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
DMBT1	1755	broad.mit.edu	36	10	124341961	124341961	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:124341961G>A	uc001lgk.1	+	c.2360G>A	c.(2359-2361)CGG>CAG	p.R787Q	DMBT1_uc001lgl.1_Missense_Mutation_p.R777Q|DMBT1_uc001lgm.1_Intron|DMBT1_uc009xzz.1_Missense_Mutation_p.R787Q|DMBT1_uc009yaa.1_Missense_Mutation_p.R400Q	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	787	SRCR 6.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				Ovarian(182;93 2026 18125 22222 38972)								0.688976	589.117712	597.212991	175	79	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124341961	124341961	4757	10	G	A	A	39	39	DMBT1	A	1	1
EPC1	80314	broad.mit.edu	36	10	32620108	32620108	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5136-01	TCGA-26-5136-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:32620108T>C	uc001iwg.1	-	c.964A>G	c.(964-966)AAA>GAA	p.K322E	EPC1_uc001iwh.1_Missense_Mutation_p.K322E|EPC1_uc001iwi.2_Missense_Mutation_p.K272E|EPC1_uc009xlt.1_Missense_Mutation_p.K272E	NM_025209	NP_079485	Q9H2F5	EPC1_HUMAN	enhancer of polycomb 1	322					histone H2A acetylation|histone H4 acetylation|negative regulation of gene expression, epigenetic|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear membrane|Piccolo NuA4 histone acetyltransferase complex	transcription activator activity|transcription repressor activity			ovary(3)|central_nervous_system(1)	4		Prostate(175;0.0199)												0.685714	176.527347	178.676723	48	22	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32620108	32620108	5353	10	T	C	C	63	63	EPC1	C	4	4
TBC1D12	23232	broad.mit.edu	36	10	96153256	96153256	+	Missense_Mutation	SNP	C	A	A			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:96153256C>A	uc001kjr.2	+	c.896C>A	c.(895-897)CCC>CAC	p.P299H		NM_015188	NP_056003	O60347	TBC12_HUMAN	TBC1 domain family, member 12	299						intracellular	Rab GTPase activator activity				0		Colorectal(252;0.0429)												0.9	28.766299	29.683446	9	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	96153256	96153256	16123	10	C	A	A	22	22	TBC1D12	A	3	3
ANGPTL5	253935	broad.mit.edu	36	11	101267460	101267460	+	Silent	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:101267460C>T	uc001pgl.1	-	c.927G>A	c.(925-927)GGG>GGA	p.G309G		NM_178127	NP_835228	Q86XS5	ANGL5_HUMAN	angiopoietin-like 5	309	Fibrinogen C-terminal.				signal transduction	extracellular space	receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043)												0.406593	218.50264	219.893226	74	108	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;0.0328)	Silent	SNP	101267460	101267460	620	11	C	T	T	18	18	ANGPTL5	T	2	2
RIC3	79608	broad.mit.edu	36	11	8147009	8147009	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5136-01	TCGA-26-5136-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:8147009T>C	uc001mgd.1	-	c.104A>G	c.(103-105)GAG>GGG	p.E35G	RIC3_uc001mgc.1_Missense_Mutation_p.E35G|RIC3_uc009yfm.1_Missense_Mutation_p.E35G|RIC3_uc001mge.1_Missense_Mutation_p.E35G|RIC3_uc009yfn.1_5'UTR|RIC3_uc001mgf.2_Missense_Mutation_p.E35G	NM_024557	NP_078833	Q7Z5B4	RIC3_HUMAN	resistance to inhibitors of cholinesterase 3	35	Lumenal (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				large_intestine(1)|ovary(1)|pancreas(1)	3														0.25	8.082566	9.508149	6	18	TT		KEEP	---	---	---	---	capture		Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)	Missense_Mutation	SNP	8147009	8147009	13829	11	T	C	C	54	54	RIC3	C	4	4
TRIM49	57093	broad.mit.edu	36	11	89171115	89171115	+	Missense_Mutation	SNP	A	T	T			TCGA-26-5136-01	TCGA-26-5136-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:89171115A>T	uc001pdb.1	-	c.1190T>A	c.(1189-1191)CTT>CAT	p.L397H		NM_020358	NP_065091	P0CI25	TRI49_HUMAN	ring finger protein 18	397	B30.2/SPRY.					intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)												0.315789	126.140066	130.730772	48	104	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89171115	89171115	17069	11	A	T	T	3	3	TRIM49	T	4	4
TSPAN9	10867	broad.mit.edu	36	12	3259886	3259886	+	Silent	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:3259886C>T	uc001qlp.1	+	c.408C>T	c.(406-408)AAC>AAT	p.N136N		NM_006675	NP_006666	O75954	TSN9_HUMAN	tetraspanin 9	136	Extracellular (Potential).					integral to plasma membrane|membrane fraction				ovary(1)	1														0.181818	19.320798	24.549824	10	45	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)		Silent	SNP	3259886	3259886	17205	12	C	T	T	19	19	TSPAN9	T	1	1
