	51361	broad.mit.edu	36	1	60067070	60067070	+	Missense_Mutation	SNP	A	T	T			TCGA-02-0055-01	TCGA-02-0055-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:60067070A>T	uc009wad.1	+	c.180A>T	c.(178-180)TTA>TTT	p.L60F	HOOK1_uc001czo.1_Missense_Mutation_p.L60F|HOOK1_uc001czp.1_Non-coding_Transcript	NM_015888	NP_056972	Q9UJC3	HOOK1_HUMAN	hook homolog 1	60	Sufficient for interaction with microtubules.				early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|multicellular organismal development|protein transport	FHF complex|microtubule	identical protein binding			ovary(1)|breast(1)	2	all_cancers(7;0.000129)													0.314607	75.871604	78.591279	28	61	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60067070	60067070	7574	1	A	T	T	13	13	HOOK1	T	4	4
DEFB118	117285	broad.mit.edu	36	20	29424416	29424416	+	Nonsense_Mutation	SNP	C	T	T	rs34328728	unknown	TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:29424416C>T	uc002wvr.1	+	c.154C>T	c.(154-156)CGA>TGA	p.R52*		NM_054112	NP_473453	Q96PH6	DB118_HUMAN	beta-defensin 118	52					cell-matrix adhesion|defense response to bacterium|innate immune response|spermatogenesis	extracellular region				ovary(3)|pancreas(1)	4	all_hematologic(12;0.158)													0.319797	168.450069	174.13721	63	134	CC		KEEP	---	---	---	---	capture	Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)		Nonsense_Mutation	SNP	29424416	29424416	4583	20	C	T	T	31	31	DEFB118	T	5	1
ASXL1	171023	broad.mit.edu	36	20	30486006	30486006	+	Silent	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:30486006C>T	uc002wxs.1	+	c.1830C>T	c.(1828-1830)GGC>GGT	p.G610G	ASXL1_uc010gea.1_Silent_p.G610G|ASXL1_uc010geb.1_Silent_p.G501G	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1	610					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding	p.G610G(1)		haematopoietic_and_lymphoid_tissue(131)|large_intestine(6)|central_nervous_system(2)|ovary(1)	140														0.295918	72.950212	76.593582	29	69	CC		KEEP	---	---	---	---	capture			Silent	SNP	30486006	30486006	1085	20	C	T	T	27	27	ASXL1	T	1	1
DLGAP4	22839	broad.mit.edu	36	20	34508554	34508554	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:34508554G>A	uc002xff.1	+	c.1448G>A	c.(1447-1449)TGC>TAC	p.C483Y		NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a	483					cell-cell signaling	membrane	protein binding			ovary(1)|skin(1)	2	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)												0.342466	61.448217	63.050902	25	48	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34508554	34508554	4742	20	G	A	A	46	46	DLGAP4	A	2	2
KRTAP19-3	337970	broad.mit.edu	36	21	30786135	30786135	+	Silent	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:30786135G>A	uc002yog.1	-	c.12C>T	c.(10-12)TAC>TAT	p.Y4Y		NM_181609	NP_853640	Q7Z4W3	KR193_HUMAN	keratin associated protein 19-3	4						intermediate filament					0														0.327128	320.793061	330.76108	123	253	GG		KEEP	---	---	---	---	capture			Silent	SNP	30786135	30786135	8845	21	G	A	A	40	40	KRTAP19-3	A	1	1
TPST2	8459	broad.mit.edu	36	22	25267269	25267269	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:25267269G>A	uc003acv.1	-	c.328C>T	c.(328-330)CGC>TGC	p.R110C	TPST2_uc003acx.1_Missense_Mutation_p.R110C|TPST2_uc003acw.1_Missense_Mutation_p.R110C	NM_003595	NP_003586	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	110	Lumenal (Potential).				peptidyl-tyrosine sulfation	endoplasmic reticulum|Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity			central_nervous_system(1)	1														0.347368	85.043281	86.998046	33	62	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25267269	25267269	16972	22	G	A	A	38	38	TPST2	A	1	1
