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
SORCS1	114815	broad.mit.edu	36	10	108370200	108370200	+	Silent	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:108370200C>T	uc001kyl.1	-	c.2772G>A	c.(2770-2772)GTG>GTA	p.V924V	SORCS1_uc001kym.1_Silent_p.V924V|SORCS1_uc009xxs.1_Silent_p.V924V|SORCS1_uc001kyn.1_Silent_p.V924V|SORCS1_uc001kyo.2_Silent_p.V924V	NM_001013031	NP_001013049	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform b	924	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)	1		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)										0.148256	90.393951	131.255118	51	293	CC		KEEP	---	---	---	---	capture			Silent	SNP	108370200	108370200	15430	10	C	T	T	17	17	SORCS1	T	2	2
XPNPEP1	7511	broad.mit.edu	36	10	111623121	111623121	+	Silent	SNP	G	A	A			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:111623121G>A	uc009xxt.1	-	c.1374C>T	c.(1372-1374)TAC>TAT	p.Y458Y	XPNPEP1_uc001kyp.1_Silent_p.Y439Y|XPNPEP1_uc001kyq.1_Silent_p.Y368Y	NM_020383	NP_065116	Q9NQW7	XPP1_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 1,	439					bradykinin catabolic process|proteolysis		manganese ion binding|metalloaminopeptidase activity|protein homodimerization activity			ovary(3)|pancreas(1)	4		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)										0.571429	39.702225	39.795631	12	9	GG		KEEP	---	---	---	---	capture			Silent	SNP	111623121	111623121	18025	10	G	A	A	40	40	XPNPEP1	A	1	1
ST8SIA6	338596	broad.mit.edu	36	10	17402888	17402888	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:17402888C>T	uc001ipd.1	-	c.1192G>A	c.(1192-1194)GCC>ACC	p.A398T		NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide	398	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1														0.389423	210.592541	212.829728	81	127	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17402888	17402888	15754	10	C	T	T	27	27	ST8SIA6	T	1	1
KIAA1217	56243	broad.mit.edu	36	10	24849173	24849173	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:24849173G>T	uc001iru.2	+	c.2293G>T	c.(2293-2295)GTA>TTA	p.V765L	KIAA1217_uc001irs.1_Missense_Mutation_p.V685L|KIAA1217_uc001irt.2_Missense_Mutation_p.V730L|KIAA1217_uc009xki.1_Missense_Mutation_p.V650L|KIAA1217_uc001irv.1_Missense_Mutation_p.V580L|KIAA1217_uc001irw.2_Missense_Mutation_p.V448L|KIAA1217_uc001irx.2_Missense_Mutation_p.V448L|KIAA1217_uc001iry.2_Missense_Mutation_p.V448L|KIAA1217_uc001irz.2_Missense_Mutation_p.V448L	NM_019590	NP_062536	Q5T5P2	SKT_HUMAN	sickle tail isoform 1	765					embryonic skeletal system development	cytoplasm				ovary(5)	5														0.621622	73.731865	74.213435	23	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24849173	24849173	8524	10	G	T	T	48	48	KIAA1217	T	3	3
DSCAML1	57453	broad.mit.edu	36	11	116804556	116804556	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:116804556C>G	uc001prh.1	-	c.6040G>C	c.(6040-6042)GGC>CGC	p.G2014R		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1954	Cytoplasmic (Potential).				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)	5	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)										0.184211	8.700487	12.264241	7	31	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116804556	116804556	4953	11	C	G	G	22	22	DSCAML1	G	3	3
TMPRSS4	56649	broad.mit.edu	36	11	117479118	117479118	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:117479118C>A	uc009yzt.1	+	c.250C>A	c.(250-252)CCC>ACC	p.P84T	TMPRSS4_uc001psd.2_Missense_Mutation_p.P84T|TMPRSS4_uc009yzu.1_Non-coding_Transcript|TMPRSS4_uc009yzv.1_Missense_Mutation_p.P59T	NM_019894	NP_063947	Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4 isoform 1	84	Extracellular (Potential).|LDL-receptor class A.				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)										0.204545	10.93551	14.520889	9	35	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117479118	117479118	16790	11	C	A	A	30	30	TMPRSS4	A	3	3