ANKRD33	341405	broad.mit.edu	36	12	50571129	50571129	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:50571129G>A	uc001rzd.1	+	c.1132G>A	c.(1132-1134)GGC>AGC	p.G378S	ANKRD33_uc001rze.1_Missense_Mutation_p.G274S|ANKRD33_uc001rzf.2_Intron|ANKRD33_uc001rzg.2_Intron|ANKRD33_uc001rzh.2_3'UTR|ANKRD33_uc001rzi.2_Intron	NM_182608	NP_872414	Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33 isoform 2	13											0														0.320513	71.249647	73.480824	25	53	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.0969)	Missense_Mutation	SNP	50571129	50571129	667	12	G	A	A	43	43	ANKRD33	A	2	2
UGGT2	55757	broad.mit.edu	36	13	95328055	95328055	+	Silent	SNP	T	C	C			TCGA-26-5136-01	TCGA-26-5136-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:95328055T>C	uc001vmt.1	-	c.3285A>G	c.(3283-3285)CAA>CAG	p.Q1095Q	UGGT2_uc001vmu.1_Silent_p.Q182Q	NM_020121	NP_064506	Q9NYU1	UGGG2_HUMAN	UDP-glucose ceramide glucosyltransferase-like 2	1095					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3														0.739645	468.26112	477.053361	125	44	TT		KEEP	---	---	---	---	capture			Silent	SNP	95328055	95328055	17500	13	T	C	C	52	52	UGGT2	C	4	4
PEX11A	8800	broad.mit.edu	36	15	88027624	88027624	+	Silent	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:88027624C>T	uc002boi.1	-	c.732G>A	c.(730-732)CTG>CTA	p.L244L		NM_003847	NP_003838	O75192	PX11A_HUMAN	peroxisomal biogenesis factor 11 alpha	244	Cytoplasmic (Potential).			KLK->SLS: No effect on peroxisomal location.	cellular lipid metabolic process|peroxisome fission|signal transduction	integral to peroxisomal membrane					0	Lung NSC(78;0.0237)|all_lung(78;0.0478)													0.38488	635.148626	641.914736	224	358	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)		Silent	SNP	88027624	88027624	12159	15	C	T	T	29	29	PEX11A	T	2	2
CDH5	1003	broad.mit.edu	36	16	64987473	64987473	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:64987473C>T	uc002eom.2	+	c.1228C>T	c.(1228-1230)CGC>TGC	p.R410C		NM_001795	NP_001786	P33151	CADH5_HUMAN	cadherin 5, type 2 preproprotein	410	Cadherin 4.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|regulation of establishment of cell polarity	integral to membrane|membrane fraction	beta-catenin binding|calcium ion binding|ion channel binding|receptor binding			ovary(2)|central_nervous_system(1)	3		Ovarian(137;0.0955)												0.354037	170.233658	173.254898	57	104	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Missense_Mutation	SNP	64987473	64987473	3242	16	C	T	T	23	23	CDH5	T	1	1
CDH15	1013	broad.mit.edu	36	16	87779238	87779238	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:87779238G>A	uc002fmt.1	+	c.659G>A	c.(658-660)CGC>CAC	p.R220H	CDH15_uc010cij.1_Missense_Mutation_p.R220H	NM_004933	NP_004924	P55291	CAD15_HUMAN	cadherin 15 preproprotein	220	Cadherin 2.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	calcium ion binding				0														0.421053	21.694957	21.798647	8	11	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(80;0.0261)	Missense_Mutation	SNP	87779238	87779238	3229	16	G	A	A	38	38	CDH15	A	1	1
CHMP1A	5119	broad.mit.edu	36	16	88239867	88239867	+	Missense_Mutation	SNP	C	G	G			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:88239867C>G	uc002fnv.1	-	c.679G>C	c.(679-681)GCA>CCA	p.A227P	CHMP1A_uc002fnt.1_Missense_Mutation_p.A122P|CHMP1A_uc002fnu.1_3'UTR	NM_001083314	NP_001076783	Q9HD42	CHM1A_HUMAN	chromatin modifying protein 1A isoform 1	Error:Variant_position_missing_in_Q9HD42_after_alignment					cell division|gene silencing|mitotic chromosome condensation|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription by glucose|protein transport|transcription, DNA-dependent|vesicle-mediated transport	condensed nuclear chromosome|early endosome|endomembrane system|endosome membrane|microtubule organizing center|nuclear matrix	metallopeptidase activity|protein domain specific binding|zinc ion binding				0		all_lung(18;3.07e-05)|all_hematologic(23;0.0256)												0.307692	8.492594	8.922751	4	9	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(80;0.048)	Missense_Mutation	SNP	88239867	88239867	3486	16	C	G	G	26	26	CHMP1A	G	3	3