PPIG	9360	broad.mit.edu	36	2	170202275	170202275	+	Missense_Mutation	SNP	G	C	C			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:170202275G>C	uc002uez.1	+	c.2261G>C	c.(2260-2262)GGA>GCA	p.G754A	PPIG_uc010fpx.1_Missense_Mutation_p.G739A|PPIG_uc010fpy.1_Missense_Mutation_p.G747A|PPIG_uc002ufb.1_Missense_Mutation_p.G754A|PPIG_uc002ufd.1_Missense_Mutation_p.G751A	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G	754					protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)									0.162162	27.451008	35.482142	12	62	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	170202275	170202275	12759	2	G	C	C	41	41	PPIG	C	3	3
TTN	7273	broad.mit.edu	36	2	179120509	179120509	+	Missense_Mutation	SNP	T	C	C			TCGA-02-0055-01	TCGA-02-0055-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179120509T>C	uc002umr.1	-	c.86386A>G	c.(86386-86388)AAG>GAG	p.K28796E	TTN_uc002ums.1_Missense_Mutation_p.K22491E|TTN_uc010frc.1_Missense_Mutation_p.K22424E|TTN_uc010frd.1_Missense_Mutation_p.K22299E	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	29723										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.471429	109.874525	109.923773	33	37	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179120509	179120509	17290	2	T	C	C	63	63	TTN	C	4	4
COL6A3	1293	broad.mit.edu	36	2	237940402	237940402	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237940402G>A	uc002vwl.2	-	c.5167C>T	c.(5167-5169)CTT>TTT	p.L1723F	COL6A3_uc002vwk.2_Missense_Mutation_p.L1556F|COL6A3_uc002vwm.2_Missense_Mutation_p.L1522F|COL6A3_uc002vwn.2_Missense_Mutation_p.L1523F|COL6A3_uc002vwo.2_Missense_Mutation_p.L1517F	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1723	VWFA 9.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)												0.311111	80.869387	83.727703	28	62	GG		KEEP	---	---	---	---	capture		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)	Missense_Mutation	SNP	237940402	237940402	3839	2	G	A	A	35	35	COL6A3	A	2	2
TMEM17	200728	broad.mit.edu	36	2	62586733	62586733	+	Silent	SNP	T	C	C			TCGA-02-0055-01	TCGA-02-0055-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:62586733T>C	uc002sbt.1	-	c.36A>G	c.(34-36)GGA>GGG	p.G12G	TMEM17_uc002sbu.1_Silent_p.G12G|TMEM17_uc002sbv.1_Intron	NM_198276	NP_938017	Q86X19	TMM17_HUMAN	transmembrane protein 17	12						integral to membrane					0	Lung NSC(7;0.0274)|all_lung(7;0.0568)													0.190476	6.790026	8.671384	4	17	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)		Silent	SNP	62586733	62586733	16619	2	T	C	C	62	62	TMEM17	C	4	4
FGD5	152273	broad.mit.edu	36	3	14880726	14880726	+	Silent	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14880726G>A	uc003bzc.1	+	c.1890G>A	c.(1888-1890)TCG>TCA	p.S630S		NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	871					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5														0.368421	122.829545	124.560469	42	72	GG		KEEP	---	---	---	---	capture			Silent	SNP	14880726	14880726	6073	3	G	A	A	39	39	FGD5	A	1	1
ITPR1	3708	broad.mit.edu	36	3	4791936	4791936	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:4791936G>A	uc003bqa.2	+	c.5846G>A	c.(5845-5847)CGT>CAT	p.R1949H	ITPR1_uc010hca.1_Missense_Mutation_p.R1934H|ITPR1_uc003bqc.2_Missense_Mutation_p.R919H	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1	1997	Cytoplasmic (Potential).				activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			ovary(4)|breast(2)|large_intestine(1)|kidney(1)|liver(1)|skin(1)|pancreas(1)	11										2114				0.285256	233.952992	246.863328	89	223	GG		KEEP	---	---	---	---	capture		Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Missense_Mutation	SNP	4791936	4791936	8224	3	G	A	A	40	40	ITPR1	A	1	1