KCNJ5	3762	broad.mit.edu	36	11	128287122	128287122	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:128287122G>T	uc001qet.1	+	c.744G>T	c.(742-744)GAG>GAT	p.E248D	KCNJ5_uc009zck.1_Missense_Mutation_p.E248D|KCNJ5_uc001qew.1_Missense_Mutation_p.E248D	NM_000890	NP_000881	P48544	IRK5_HUMAN	potassium inwardly-rectifying channel J5	248	Cytoplasmic (By similarity).				synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding				0	all_hematologic(175;0.0641)	Lung NSC(97;0.00038)|all_lung(97;0.000817)|Breast(109;0.00123)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0059)|LUSC - Lung squamous cell carcinoma(976;0.021)|Lung(977;0.0215)	Glibenclamide(DB01016)	Pancreas(108;2548 5082)|Esophageal Squamous(165;4544 6231)								0.533333	120.599804	120.672639	40	35	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128287122	128287122	8359	11	G	T	T	36	36	KCNJ5	T	3	3
KCNQ1	3784	broad.mit.edu	36	11	2550773	2550774	+	Missense_Mutation	DNP	AT	CC	CC			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:2550773_2550774AT>CC	uc001lwn.1	+	c.902_903AT>CC	c.(901-903)GAT>GCC	p.D301A	KCNQ1_uc009ydp.1_Missense_Mutation_p.D85A|KCNQ1_uc001lwo.1_Missense_Mutation_p.D174A	NM_000218	NP_000209	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like	301					blood circulation|membrane depolarization|muscle contraction|regulation of heart contraction|sensory perception of sound	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			ovary(1)	1		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)									0.818182	23.474527	24.518066	9	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	2550773	2550774	8387	11	AT	CC	CC	12	12	KCNQ1	CC	4	4
OR4C6	219432	broad.mit.edu	36	11	55189543	55189543	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55189543G>T	uc001nht.2	+	c.325G>T	c.(325-327)GGG>TGG	p.G109W	OR4C6_uc009ymc.1_Missense_Mutation_p.G109W	NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C,	109	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.255474	82.755908	90.192504	35	102	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55189543	55189543	11459	11	G	T	T	43	43	OR4C6	T	3	3
COX8A	1351	broad.mit.edu	36	11	63498747	63498747	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:63498747C>A	uc001nye.1	+	c.19C>A	c.(19-21)CTG>ATG	p.L7M		NM_004074	NP_004065	P10176	COX8A_HUMAN	cytochrome c oxidase subunit VIIIa	7					respiratory electron transport chain	integral to membrane|mitochondrial inner membrane	cytochrome-c oxidase activity				0														0.108434	9.717217	22.326221	9	74	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63498747	63498747	3923	11	C	A	A	28	28	COX8A	A	3	3
OR10A3	26496	broad.mit.edu	36	11	7916705	7916705	+	Silent	SNP	T	A	A			TCGA-12-1088-01	TCGA-12-1088-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:7916705T>A	uc001mfu.1	-	c.939A>T	c.(937-939)ACA>ACT	p.T313T		NM_001003745	NP_001003745	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A,	313	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)										0.822581	162.508137	168.755513	51	11	TT		KEEP	---	---	---	---	capture			Silent	SNP	7916705	7916705	11297	11	T	A	A	51	51	OR10A3	A	4	4
TPCN1	53373	broad.mit.edu	36	12	112210403	112210403	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:112210403C>A	uc001tux.1	+	c.1903C>A	c.(1903-1905)CTG>ATG	p.L635M	TPCN1_uc001tuw.1_Missense_Mutation_p.L563M	NM_017901	NP_060371	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1 isoform 2	563	Cytoplasmic (Potential).					endosome membrane|integral to membrane|lysosomal membrane	calcium channel activity|voltage-gated ion channel activity			ovary(1)	1														0.428571	6.32147	6.352919	3	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	112210403	112210403	16939	12	C	A	A	28	28	TPCN1	A	3	3