PHF12	57649	broad.mit.edu	36	17	24264271	24264271	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5136-01	TCGA-26-5136-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:24264271T>C	uc002hdg.1	-	c.1444A>G	c.(1444-1446)ACA>GCA	p.T482A	PHF12_uc002hdh.1_Missense_Mutation_p.T265A|PHF12_uc002hdi.1_Missense_Mutation_p.T478A|PHF12_uc002hdj.1_Missense_Mutation_p.T482A|PHF12_uc010crw.1_Missense_Mutation_p.T185A	NM_001033561	NP_001028733	Q96QT6	PHF12_HUMAN	PHD finger protein 12 isoform 1	482	Interaction with SIN3A.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	protein binding|transcription repressor activity|zinc ion binding			ovary(1)	1	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)													0.358885	345.73823	350.773167	103	184	TT		KEEP	---	---	---	---	capture	Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)		Missense_Mutation	SNP	24264271	24264271	12246	17	T	C	C	60	60	PHF12	C	4	4
TP53	7157	broad.mit.edu	36	17	7519259	7519259	+	Missense_Mutation	SNP	C	A	A			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519259C>A	uc002gim.2	-	c.396G>T	c.(394-396)AAG>AAT	p.K132N	TP53_uc002gig.1_Missense_Mutation_p.K132N|TP53_uc002gih.1_Missense_Mutation_p.K132N|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'UTR|TP53_uc010cng.1_5'UTR|TP53_uc002gii.1_5'UTR|TP53_uc010cnh.1_Missense_Mutation_p.K132N|TP53_uc010cni.1_Missense_Mutation_p.K132N|TP53_uc002gij.2_Missense_Mutation_p.K132N|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.K39N|TP53_uc002gio.2_5'UTR	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	132	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		K -> T (in sporadic cancers; somatic mutation).|KM -> NL (in a sporadic cancer; somatic mutation).|K -> W (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|K -> R (in sporadic cancers; somatic mutation).|K -> M (in sporadic cancers; somatic mutation).|K -> N (in sporadic cancers; somatic mutation).|K -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|K -> Q (in sporadic cancers; somatic mutation).|K -> E (in LFS; germline mutation and 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.K132N(39)|p.0?(6)|p.Y126_K132delYSPALNK(6)|p.N131fs*27(2)|p.V73fs*9(1)|p.S127fs*36(1)|p.A129_K132delALNK(1)|p.Y126fs*11(1)|p.K132K(1)|p.K132_A138delKMFCQLA(1)|p.S127_Q136del10(1)|p.L130_M133delLNKM(1)|p.M133fs*37(1)|p.M133fs*16(1)|p.K132E(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.K132N(EJM-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.794118	168.177382	173.626553	54	14	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7519259	7519259	16923	17	C	A	A	32	32	TP53	A	3	3
EPB41L3	23136	broad.mit.edu	36	18	5405838	5405838	+	Silent	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:5405838C>T	uc002kmt.1	-	c.2046G>A	c.(2044-2046)CCG>CCA	p.P682P	EPB41L3_uc002kmu.1_Intron|EPB41L3_uc010dkq.1_Intron|EPB41L3_uc002kms.1_Intron|EPB41L3_uc010dkr.1_Intron	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	682	Spectrin--actin-binding (Potential).				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5														0.226601	106.342422	120.275117	46	157	CC		KEEP	---	---	---	---	capture			Silent	SNP	5405838	5405838	5347	18	C	T	T	31	31	EPB41L3	T	1	1
KDSR	2531	broad.mit.edu	36	18	59185315	59185315	+	Missense_Mutation	SNP	G	C	C			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59185315G>C	uc010dpw.1	-	c.17C>G	c.(16-18)GCC>GGC	p.A6G		NM_002035	NP_002026	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase precursor	6					3-keto-sphinganine metabolic process|oxidation-reduction process	endoplasmic reticulum membrane|extracellular space|integral to membrane	3-dehydrosphinganine reductase activity|binding				0									p.A6G(SNU719-Tumor)	107				0.333333	7.134698	7.3498	3	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59185315	59185315	8446	18	G	C	C	42	42	KDSR	C	3	3
NWD1	284434	broad.mit.edu	36	19	16721196	16721196	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:16721196G>A	uc002net.2	+	c.338G>A	c.(337-339)CGC>CAC	p.R113H	NWD1_uc002neu.2_Missense_Mutation_p.R248H|NWD1_uc002nev.2_Missense_Mutation_p.R42H	NM_001007525	NP_001007526	Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	248							ATP binding			ovary(2)|pancreas(2)	4														0.640351	218.982934	220.955806	73	41	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16721196	16721196	11186	19	G	A	A	38	38	NWD1	A	1	1
MAST3	23031	broad.mit.edu	36	19	18079415	18079415	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18079415C>T	uc002nhz.2	+	c.58C>T	c.(58-60)CGC>TGC	p.R20C		NM_015016	NP_055831	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase	20					protein phosphorylation		ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			large_intestine(2)|ovary(2)	4										374				0.55618	300.425122	300.912786	99	79	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18079415	18079415	9710	19	C	T	T	19	19	MAST3	T	1	1