MST1	4485	broad.mit.edu	36	3	49698920	49698920	+	Splice_Site_SNP	SNP	T	G	G			TCGA-02-0055-01	TCGA-02-0055-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49698920T>G	uc003cxg.1	-	c.806_splice	c.e8-1	p.G269_splice	MST1_uc010hkx.1_Intron	NM_020998	NP_066278			macrophage stimulating 1 (hepatocyte growth						proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)	1						GBM(110;181 1524 8005 22865 46297)								0.148936	12.903648	18.452971	7	40	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Splice_Site_SNP	SNP	49698920	49698920	10283	3	T	G	G	56	56	MST1	G	5	4
FLNB	2317	broad.mit.edu	36	3	58070810	58070810	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:58070810G>A	uc010hne.1	+	c.2357G>A	c.(2356-2358)CGG>CAG	p.R786Q	FLNB_uc003djj.1_Missense_Mutation_p.R786Q|FLNB_uc003djk.1_Missense_Mutation_p.R786Q|FLNB_uc010hnf.1_Missense_Mutation_p.R786Q|FLNB_uc003djl.1_Missense_Mutation_p.R617Q|FLNB_uc003djm.1_Missense_Mutation_p.R617Q	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B, beta (actin binding protein 278)	786	Filamin 6.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(6)|ovary(3)	9										676				0.135417	83.231236	132.718037	52	332	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)	Missense_Mutation	SNP	58070810	58070810	6176	3	G	A	A	39	39	FLNB	A	1	1
HGFAC	3083	broad.mit.edu	36	4	3419033	3419033	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:3419033G>A	uc010icw.1	+	c.1393G>A	c.(1393-1395)GTC>ATC	p.V465I	HGFAC_uc003ghc.1_Missense_Mutation_p.V458I	NM_001528	NP_001519	Q04756	HGFA_HUMAN	HGF activator preproprotein	458	Peptidase S1.				proteolysis	extracellular space	protein binding|serine-type endopeptidase activity			central_nervous_system(2)	2														0.3125	252.239526	261.740429	95	209	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Missense_Mutation	SNP	3419033	3419033	7370	4	G	A	A	40	40	HGFAC	A	1	1
ADRA2C	152	broad.mit.edu	36	4	3739210	3739210	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:3739210G>A	uc003ghm.1	+	c.1079G>A	c.(1078-1080)CGG>CAG	p.R360Q	ADRA2C_uc010icx.1_Intron	NM_000683	NP_000674	P18825	ADA2C_HUMAN	alpha-2C-adrenergic receptor	360	Cytoplasmic (By similarity).				activation of MAPK activity by adrenergic receptor signaling pathway|activation of protein kinase B activity|blood coagulation|cell-cell signaling|energy reserve metabolic process|epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway|negative regulation of epinephrine secretion|negative regulation of norepinephrine secretion|positive regulation of neuron differentiation|regulation of insulin secretion	endosome|integral to plasma membrane	alpha-2A adrenergic receptor binding|alpha2-adrenergic receptor activity|epinephrine binding|protein heterodimerization activity|protein homodimerization activity				0					Bethanidine(DB00217)|Brimonidine(DB00484)|Debrisoquin(DB04840)|Fenoldopam(DB00800)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Lofexidine(DB04948)|Norepinephrine(DB00368)|Yohimbine(DB01392)	Esophageal Squamous(12;454 628 4517 14479)								0.394737	42.887246	43.231891	15	23	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Missense_Mutation	SNP	3739210	3739210	340	4	G	A	A	39	39	ADRA2C	A	1	1
AFM	173	broad.mit.edu	36	4	74573270	74573270	+	Missense_Mutation	SNP	T	C	C			TCGA-02-0055-01	TCGA-02-0055-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:74573270T>C	uc003hhb.1	+	c.773T>C	c.(772-774)CTT>CCT	p.L258P		NM_001133	NP_001124	P43652	AFAM_HUMAN	afamin precursor	258	Albumin 2.				transport					ovary(2)	2	Breast(15;0.00102)													0.358382	204.10628	207.160125	62	111	TT		KEEP	---	---	---	---	capture	Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)		Missense_Mutation	SNP	74573270	74573270	362	4	T	C	C	56	56	AFM	C	4	4