C14orf138	79609	broad.mit.edu	36	14	49652836	49652836	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:49652836C>G	uc001wxo.1	-	c.185G>C	c.(184-186)GGG>GCG	p.G62A	C14orf138_uc001wxn.1_5'Flank|C14orf138_uc001wxp.1_Missense_Mutation_p.G62A|C14orf138_uc001wxq.1_Non-coding_Transcript	NM_024558	NP_078834	Q9H867	MT21D_HUMAN	hypothetical protein LOC79609 isoform a	62							methyltransferase activity				0	all_epithelial(31;0.000822)|Breast(41;0.0065)													0.928571	30.604206	32.498649	13	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49652836	49652836	1794	14	C	G	G	22	22	C14orf138	G	3	3
C14orf138	79609	broad.mit.edu	36	14	49652838	49652838	+	Missense_Mutation	SNP	G	C	C			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:49652838G>C	uc001wxo.1	-	c.183C>G	c.(181-183)GAC>GAG	p.D61E	C14orf138_uc001wxn.1_5'Flank|C14orf138_uc001wxp.1_Missense_Mutation_p.D61E|C14orf138_uc001wxq.1_Non-coding_Transcript	NM_024558	NP_078834	Q9H867	MT21D_HUMAN	hypothetical protein LOC79609 isoform a	61							methyltransferase activity				0	all_epithelial(31;0.000822)|Breast(41;0.0065)													0.913043	57.327567	58.962796	21	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49652838	49652838	1794	14	G	C	C	40	40	C14orf138	C	3	3
TK2	7084	broad.mit.edu	36	16	65141509	65141509	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65141509G>A	uc002eos.1	-	c.83C>T	c.(82-84)TCG>TTG	p.S28L	TK2_uc002eor.1_Intron|TK2_uc010cdq.1_Intron|TK2_uc010cdr.1_5'UTR	NM_004614	NP_004605	O00142	KITM_HUMAN	thymidine kinase 2, mitochondrial	Error:Variant_position_missing_in_O00142_after_alignment					pyrimidine base metabolic process|pyrimidine nucleoside salvage	mitochondrial matrix	ATP binding|phosphotransferase activity, alcohol group as acceptor|thymidine kinase activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0736)|Epithelial(162;0.237)										0.5	8.293031	8.293031	4	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65141509	65141509	16462	16	G	A	A	37	37	TK2	A	1	1
MPO	4353	broad.mit.edu	36	17	53705800	53705800	+	Missense_Mutation	SNP	A	T	T			TCGA-12-1088-01	TCGA-12-1088-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53705800A>T	uc002ivu.1	-	c.1595T>A	c.(1594-1596)TTT>TAT	p.F532Y		NM_000250	NP_000241	P05164	PERM_HUMAN	myeloperoxidase	532					anti-apoptosis|hydrogen peroxide catabolic process|low-density lipoprotein particle remodeling|oxidation-reduction process	extracellular space|lysosome|nucleus|stored secretory granule	chromatin binding|heme binding|heparin binding|peroxidase activity			ovary(2)|large_intestine(1)|pancreas(1)	4					Cefdinir(DB00535)									0.177778	7.662915	12.085017	8	37	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53705800	53705800	10124	17	A	T	T	1	1	MPO	T	4	4
TP53	7157	broad.mit.edu	36	17	7519015	7519015	+	Splice_Site_SNP	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519015C>T	uc002gim.2	-	c.e6_splice_site			TP53_uc002gig.1_Splice_Site_SNP|TP53_uc002gih.1_Splice_Site_SNP|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Splice_Site_SNP|TP53_uc010cng.1_Splice_Site_SNP|TP53_uc002gii.1_Splice_Site_SNP|TP53_uc010cnh.1_Splice_Site_SNP|TP53_uc010cni.1_Splice_Site_SNP|TP53_uc002gij.2_Splice_Site_SNP|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Splice_Site_SNP|TP53_uc002gio.2_Splice_Site_SNP	NM_001126112	NP_001119584			tumor protein p53 isoform a						activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.?(22)|p.0?(6)|p.G187fs*16(2)|p.D186_P191delDGLAPP(1)|p.L188fs*19(1)|p.G187_L188delGL(1)|p.G187fs*22(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	(CHAGOK1-Tumor)|(HH-Tumor)|(NCIH3255-Tumor)|(T84-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.686131	310.879478	315.100281	94	43	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	7519015	7519015	16923	17	C	T	T	24	24	TP53	T	5	2