AMPD1	270	broad.mit.edu	36	1	115021592	115021592	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:115021592G>A	uc001efe.1	-	c.1291C>T	c.(1291-1293)CGC>TGC	p.R431C	AMPD1_uc001eff.1_Missense_Mutation_p.R427C	NM_000036	NP_000027	P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1 (isoform M)	431					purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			large_intestine(1)|ovary(1)	2	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)			Adenosine monophosphate(DB00131)									0.356322	177.900219	181.06494	62	112	GG		KEEP	---	---	---	---	capture		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Missense_Mutation	SNP	115021592	115021592	588	1	G	A	A	39	39	AMPD1	A	1	1
PEAR1	375033	broad.mit.edu	36	1	155146246	155146246	+	Silent	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:155146246C>T	uc001fqj.1	+	c.1491C>T	c.(1489-1491)GCC>GCT	p.A497A	PEAR1_uc001fqk.1_Silent_p.A122A	NM_001080471	NP_001073940	Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	497	EGF-like 6.					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)													0.319328	102.406618	105.859513	38	81	CC		KEEP	---	---	---	---	capture			Silent	SNP	155146246	155146246	12133	1	C	T	T	22	22	PEAR1	T	2	2
PVRL4	81607	broad.mit.edu	36	1	159316153	159316153	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159316153C>T	uc001fxo.1	-	c.290G>A	c.(289-291)CGC>CAC	p.R97H		NM_030916	NP_112178	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4	97	Ig-like V-type 1.|Extracellular (Potential).				adherens junction organization|cell adhesion|cell junction assembly	adherens junction|extracellular region|integral to membrane				ovary(2)	2	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)					NSCLC(76;1160 1387 14476 16172 29359)								0.464789	87.966107	88.042441	33	38	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00165)		Missense_Mutation	SNP	159316153	159316153	13300	1	C	T	T	27	27	PVRL4	T	1	1
SIPA1L2	57568	broad.mit.edu	36	1	230628043	230628043	+	Silent	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:230628043G>A	uc001hvg.1	-	c.4545C>T	c.(4543-4545)AAC>AAT	p.N1515N	SIPA1L2_uc001hvf.1_Silent_p.N589N	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	1515					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)												0.308824	50.943068	53.162189	21	47	GG		KEEP	---	---	---	---	capture			Silent	SNP	230628043	230628043	14825	1	G	A	A	40	40	SIPA1L2	A	1	1
SIPA1L2	57568	broad.mit.edu	36	1	230693302	230693302	+	Nonsense_Mutation	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:230693302G>A	uc001hvg.1	-	c.1747C>T	c.(1747-1749)CGA>TGA	p.R583*		NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	583					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)												0.373786	206.948657	209.819303	77	129	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	230693302	230693302	14825	1	G	A	A	38	38	SIPA1L2	A	5	1
OR2T6	254879	broad.mit.edu	36	1	246617633	246617633	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5136-01	TCGA-26-5136-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246617633T>C	uc001iei.1	+	c.101T>C	c.(100-102)GTC>GCC	p.V34A		NM_001005471	NP_001005471	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T,	34	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)													0.369318	216.222902	218.86658	65	111	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		Missense_Mutation	SNP	246617633	246617633	11435	1	T	C	C	58	58	OR2T6	C	4	4
ZNF644	84146	broad.mit.edu	36	1	91176981	91176981	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:91176981C>T	uc001dnw.1	-	c.2518G>A	c.(2518-2520)GTT>ATT	p.V840I	ZNF644_uc001dnv.1_Intron|ZNF644_uc001dnx.1_Intron|ZNF644_uc001dny.1_Missense_Mutation_p.V840I	NM_201269	NP_958357	Q9H582	ZN644_HUMAN	zinc finger protein 644 isoform 1	840					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)												0.368852	245.894939	249.579451	90	154	CC		KEEP	---	---	---	---	capture		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)	Missense_Mutation	SNP	91176981	91176981	18655	1	C	T	T	19	19	ZNF644	T	1	1
PIK3CD	5293	broad.mit.edu	36	1	9702818	9702818	+	Silent	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:9702818C>T	uc001aqe.2	+	c.1296C>T	c.(1294-1296)AGC>AGT	p.S432S	PIK3CD_uc001aqb.2_Silent_p.S467S	NM_005026	NP_005017	O00329	PK3CD_HUMAN	phosphoinositide-3-kinase, catalytic, delta	467					phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(2)|central_nervous_system(1)	3	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)								859				0.425926	123.860034	124.368754	46	62	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Silent	SNP	9702818	9702818	12339	1	C	T	T	27	27	PIK3CD	T	1	1