SLC27A6	28965	broad.mit.edu	36	5	128329829	128329829	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:128329829G>A	uc003kuy.1	+	c.100G>A	c.(100-102)GTG>ATG	p.V34M	SLC27A6_uc003kuz.1_Missense_Mutation_p.V34M	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid	34	Helical; (Potential).				long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)												0.146552	55.008665	82.853682	34	198	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)	Missense_Mutation	SNP	128329829	128329829	15027	5	G	A	A	40	40	SLC27A6	A	1	1
PCDHGA1	56114	broad.mit.edu	36	5	140692584	140692584	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140692584C>T	uc003lji.1	+	c.2149C>T	c.(2149-2151)CGG>TGG	p.R717W	PCDHGA1_uc003ljh.1_Missense_Mutation_p.R717W	NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1	717	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3														0.43125	191.868349	192.522132	69	91	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140692584	140692584	11970	5	C	T	T	27	27	PCDHGA1	T	1	1
FAM153C	653316	broad.mit.edu	36	5	177399016	177399016	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:177399016G>A	uc003mig.1	+	c.131G>A	c.(130-132)CGT>CAT	p.R44H		NM_001079527	NP_001072995	Q494X1	F153C_HUMAN	hypothetical protein LOC653316	44											0	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)												0.354331	377.006082	384.135324	135	246	GG		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Missense_Mutation	SNP	177399016	177399016	5660	5	G	A	A	40	40	FAM153C	A	1	1
PLEKHG4B	153478	broad.mit.edu	36	5	216558	216558	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:216558C>T	uc003jak.2	+	c.2303C>T	c.(2302-2304)CCG>CTG	p.P768L		NM_052909	NP_443141	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G	768					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)	1														0.277174	127.664729	135.876182	51	133	CC		KEEP	---	---	---	---	capture	all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)	Missense_Mutation	SNP	216558	216558	12498	5	C	T	T	23	23	PLEKHG4B	T	1	1
ZC3H12D	340152	broad.mit.edu	36	6	149837304	149837304	+	Silent	SNP	C	A	A			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:149837304C>A	uc003qmm.2	-	c.69G>T	c.(67-69)GTG>GTT	p.V23V	PPIL4_uc010kic.1_Intron|ZC3H12D_uc010kid.1_Silent_p.V23V|ZC3H12D_uc003qmn.1_Silent_p.V23V	NM_207360	NP_997243	A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	23						cytoplasm|nucleus	endonuclease activity|nucleic acid binding|zinc ion binding				0		Ovarian(120;0.0907)												0.481481	39.673547	39.681597	13	14	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)	Silent	SNP	149837304	149837304	18152	6	C	A	A	17	17	ZC3H12D	A	3	3
GTPBP2	54676	broad.mit.edu	36	6	43704770	43704770	+	Missense_Mutation	SNP	G	C	C			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43704770G>C	uc003ovt.1	-	c.108C>G	c.(106-108)TGC>TGG	p.C36W	GTPBP2_uc010jyv.1_5'Flank|GTPBP2_uc003ovs.1_Missense_Mutation_p.C36W|MAD2L1BP_uc003ovu.1_5'Flank	NM_019096	NP_061969	Q9BX10	GTPB2_HUMAN	GTP binding protein 2	36							GTP binding|GTPase activity			liver(1)	1	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)					GBM(116;405 1620 28302 32150 44768)								0.388889	12.414377	12.609085	7	11	GG		KEEP	---	---	---	---	capture	all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)		Missense_Mutation	SNP	43704770	43704770	7160	6	G	C	C	38	38	GTPBP2	C	3	3