ZNF564	163050	broad.mit.edu	36	19	12500389	12500389	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12500389C>A	uc002mty.1	-	c.125G>T	c.(124-126)TGT>TTT	p.C42F	ZNF709_uc002mtx.2_Intron	NM_144976	NP_659413	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	42	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.368421	128.019056	129.754372	42	72	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12500389	12500389	18590	19	C	A	A	17	17	ZNF564	A	3	3
HAUS8	93323	broad.mit.edu	36	19	17031456	17031456	+	Missense_Mutation	SNP	T	G	G			TCGA-12-1088-01	TCGA-12-1088-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17031456T>G	uc002nfe.1	-	c.331A>C	c.(331-333)AGC>CGC	p.S111R	HAUS8_uc002nff.1_Missense_Mutation_p.S110R|HAUS8_uc002nfg.1_Missense_Mutation_p.S50R|HAUS8_uc002nfh.1_Missense_Mutation_p.S111R	NM_033417	NP_219485	Q9BT25	HAUS8_HUMAN	sarcoma antigen NY-SAR-48 isoform a	111					cell division|centrosome organization|mitosis|spindle assembly	HAUS complex|microtubule|microtubule organizing center|spindle pole					0														0.181818	7.826329	10.97418	6	27	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17031456	17031456	7254	19	T	G	G	56	56	HAUS8	G	4	4
MLL4	9757	broad.mit.edu	36	19	40905875	40905876	+	Missense_Mutation	DNP	CC	TG	TG			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40905875_40905876CC>TG	uc010eei.1	+	c.2861_2862CC>TG	c.(2860-2862)CCC>CTG	p.P954L		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	954					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)											0.181818	13.047976	19.352403	12	54	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	40905875	40905876	10013	19	CC	TG	TG	22	22	MLL4	TG	2	2
IL28B	282617	broad.mit.edu	36	19	44426601	44426601	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:44426601C>A	uc002oks.1	-	c.295G>T	c.(295-297)GCC>TCC	p.A99S	IL28B_uc002okt.1_Missense_Mutation_p.A99S	NM_172139	NP_742151	Q8IZI9	IL28B_HUMAN	interleukin 28B	99					response to virus	extracellular space	cytokine activity				0	all_cancers(60;2.81e-07)|all_lung(34;7.81e-08)|Lung NSC(34;9.29e-08)|all_epithelial(25;3.9e-07)|Ovarian(47;0.0315)		Epithelial(26;1.55e-27)|all cancers(26;1.41e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)											0.4	7.791402	7.880502	4	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44426601	44426601	7984	19	C	A	A	26	26	IL28B	A	3	3
SIGLEC7	27036	broad.mit.edu	36	19	56340943	56340943	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56340943C>G	uc002pvv.1	+	c.780C>G	c.(778-780)AAC>AAG	p.N260K	SIGLEC7_uc002pvw.1_Missense_Mutation_p.N167K|SIGLEC7_uc010eoq.1_Intron|SIGLEC7_uc010eor.1_Intron	NM_014385	NP_055200	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7 isoform 1	260	Ig-like C2-type 2.|Extracellular (Potential).				cell adhesion	integral to plasma membrane	receptor activity|sugar binding			large_intestine(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)										0.11215	46.593768	94.273823	36	285	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56340943	56340943	14808	19	C	G	G	17	17	SIGLEC7	G	3	3
DFFA	1676	broad.mit.edu	36	1	10449888	10449888	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:10449888C>A	uc001arj.1	-	c.387G>T	c.(385-387)AGG>AGT	p.R129S	DFFA_uc001ark.1_Missense_Mutation_p.R129S	NM_004401	NP_004392	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha	129					DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction|negative regulation of apoptosis	cytosol|mitochondrion|nucleoplasm|plasma membrane	deoxyribonuclease activity|identical protein binding				0	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)						120				0.088319	9.373185	69.503053	31	320	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10449888	10449888	4631	1	C	A	A	26	26	DFFA	A	3	3