SAMHD1	25939	broad.mit.edu	36	20	34981303	34981303	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:34981303G>A	uc002xgh.1	-	c.730C>T	c.(730-732)CTT>TTT	p.L244F		NM_015474	NP_056289	Q9Y3Z3	SAMH1_HUMAN	SAM domain- and HD domain-containing protein 1	244	HD.				defense response to virus|innate immune response|regulation of innate immune response	nucleus	hydrolase activity				0		Myeloproliferative disorder(115;0.00878)												0.345455	117.516017	119.836353	38	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34981303	34981303	14308	20	G	A	A	35	35	SAMHD1	A	2	2
MYCN	4613	broad.mit.edu	36	2	15999810	15999810	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:15999810C>T	uc002rci.1	+	c.173C>T	c.(172-174)ACG>ATG	p.T58M	MYCNOS_uc002rcg.1_5'Flank|MYCNOS_uc002rch.1_5'Flank|MYCN_uc002rcj.1_Missense_Mutation_p.T58M	NM_005378	NP_005369	P04198	MYCN_HUMAN	v-myc myelocytomatosis viral related oncogene,	58					regulation of transcription from RNA polymerase II promoter	chromatin|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)									50				0.404255	50.12984	50.501326	19	28	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(3;0.000332)		Missense_Mutation	SNP	15999810	15999810	10416	2	C	T	T	19	19	MYCN	T	1	1
SCN9A	6335	broad.mit.edu	36	2	166849429	166849429	+	Missense_Mutation	SNP	C	G	G			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:166849429C>G	uc002udq.2	-	c.1754G>C	c.(1753-1755)AGG>ACG	p.R585T	SCN9A_uc002udr.1_Missense_Mutation_p.R456T|SCN9A_uc002uds.1_Missense_Mutation_p.R456T|SCN9A_uc002udt.1_Missense_Mutation_p.R456T	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	585						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.39779	222.564107	224.217863	72	109	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166849429	166849429	14407	2	C	G	G	24	24	SCN9A	G	3	3
COL6A3	1293	broad.mit.edu	36	2	237935214	237935214	+	Splice_Site_SNP	SNP	C	G	G			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237935214C>G	uc002vwl.2	-	c.6064_splice	c.e15-1	p.D2022_splice	COL6A3_uc002vwk.2_Splice_Site_SNP_p.D1855_splice|COL6A3_uc002vwm.2_Splice_Site_SNP_p.D1821_splice|COL6A3_uc002vwn.2_Splice_Site_SNP_p.D1822_splice|COL6A3_uc002vwo.2_Splice_Site_SNP_p.D1816_splice	NM_004369	NP_004360			alpha 3 type VI collagen isoform 1 precursor						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)												0.367568	211.23805	214.095558	68	117	CC		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)	Splice_Site_SNP	SNP	237935214	237935214	3839	2	C	G	G	24	24	COL6A3	G	5	3
VWA3B	200403	broad.mit.edu	36	2	98294831	98294831	+	Missense_Mutation	SNP	G	C	C			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:98294831G>C	uc002syo.1	+	c.3639G>C	c.(3637-3639)AAG>AAC	p.K1213N	VWA3B_uc002syn.1_Non-coding_Transcript|VWA3B_uc002syp.1_Missense_Mutation_p.K605N|VWA3B_uc002syq.1_Missense_Mutation_p.K489N|VWA3B_uc002syr.1_Missense_Mutation_p.K530N|VWA3B_uc002sys.2_Non-coding_Transcript	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	1213										ovary(3)|large_intestine(2)	5														0.375	8.423437	8.532998	3	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	98294831	98294831	17810	2	G	C	C	34	34	VWA3B	C	3	3
OXSM	54995	broad.mit.edu	36	3	25807624	25807624	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5136-01	TCGA-26-5136-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:25807624A>G	uc003cdn.1	+	c.109A>G	c.(109-111)ATA>GTA	p.I37V	OXSM_uc010hfh.1_Missense_Mutation_p.I37V	NM_017897	NP_060367	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial isoform 1	37					acyl-CoA metabolic process|medium-chain fatty acid biosynthetic process|short-chain fatty acid biosynthetic process	mitochondrion	3-oxoacyl-[acyl-carrier-protein] synthase activity			ovary(1)|breast(1)	2														0.394444	491.78639	495.293713	142	218	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25807624	25807624	11748	3	A	G	G	4	4	OXSM	G	4	4
UGT2B10	7365	broad.mit.edu	36	4	69731081	69731081	+	Silent	SNP	G	T	T			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:69731081G>T	uc003hee.1	+	c.1482G>T	c.(1480-1482)GGG>GGT	p.G494G		NM_001075	NP_001066	P36537	UDB10_HUMAN	UDP glucuronosyltransferase 2 family,	494	Helical; (Potential).				lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(2)	2						Melanoma(133;755 1763 25578 26334 46021)								0.365385	341.3717	346.342068	114	198	GG		KEEP	---	---	---	---	capture			Silent	SNP	69731081	69731081	17514	4	G	T	T	44	44	UGT2B10	T	3	3