JHDM1D	80853	broad.mit.edu	36	7	139471003	139471003	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:139471003C>T	uc003vvm.1	-	c.938G>A	c.(937-939)CGT>CAT	p.R313H		NM_030647	NP_085150	Q6ZMT4	KDM7_HUMAN	jumonji C domain containing histone demethylase	313	JmjC.				midbrain development|oxidation-reduction process|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1	Melanoma(164;0.0142)													0.274725	60.633632	64.795353	25	66	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139471003	139471003	8252	7	C	T	T	19	19	JHDM1D	T	1	1
OR2A2	442361	broad.mit.edu	36	7	143438181	143438181	+	Silent	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:143438181C>T	uc003wdx.1	+	c.573C>T	c.(571-573)ACC>ACT	p.T191T		NM_001005480	NP_001005480	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A,	191	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Melanoma(164;0.0783)													0.247525	195.554133	213.149901	75	228	CC		KEEP	---	---	---	---	capture			Silent	SNP	143438181	143438181	11383	7	C	T	T	24	24	OR2A2	T	2	2
TNRC18	84629	broad.mit.edu	36	7	5396781	5396781	+	Silent	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:5396781G>A	uc003soi.2	-	c.348C>T	c.(346-348)TTC>TTT	p.F116F	TNRC18_uc010ksx.1_Silent_p.F42F|TNRC18_uc003sok.1_Silent_p.F42F	NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	116							DNA binding				0		Ovarian(82;0.142)												0.277778	8.261162	9.067646	5	13	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)	Silent	SNP	5396781	5396781	16880	7	G	A	A	33	33	TNRC18	A	2	2
TAF6	6878	broad.mit.edu	36	7	99543561	99543561	+	Missense_Mutation	SNP	G	C	C			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99543561G>C	uc003uth.1	-	c.1751C>G	c.(1750-1752)GCC>GGC	p.A584G	AP4M1_uc003utd.2_Intron|TAF6_uc003utg.1_Missense_Mutation_p.A449G|TAF6_uc003uti.1_Missense_Mutation_p.A527G|TAF6_uc003utk.1_Missense_Mutation_p.A527G|TAF6_uc003utj.1_Missense_Mutation_p.A517G|TAF6_uc003utm.1_Missense_Mutation_p.A527G|TAF6_uc003utl.1_Missense_Mutation_p.A517G	NM_139315	NP_647476	P49848	TAF6_HUMAN	TBP-associated factor 6 isoform alpha	527					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)													0.26	14.577904	17.278536	13	37	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99543561	99543561	16051	7	G	C	C	42	42	TAF6	C	3	3
NEFM	4741	broad.mit.edu	36	8	24827261	24827261	+	Missense_Mutation	SNP	T	G	G			TCGA-02-0055-01	TCGA-02-0055-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:24827261T>G	uc003xed.2	+	c.50T>G	c.(49-51)GTA>GGA	p.V17G	NEFM_uc010lud.1_Missense_Mutation_p.V17G|NEFM_uc010lue.1_5'Flank	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	17	Head.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)												0.333333	7.67374	8.152228	6	12	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)	Missense_Mutation	SNP	24827261	24827261	10715	8	T	G	G	57	57	NEFM	G	4	4
XKR4	114786	broad.mit.edu	36	8	56598409	56598409	+	Missense_Mutation	SNP	C	G	G			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:56598409C>G	uc003xsf.1	+	c.1022C>G	c.(1021-1023)GCT>GGT	p.A341G		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	341	Helical; (Potential).					integral to membrane				pancreas(2)	2														0.282051	7.787195	9.629359	11	28	CC		KEEP	---	---	---	---	capture	Epithelial(17;0.000117)|all cancers(17;0.000836)		Missense_Mutation	SNP	56598409	56598409	18014	8	C	G	G	28	28	XKR4	G	3	3
PLAG1	5324	broad.mit.edu	36	8	57241776	57241776	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:57241776C>T	uc003xsq.2	-	c.1083G>A	c.(1081-1083)ATG>ATA	p.M361I	PLAG1_uc003xsr.2_Missense_Mutation_p.M361I|PLAG1_uc010lyi.1_Missense_Mutation_p.M361I|PLAG1_uc010lyj.1_Missense_Mutation_p.M279I	NM_001114635	NP_001108107	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1 isoform b	361	Activates transcription; Inhibition of nuclear import due to lack of NLS and KPNA2 interaction.|Repression domain; contains 3 sumoylation motifs and massively decrease transcription activity.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	p.M361I(1)		central_nervous_system(1)	1		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)								45				0.316832	262.172588	271.223068	96	207	CC		KEEP	---	---	---	---	capture	Epithelial(17;0.00179)|all cancers(17;0.0125)		Missense_Mutation	SNP	57241776	57241776	12444	8	C	T	T	21	21	PLAG1	T	2	2