KANK4	163782	broad.mit.edu	36	1	62485832	62485832	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1088-01	TCGA-12-1088-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:62485832T>C	uc001dah.2	-	c.2783A>G	c.(2782-2784)GAT>GGT	p.D928G	KANK4_uc001dai.2_Missense_Mutation_p.D300G|KANK4_uc001daf.2_Missense_Mutation_p.D66G|KANK4_uc001dag.2_Missense_Mutation_p.D284G	NM_181712	NP_859063	Q5T7N3	KANK4_HUMAN	ankyrin repeat domain 38	928	ANK 4.									ovary(3)|lung(1)	4														0.25	7.790994	8.70175	4	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62485832	62485832	8283	1	T	C	C	50	50	KANK4	C	4	4
ITGB6	3694	broad.mit.edu	36	2	160691168	160691168	+	Nonsense_Mutation	SNP	A	T	T			TCGA-12-1088-01	TCGA-12-1088-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:160691168A>T	uc002ubh.2	-	c.1851T>A	c.(1849-1851)TGT>TGA	p.C617*	ITGB6_uc010fou.1_Nonsense_Mutation_p.C617*|ITGB6_uc010fov.1_Nonsense_Mutation_p.C617*	NM_000888	NP_000879	P18564	ITB6_HUMAN	integrin, beta 6	617	Extracellular (Potential).|IV.|Cysteine-rich tandem repeats.				cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development	integrin complex	receptor activity			ovary(1)|lung(1)|skin(1)	3										575				0.193548	19.373512	27.574793	18	75	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	160691168	160691168	8203	2	A	T	T	10	10	ITGB6	T	5	4
TTN	7273	broad.mit.edu	36	2	179106848	179106848	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179106848C>T	uc002umr.1	-	c.95036G>A	c.(95035-95037)AGA>AAA	p.R31679K	TTN_uc002ums.1_Missense_Mutation_p.R25374K|TTN_uc010frc.1_Missense_Mutation_p.R25307K|TTN_uc010frd.1_Missense_Mutation_p.R25182K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	32606										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			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.45	1034.140413	1035.825255	351	429	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	179106848	179106848	17290	2	C	T	T	32	32	TTN	T	2	2
FZD5	7855	broad.mit.edu	36	2	208341372	208341372	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1088-01	TCGA-12-1088-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:208341372T>C	uc002vcj.1	-	c.337A>G	c.(337-339)AAG>GAG	p.K113E	FZD5_uc010ful.1_Missense_Mutation_p.K113E	NM_003468	NP_003459	Q13467	FZD5_HUMAN	frizzled 5 precursor	113	FZ.|Extracellular (Potential).				angiogenesis|anterior/posterior axis specification, embryo|axonogenesis|brain development|canonical Wnt receptor signaling pathway|cellular response to molecule of bacterial origin|embryonic camera-type eye development|gonad development|labyrinthine layer blood vessel development|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of interferon-gamma production|post-embryonic camera-type eye development|Spemann organizer formation|T cell differentiation in thymus|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell projection|cell surface|Golgi membrane|integral to membrane|plasma membrane	G-protein coupled receptor activity|PDZ domain binding|protein kinase binding|Wnt receptor activity|Wnt-protein binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.13)|Lung(261;0.134)										0.363636	7.59328	7.774513	4	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	208341372	208341372	6384	2	T	C	C	63	63	FZD5	C	4	4
COL6A3	1293	broad.mit.edu	36	2	237961438	237961438	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237961438G>A	uc002vwl.2	-	c.838C>T	c.(838-840)CGA>TGA	p.R280*	COL6A3_uc002vwk.2_Nonsense_Mutation_p.R280*|COL6A3_uc002vwm.2_Intron|COL6A3_uc002vwn.2_Nonsense_Mutation_p.R280*|COL6A3_uc002vwo.2_Nonsense_Mutation_p.R74*|COL6A3_uc002vwq.2_Nonsense_Mutation_p.R74*|COL6A3_uc002vwr.2_Intron	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	280	VWFA 2.|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)		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)										0.358491	118.959981	120.812193	38	68	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	237961438	237961438	3839	2	G	A	A	39	39	COL6A3	A	5	1