FAM13A	10144	broad.mit.edu	36	4	90160665	90160665	+	Silent	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:90160665C>T	uc003hse.1	-	c.396G>A	c.(394-396)GCG>GCA	p.A132A	FAM13A_uc003hsf.1_5'UTR|FAM13A_uc003hsh.1_5'UTR|FAM13A_uc003hsi.2_Silent_p.A132A|FAM13A_uc003hsj.2_Silent_p.A132A	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1	132	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2														0.382353	69.93711	70.760951	26	42	CC		KEEP	---	---	---	---	capture			Silent	SNP	90160665	90160665	5649	4	C	T	T	19	19	FAM13A	T	1	1
HSP90AB1	3326	broad.mit.edu	36	6	44325299	44325299	+	Splice_Site_SNP	SNP	G	T	T			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:44325299G>T	uc003oxa.1	+	c.354_splice	c.e3+1	p.Q118_splice	HSP90AB1_uc003oxb.1_Splice_Site_SNP_p.Q118_splice|HSP90AB1_uc003oxc.1_5'Flank	NM_007355	NP_031381			heat shock 90kDa protein 1, beta						axon guidance|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of nitric oxide biosynthetic process|protein folding|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to unfolded protein	cytosol|melanosome	ATP binding|nitric-oxide synthase regulator activity|TPR domain binding|unfolded protein binding				0	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)									186				0.385714	243.447804	245.84406	81	129	GG		KEEP	---	---	---	---	capture	Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Splice_Site_SNP	SNP	44325299	44325299	7701	6	G	T	T	44	44	HSP90AB1	T	5	3
PARP12	64761	broad.mit.edu	36	7	139370836	139370836	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:139370836C>T	uc003vvl.1	-	c.2099G>A	c.(2098-2100)CGA>CAA	p.R700Q	PARP12_uc003vvk.1_Missense_Mutation_p.R486Q|PARP12_uc010lnf.1_Non-coding_Transcript	NM_022750	NP_073587	Q9H0J9	PAR12_HUMAN	zinc finger CCCH-type domain containing 1	700						nucleus	NAD+ ADP-ribosyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)	3	Melanoma(164;0.0142)													0.354839	90.744514	92.473217	33	60	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139370836	139370836	11874	7	C	T	T	31	31	PARP12	T	1	1
OR2F2	135948	broad.mit.edu	36	7	143263515	143263515	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5136-01	TCGA-26-5136-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:143263515T>C	uc003wdq.1	+	c.257T>C	c.(256-258)CTT>CCT	p.L86P		NM_001004685	NP_001004685	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F,	86	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0903)													0.310665	661.15016	681.799983	201	446	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143263515	143263515	11403	7	T	C	C	56	56	OR2F2	C	4	4
SLC4A2	6522	broad.mit.edu	36	7	150390027	150390027	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150390027G>A	uc003wit.2	+	c.20G>A	c.(19-21)CGC>CAC	p.R7H	SLC4A2_uc003wiu.2_5'Flank	NM_003040	NP_003031	P04920	B3A2_HUMAN	solute carrier family 4, anion exchanger, member	7	Cytoplasmic (Potential).|Pro-rich.			R -> L (in Ref. 1; CAA44067).	bicarbonate transport	integral to membrane|membrane fraction	inorganic anion exchanger activity				0										2				0.272727	37.751913	40.808498	18	48	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	150390027	150390027	15151	7	G	A	A	38	38	SLC4A2	A	1	1
RABGEF1	27342	broad.mit.edu	36	7	65899905	65899905	+	Silent	SNP	T	C	C			TCGA-26-5136-01	TCGA-26-5136-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:65899905T>C	uc003tvh.1	+	c.705T>C	c.(703-705)GAT>GAC	p.D235D	RABGEF1_uc003tvf.1_Silent_p.D108D|RABGEF1_uc003tvg.1_Silent_p.D43D|RABGEF1_uc010lag.1_Silent_p.D235D|RABGEF1_uc003tvi.1_Silent_p.D69D	NM_014504	NP_055319	Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	452	VPS9.				endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1														0.263889	173.838886	184.761957	57	159	TT		KEEP	---	---	---	---	capture			Silent	SNP	65899905	65899905	13425	7	T	C	C	50	50	RABGEF1	C	4	4
TRIM50	135892	broad.mit.edu	36	7	72372095	72372095	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:72372095C>T	uc010lbd.1	-	c.482G>A	c.(481-483)CGG>CAG	p.R161Q	FKBP6_uc003twz.2_Intron|TRIM50_uc003txy.1_Missense_Mutation_p.R161Q|TRIM50_uc003txz.1_Missense_Mutation_p.R161Q	NM_178125	NP_835226	Q86XT4	TRI50_HUMAN	tripartite motif protein 50A	161	Potential.					cytoplasm|intracellular membrane-bounded organelle	ligase activity|zinc ion binding				0														0.240088	272.284265	300.251827	109	345	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72372095	72372095	17072	7	C	T	T	23	23	TRIM50	T	1	1