MATN2	4147	broad.mit.edu	36	8	99113681	99113681	+	Silent	SNP	T	C	C			TCGA-02-0055-01	TCGA-02-0055-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:99113681T>C	uc003yic.1	+	c.2541T>C	c.(2539-2541)TCT>TCC	p.S847S	MATN2_uc010mbh.1_Silent_p.S806S|MATN2_uc003yid.1_Silent_p.S847S|MATN2_uc003yie.1_Silent_p.S847S|MATN2_uc010mbi.1_Silent_p.S680S|MATN2_uc010mbj.1_Silent_p.S208S|RPL30_uc010mbk.1_Intron	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor	847						proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)													0.296296	24.390218	25.391738	8	19	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;0.244)		Silent	SNP	99113681	99113681	9718	8	T	C	C	54	54	MATN2	C	4	4
SUSD3	203328	broad.mit.edu	36	9	94877910	94877910	+	Missense_Mutation	SNP	C	A	A			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:94877910C>A	uc004atb.1	+	c.112C>A	c.(112-114)CCC>ACC	p.P38T	SUSD3_uc004atc.1_Missense_Mutation_p.P25T	NM_145006	NP_659443	Q96L08	SUSD3_HUMAN	sushi domain containing 3	38	Sushi.|Extracellular (Potential).					integral to membrane				breast(2)|skin(2)|ovary(1)|lung(1)	6														0.283951	34.888969	38.309144	23	58	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94877910	94877910	15929	9	C	A	A	18	18	SUSD3	A	3	3
CLCN4	1183	broad.mit.edu	36	X	10141962	10141962	+	Missense_Mutation	SNP	G	C	C			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:10141962G>C	uc004csy.2	+	c.1818G>C	c.(1816-1818)GAG>GAC	p.E606D		NM_001830	NP_001821	P51793	CLCN4_HUMAN	chloride channel 4	606	CBS 1.|Cytoplasmic (By similarity).					early endosome membrane|integral to membrane|late endosome membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			ovary(2)|lung(2)	4						Melanoma(74;1050 1296 1576 30544 38374)								0.321429	14.351649	15.153311	9	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10141962	10141962	3601	23	G	C	C	34	34	CLCN4	C	3	3
H2BFWT	158983	broad.mit.edu	36	X	103154558	103154558	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:103154558G>A	uc004elr.1	-	c.331C>T	c.(331-333)CAT>TAT	p.H111Y		NM_001002916	NP_001002916	Q7Z2G1	H2BWT_HUMAN	H2B histone family, member W, testis-specific	111					nucleosome assembly	nuclear membrane|nucleosome	DNA binding			ovary(1)	1														0.42735	136.594327	137.1387	50	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	103154558	103154558	7214	23	G	A	A	45	45	H2BFWT	A	2	2
GEMIN8	54960	broad.mit.edu	36	X	13937206	13937206	+	Missense_Mutation	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:13937206C>T	uc004cwb.1	-	c.476G>A	c.(475-477)CGG>CAG	p.R159Q	GEMIN8_uc004cwc.1_Missense_Mutation_p.R159Q|GEMIN8_uc004cwd.1_Missense_Mutation_p.R159Q	NM_017856	NP_060326	Q9NWZ8	GEMI8_HUMAN	gem (nuclear organelle) associated protein 8	159	Potential.				spliceosomal snRNP assembly	Cajal body|cytoplasm|SMN complex|spliceosomal complex	protein binding				0														0.398268	269.871798	271.956507	92	139	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13937206	13937206	6602	23	C	T	T	23	23	GEMIN8	T	1	1