CNNM3	26505	broad.mit.edu	36	2	96846889	96846889	+	Missense_Mutation	SNP	C	A	A			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:96846889C>A	uc002swy.1	+	c.1148C>A	c.(1147-1149)ACT>AAT	p.T383N	CNNM3_uc002swz.1_Missense_Mutation_p.T383N	NM_017623	NP_060093	Q8NE01	CNNM3_HUMAN	cyclin M3 isoform 1	383					ion transport	integral to membrane|plasma membrane	protein binding			ovary(1)	1														0.307692	7.494579	7.923775	4	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	96846889	96846889	3752	2	C	A	A	20	20	CNNM3	A	3	3
MED12L	116931	broad.mit.edu	36	3	152611934	152611934	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1088-01	TCGA-12-1088-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:152611934A>G	uc003eyp.1	+	c.5984A>G	c.(5983-5985)TAT>TGT	p.Y1995C		NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1995	Gln-rich.				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	RNA polymerase II transcription mediator activity			ovary(4)|large_intestine(1)	5			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)							59				0.419355	126.817175	127.342711	39	54	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152611934	152611934	9818	3	A	G	G	16	16	MED12L	G	4	4
ARPM1	84517	broad.mit.edu	36	3	170968617	170968617	+	Missense_Mutation	SNP	A	C	C			TCGA-12-1088-01	TCGA-12-1088-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:170968617A>C	uc003ffs.1	-	c.416T>G	c.(415-417)CTG>CGG	p.L139R		NM_032487	NP_115876	Q9BYD9	ARPM1_HUMAN	actin related protein M1	139						cytoplasm|cytoskeleton					0	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;5.01e-59)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)											0.375	6.520613	6.631159	3	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	170968617	170968617	994	3	A	C	C	7	7	ARPM1	C	4	4
CCR9	10803	broad.mit.edu	36	3	45917468	45917468	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:45917468G>T	uc003coz.1	+	c.184G>T	c.(184-186)GGT>TGT	p.G62C	LZTFL1_uc003coy.1_Intron|CCR9_uc010hiv.1_Missense_Mutation_p.G50C|CCR9_uc003cpa.1_Missense_Mutation_p.G50C|CCR9_uc010hiw.1_Missense_Mutation_p.G50C	NM_031200	NP_006632	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9 isoform A	62	Helical; Name=1; (Potential).				cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane				ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)										0.658436	926.066785	936.794739	320	166	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45917468	45917468	3075	3	G	T	T	43	43	CCR9	T	3	3
PLXNB1	5364	broad.mit.edu	36	3	48425782	48425782	+	Missense_Mutation	SNP	A	T	T			TCGA-12-1088-01	TCGA-12-1088-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:48425782A>T	uc003csv.1	-	c.6046T>A	c.(6046-6048)TTC>ATC	p.F2016I	PLXNB1_uc003cst.1_Missense_Mutation_p.F466I|PLXNB1_uc003csu.1_Missense_Mutation_p.F1833I|PLXNB1_uc003csw.1_Missense_Mutation_p.F2016I|PLXNB1_uc003csx.1_Missense_Mutation_p.F2016I	NM_002673	NP_002664	O43157	PLXB1_HUMAN	plexin B1	2016	Cytoplasmic (Potential).				axon guidance|cell migration|intracellular signal transduction|regulation of cell shape|regulation of cytoskeleton organization|regulation of small GTPase mediated signal transduction|semaphorin-plexin signaling pathway	extracellular region|integral to plasma membrane|intracellular|semaphorin receptor complex	GTPase activator activity|semaphorin receptor activity|semaphorin receptor binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)										0.257576	31.338344	34.861254	17	49	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48425782	48425782	12549	3	A	T	T	3	3	PLXNB1	T	4	4