BAIAP2L1	55971	broad.mit.edu	36	7	97760800	97760800	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:97760800G>A	uc003upj.1	-	c.1505C>T	c.(1504-1506)ACG>ATG	p.T502M		NM_018842	NP_061330	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	502	Binds F-actin.			Missing: Loss ability to induce the formation of actin clusters; induce the formation of long filopodia.	filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)													0.277027	303.836367	323.703567	123	321	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)		Missense_Mutation	SNP	97760800	97760800	1323	7	G	A	A	40	40	BAIAP2L1	A	1	1
CYP11B2	1585	broad.mit.edu	36	8	143996174	143996174	+	Missense_Mutation	SNP	C	T	T	rs6438	by-cluster,by-frequency,by-hapmap,by-1000genomes	TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:143996174C>T	uc003yxk.1	-	c.85G>A	c.(85-87)GCT>ACT	p.A29T		NM_000498	NP_000489	P19099	C11B2_HUMAN	cytochrome P450, subfamily XIB polypeptide 2	29					aldosterone biosynthetic process|oxidation-reduction process|potassium ion homeostasis|regulation of blood volume by renal aldosterone|renal water homeostasis|sodium ion homeostasis|xenobiotic metabolic process	mitochondrial inner membrane	corticosterone 18-monooxygenase activity|electron carrier activity|heme binding|steroid 11-beta-monooxygenase activity				0	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Candesartan(DB00796)|Metyrapone(DB01011)									0.34507	122.231373	125.241281	49	93	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143996174	143996174	4311	8	C	T	T	27	27	CYP11B2	T	1	1
C9orf163	158055	broad.mit.edu	36	9	138498930	138498930	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138498930G>A	uc004chy.1	+	c.209G>A	c.(208-210)GGG>GAG	p.G70E	SEC16A_uc004chx.1_5'Flank|SEC16A_uc010nbo.1_5'Flank	NM_152571	NP_689784	Q8N9P6	CI163_HUMAN	hypothetical protein LOC158055	70							protein binding				0		Myeloproliferative disorder(178;0.0511)												0.361702	43.920139	44.727756	17	30	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;4.36e-06)|Epithelial(140;5.65e-06)	Missense_Mutation	SNP	138498930	138498930	2581	9	G	A	A	43	43	C9orf163	A	2	2
CXorf57	55086	broad.mit.edu	36	X	105742223	105742223	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:105742223C>T	uc004emi.2	+	c.257C>T	c.(256-258)ACG>ATG	p.T86M	CXorf57_uc004emj.2_Missense_Mutation_p.T86M|CXorf57_uc004emh.2_Missense_Mutation_p.T86M	NM_018015	NP_060485	Q6NSI4	CX057_HUMAN	hypothetical protein LOC55086	86										ovary(1)|lung(1)|breast(1)	3														0.298658	218.114865	228.942449	89	209	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105742223	105742223	4277	23	C	T	T	19	19	CXorf57	T	1	1
TMEM164	84187	broad.mit.edu	36	X	109133920	109133920	+	Nonsense_Mutation	SNP	G	T	T			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:109133920G>T	uc004eom.1	+	c.262G>T	c.(262-264)GAG>TAG	p.E88*	TMEM164_uc004eol.1_Intron|TMEM164_uc010npq.1_Nonsense_Mutation_p.E88*	NM_032227	NP_115603	Q5U3C3	TM164_HUMAN	transmembrane protein 164	88						integral to membrane				large_intestine(1)|lung(1)|skin(1)	3														0.363636	162.149528	165.029117	64	112	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	109133920	109133920	16613	23	G	T	T	41	41	TMEM164	T	5	3
MSL3	10943	broad.mit.edu	36	X	11700195	11700195	+	Splice_Site_SNP	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:11700195G>A	uc004cuw.1	+	c.1282_splice	c.e11-1	p.V428_splice	MSL3_uc004cux.1_Splice_Site_SNP_p.V369_splice|MSL3_uc004cuy.1_Splice_Site_SNP_p.V262_splice	NM_078629	NP_006791			male-specific lethal 3-like 1 isoform a						chromatin assembly or disassembly|histone H4-K16 acetylation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromatin|MSL complex	chromatin binding|DNA binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1														0.403471	595.569378	599.322351	186	275	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	11700195	11700195	10272	23	G	A	A	35	35	MSL3	A	5	2
TREX2	11219	broad.mit.edu	36	X	152363794	152363794	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152363794C>T	uc010nue.1	-	c.415G>A	c.(415-417)GTG>ATG	p.V139M	TREX2_uc010nuc.1_Missense_Mutation_p.V97M|TREX2_uc004fhj.1_Missense_Mutation_p.V97M|TREX2_uc010nud.1_Missense_Mutation_p.V97M|HAUS7_uc004fhl.2_Non-coding_Transcript|HAUS7_uc004fhm.2_Non-coding_Transcript	NM_080701	NP_542432	Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	140					DNA repair	nucleus	3'-5'-exodeoxyribonuclease activity|exodeoxyribonuclease III activity|nucleic acid binding			large_intestine(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.276596	29.552319	31.665849	13	34	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152363794	152363794	17021	23	C	T	T	19	19	TREX2	T	1	1