GABRA3	2556	broad.mit.edu	36	X	151087484	151087484	+	Missense_Mutation	SNP	T	A	A			TCGA-02-0055-01	TCGA-02-0055-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:151087484T>A	uc010ntk.1	-	c.1351A>T	c.(1351-1353)AGT>TGT	p.S451C		NM_000808	NP_000799	P34903	GBRA3_HUMAN	gamma-aminobutyric acid A receptor, alpha 3	451	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)				Alprazolam(DB00404)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	NSCLC(142;2578 2613 10251 16743)								0.26361	239.04366	256.677793	92	257	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151087484	151087484	6413	23	T	A	A	55	55	GABRA3	A	4	4
KLHL34	257240	broad.mit.edu	36	X	21584587	21584587	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:21584587G>A	uc004czz.1	-	c.1241C>T	c.(1240-1242)GCG>GTG	p.A414V		NM_153270	NP_695002	Q8N239	KLH34_HUMAN	kelch-like 34	414	Kelch 2.									ovary(1)	1														0.325	32.666166	33.750739	13	27	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21584587	21584587	8701	23	G	A	A	38	38	KLHL34	A	1	1
USP11	8237	broad.mit.edu	36	X	46987850	46987850	+	Silent	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46987850C>T	uc004dhp.1	+	c.1824C>T	c.(1822-1824)TAC>TAT	p.Y608Y	USP11_uc004dhq.1_Silent_p.Y335Y	NM_004651	NP_004642	P51784	UBP11_HUMAN	ubiquitin specific protease 11	608					protein deubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)|central_nervous_system(1)	2														0.259259	118.686861	128.611155	49	140	CC		KEEP	---	---	---	---	capture			Silent	SNP	46987850	46987850	17604	23	C	T	T	19	19	USP11	T	1	1
ZNF81	347344	broad.mit.edu	36	X	47660598	47660598	+	Missense_Mutation	SNP	G	A	A			TCGA-02-0055-01	TCGA-02-0055-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:47660598G>A	uc010nhy.1	+	c.1609G>A	c.(1609-1611)GAC>AAC	p.D537N		NM_007137	NP_009068	P51508	ZNF81_HUMAN	zinc finger protein 81	537	C2H2-type 8.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(315;0.0973)												0.284916	132.352812	139.784874	51	128	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47660598	47660598	18772	23	G	A	A	37	37	ZNF81	A	1	1
ERCC6L	54821	broad.mit.edu	36	X	71341664	71341664	+	Silent	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:71341664C>T	uc004eaq.1	-	c.3678G>A	c.(3676-3678)GCG>GCA	p.A1226A	PIN4_uc004eao.1_Intron|ERCC6L_uc004eap.1_Silent_p.A1103A	NM_017669	NP_060139	Q2NKX8	ERC6L_HUMAN	excision repair protein ERCC6-like	1226	TPR 2.				cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol	ATP binding|DNA binding|helicase activity|protein binding			ovary(3)	3	Renal(35;0.156)													0.263514	98.466098	105.945835	39	109	CC		KEEP	---	---	---	---	capture			Silent	SNP	71341664	71341664	5411	23	C	T	T	27	27	ERCC6L	T	1	1
TBX22	50945	broad.mit.edu	36	X	79172666	79172666	+	Silent	SNP	C	T	T			TCGA-02-0055-01	TCGA-02-0055-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:79172666C>T	uc010nmg.1	+	c.963C>T	c.(961-963)GGC>GGT	p.G321G	TBX22_uc004edi.1_Silent_p.G201G|TBX22_uc004edj.1_Silent_p.G321G	NM_001109878	NP_001103349	Q9Y458	TBX22_HUMAN	T-box 22 isoform 1	321					multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			large_intestine(3)|central_nervous_system(2)|lung(1)|ovary(1)	7										298				0.128319	36.298051	66.760043	29	197	CC		KEEP	---	---	---	---	capture			Silent	SNP	79172666	79172666	16184	23	C	T	T	28	28	TBX22	T	2	2
KRTAP5-5	439915	broad.mit.edu	36	11	1607767	1607775	+	In_Frame_Del	DEL	GGCTGTGGA	-	-			TCGA-02-0055-01	TCGA-02-0055-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1607767_1607775delGGCTGTGGA	uc001lty.1	+	c.121_129delGGCTGTGGA	c.(121-129)GGCTGTGGAdel	p.GCG47del		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	47_49						keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)										0.35			12	22				---	---	---	---	capture_indel			In_Frame_Del	DEL	1607767	1607775	8886	11	GGCTGTGGA	-	-	39	39	KRTAP5-5	-	5	5