CELSR3	1951	broad.mit.edu	36	3	48671603	48671603	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:48671603C>T	uc003cuf.1	-	c.3679G>A	c.(3679-3681)GTC>ATC	p.V1227I	CELSR3_uc003cul.1_Missense_Mutation_p.V1157I	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	1157	Extracellular (Potential).|Cadherin 8.				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)										0.160494	23.128728	32.016504	13	68	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48671603	48671603	3356	3	C	T	T	19	19	CELSR3	T	1	1
CCDC158	339965	broad.mit.edu	36	4	77524337	77524337	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:77524337C>G	uc003hkb.2	-	c.654G>C	c.(652-654)TTG>TTC	p.L218F	CCDC158_uc010ijg.1_Non-coding_Transcript|CCDC158_uc003hkd.2_Missense_Mutation_p.L218F	NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	hypothetical protein LOC339965	218										ovary(2)|pancreas(1)	3														0.28	29.020159	31.203465	14	36	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77524337	77524337	2912	4	C	G	G	21	21	CCDC158	G	3	3
TIGD2	166815	broad.mit.edu	36	4	90254140	90254140	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1088-01	TCGA-12-1088-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:90254140T>C	uc003hsk.1	+	c.992T>C	c.(991-993)CTA>CCA	p.L331P	FAM13A_uc003hsh.1_5'Flank	NM_145715	NP_663761	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	331	DDE.					chromosome, centromeric region|nucleus	DNA binding				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)										0.25	7.190176	8.101866	4	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	90254140	90254140	16425	4	T	C	C	53	53	TIGD2	C	4	4
ARAP3	64411	broad.mit.edu	36	5	141013944	141013944	+	Missense_Mutation	SNP	C	G	G			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:141013944C>G	uc003llm.1	-	c.4392G>C	c.(4390-4392)GAG>GAC	p.E1464D	ARAP3_uc003lln.1_Missense_Mutation_p.E1295D|FCHSD1_uc003llk.1_5'Flank|ARAP3_uc003lll.1_Missense_Mutation_p.E415D	NM_022481	NP_071926	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	1464	Pro-rich.				cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			breast(5)|ovary(1)|large_intestine(1)	7														0.147541	6.837207	14.130656	9	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	141013944	141013944	851	5	C	G	G	28	28	ARAP3	G	3	3
LPCAT1	79888	broad.mit.edu	36	5	1536600	1536600	+	Silent	SNP	A	C	C			TCGA-12-1088-01	TCGA-12-1088-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1536600A>C	uc003jcm.1	-	c.669T>G	c.(667-669)GGT>GGG	p.G223G		NM_024830	NP_079106	Q8NF37	PCAT1_HUMAN	acyltransferase like 2	223	Lumenal (Potential).				phospholipid biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)										0.3	6.53153	6.883095	3	7	AA		KEEP	---	---	---	---	capture			Silent	SNP	1536600	1536600	9283	5	A	C	C	6	6	LPCAT1	C	4	4
GABRA6	2559	broad.mit.edu	36	5	161045869	161045869	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:161045869G>T	uc003lyu.2	+	c.94G>T	c.(94-96)GTC>TTC	p.V32F		NM_000811	NP_000802	Q16445	GBRA6_HUMAN	gamma-aminobutyric acid A receptor, alpha 6	32	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity			ovary(7)|large_intestine(1)|central_nervous_system(1)	9	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)						TCGA Ovarian(5;0.080)			0.219251	102.940246	116.473212	41	146	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	161045869	161045869	6416	5	G	T	T	40	40	GABRA6	T	3	3
ADAMTS16	170690	broad.mit.edu	36	5	5199447	5199447	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:5199447C>T	uc003jdl.1	+	c.380C>T	c.(379-381)ACG>ATG	p.T127M	ADAMTS16_uc003jdj.1_Missense_Mutation_p.T127M|ADAMTS16_uc003jdk.1_Missense_Mutation_p.T127M	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	127					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.177778	15.571486	19.974982	8	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5199447	5199447	262	5	C	T	T	19	19	ADAMTS16	T	1	1