ATP2B3	492	broad.mit.edu	36	X	152483676	152483676	+	Missense_Mutation	SNP	A	T	T			TCGA-26-5136-01	TCGA-26-5136-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152483676A>T	uc004fht.1	+	c.3263A>T	c.(3262-3264)GAA>GTA	p.E1088V	ATP2B3_uc004fhs.1_Missense_Mutation_p.E1088V|ATP2B3_uc010nuf.1_Missense_Mutation_p.E111V|ATP2B3_uc004fhu.1_Missense_Mutation_p.E11V	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	1088	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.30303	23.835861	24.979723	10	23	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152483676	152483676	1160	23	A	T	T	9	9	ATP2B3	T	4	4
PRKX	5613	broad.mit.edu	36	X	3583336	3583336	+	Missense_Mutation	SNP	G	C	C			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:3583336G>C	uc010nde.1	-	c.453C>G	c.(451-453)TTC>TTG	p.F151L		NM_005044	NP_005035	P51817	PRKX_HUMAN	protein kinase, X-linked	151	Protein kinase.				protein phosphorylation		ATP binding|cAMP-dependent protein kinase activity			lung(1)	1		all_lung(23;0.000396)|Lung NSC(23;0.00123)								166				0.356757	218.596159	221.941042	66	119	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3583336	3583336	12970	23	G	C	C	33	33	PRKX	C	3	3
XK	7504	broad.mit.edu	36	X	37430294	37430294	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5136-01	TCGA-26-5136-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:37430294C>T	uc004ddq.1	+	c.161C>T	c.(160-162)ACG>ATG	p.T54M		NM_021083	NP_066569	P51811	XK_HUMAN	membrane transport protein XK	54	Helical; (Potential).				amino acid transport	integral to membrane	protein binding|transporter activity				0		all_lung(315;0.175)												0.282609	30.255087	32.208858	13	33	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37430294	37430294	18012	23	C	T	T	19	19	XK	T	1	1
UBA1	7317	broad.mit.edu	36	X	46954304	46954304	+	Silent	SNP	G	C	C			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46954304G>C	uc004dhj.2	+	c.2037G>C	c.(2035-2037)CTG>CTC	p.L679L	UBA1_uc004dhk.2_Silent_p.L679L|UBA1_uc004dhm.1_Silent_p.L127L	NM_153280	NP_695012	P22314	UBA1_HUMAN	ubiquitin-activating enzyme E1	679					cell death|protein modification process		ATP binding|ligase activity|protein binding|small protein activating enzyme activity			ovary(1)	1														0.374486	269.959178	273.322055	91	152	GG		KEEP	---	---	---	---	capture			Silent	SNP	46954304	46954304	17384	23	G	C	C	47	47	UBA1	C	3	3
OTUD5	55593	broad.mit.edu	36	X	48699240	48699240	+	Silent	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48699240G>A	uc004dlu.1	-	c.537C>T	c.(535-537)GAC>GAT	p.D179D	OTUD5_uc004dlt.2_Silent_p.D179D|OTUD5_uc004dlv.1_Silent_p.D179D	NM_017602	NP_060072	Q96G74	OTUD5_HUMAN	OTU domain containing 5 isoform a	179					negative regulation of type I interferon production		cysteine-type peptidase activity			pancreas(1)	1														0.315789	14.841744	15.416022	6	13	GG		KEEP	---	---	---	---	capture			Silent	SNP	48699240	48699240	11728	23	G	A	A	40	40	OTUD5	A	1	1
TEX11	56159	broad.mit.edu	36	X	69788083	69788083	+	Silent	SNP	G	A	A			TCGA-26-5136-01	TCGA-26-5136-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:69788083G>A	uc004dyl.1	-	c.1470C>T	c.(1468-1470)AAC>AAT	p.N490N	TEX11_uc004dyk.1_Silent_p.N165N|TEX11_uc004dym.1_Silent_p.N475N	NM_001003811	NP_001003811	Q8IYF3	TEX11_HUMAN	testis expressed sequence 11 isoform 1	490							protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)													0.409836	138.824913	139.691213	50	72	GG		KEEP	---	---	---	---	capture			Silent	SNP	69788083	69788083	16301	23	G	A	A	40	40	TEX11	A	1	1
MLL4	9757	broad.mit.edu	36	19	40916167	40916167	+	Frame_Shift_Del	DEL	C	-	-			TCGA-26-5136-01	TCGA-26-5136-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40916167_40916167delC	uc010eei.1	+	c.6877_6877delC	c.(6877-6879)CCCfs	p.P2293fs		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	2293					chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.43			3	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	40916167	40916167	10013	19	C	-	-	30	30	MLL4	-	5	5
PRIM2	5558	broad.mit.edu	36	6	57620875	57620876	+	Splice_Site_Ins	INS	-	T	T			TCGA-26-5136-01	TCGA-26-5136-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:57620875_57620876insT	uc003pdx.1	+	c.e16_splice_site				NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)										0.55			6	5				---	---	---	---	capture_indel			Splice_Site_Ins	INS	57620875	57620876	12934	6	-	T	T	4	4	PRIM2	T	5	5