CCNH	902	broad.mit.edu	36	5	86726669	86726669	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:86726669C>T	uc003kjb.1	-	c.881G>A	c.(880-882)AGG>AAG	p.R294K	CCNH_uc003kiy.1_Non-coding_Transcript|CCNH_uc003kiz.1_Missense_Mutation_p.R241K|CCNH_uc003kja.1_Missense_Mutation_p.R241K	NM_001239	NP_001230	P51946	CCNH_HUMAN	cyclin H	294					G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cyclin-dependent protein kinase activating kinase holoenzyme complex|holo TFIIH complex	protein binding			ovary(2)|kidney(1)	3		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;9.01e-39)|Epithelial(54;5.08e-33)|all cancers(79;4.28e-28)										0.171429	20.856445	28.004817	12	58	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86726669	86726669	3052	5	C	T	T	24	24	CCNH	T	2	2
CNKSR3	154043	broad.mit.edu	36	6	154773250	154773250	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:154773250G>A	uc003qpy.1	-	c.1288C>T	c.(1288-1290)CGG>TGG	p.R430W		NM_173515	NP_775786	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	430	DUF1170.				negative regulation of ERK1 and ERK2 cascade|negative regulation of peptidyl-serine phosphorylation|positive regulation of sodium ion transport	cytoplasm|membrane				ovary(2)|breast(1)	3		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)										0.40981	791.448592	795.924173	259	373	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154773250	154773250	3746	6	G	A	A	40	40	CNKSR3	A	1	1
HLA-DRB5	3127	broad.mit.edu	36	6	32665465	32665465	+	Silent	SNP	G	A	A	rs34396110	unknown	TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32665465G>A	uc003obk.2	-	c.33C>T	c.(31-33)TGC>TGT	p.C11C	HLA-DRB1_uc003obl.2_Silent_p.C11C|HLA-DRB1_uc003obp.2_Silent_p.C11C	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR	11					antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0														0.176471	6.915026	8.591417	3	14	GG		KEEP	---	---	---	---	capture			Silent	SNP	32665465	32665465	7500	6	G	A	A	46	46	HLA-DRB5	A	2	2
KHDRBS2	202559	broad.mit.edu	36	6	62945081	62945081	+	Nonsense_Mutation	SNP	T	A	A			TCGA-12-1088-01	TCGA-12-1088-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:62945081T>A	uc003peg.2	-	c.187A>T	c.(187-189)AGA>TGA	p.R63*		NM_152688	NP_689901	Q5VWX1	KHDR2_HUMAN	KH domain-containing, RNA-binding, signal	63					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			ovary(3)|liver(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(397;0.149)										0.134021	20.224813	32.816029	13	84	TT		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	62945081	62945081	8453	6	T	A	A	56	56	KHDRBS2	A	5	4
PHF3	23469	broad.mit.edu	36	6	64459592	64459592	+	Missense_Mutation	SNP	G	T	T			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:64459592G>T	uc003pep.1	+	c.2196G>T	c.(2194-2196)ATG>ATT	p.M732I	PHF3_uc010kaf.1_Missense_Mutation_p.M732I|PHF3_uc003pem.2_Missense_Mutation_p.M685I|PHF3_uc010kag.1_Missense_Mutation_p.M644I|PHF3_uc010kah.1_Missense_Mutation_p.M546I|PHF3_uc003pen.2_Missense_Mutation_p.M644I	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	732	PHD-type.				multicellular organismal development	nucleus	zinc ion binding			ovary(2)|lung(1)|skin(1)	4	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GBM(135;136 1820 29512 34071 46235)				350				0.148148	49.104056	71.5428	28	161	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64459592	64459592	12259	6	G	T	T	47	47	PHF3	T	3	3
EPHA7	2045	broad.mit.edu	36	6	94031032	94031032	+	Splice_Site_SNP	SNP	C	A	A			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:94031032C>A	uc003poe.1	-	c.e8_splice_site			EPHA7_uc003pof.1_Splice_Site_SNP	NM_004440	NP_004431			ephrin receptor EphA7						protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(7)|lung(6)|central_nervous_system(3)|large_intestine(2)|skin(2)|pancreas(1)	21		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)						635				0.392857	63.137615	63.700213	22	34	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	94031032	94031032	5365	6	C	A	A	18	18	EPHA7	A	5	3
TMEM106B	54664	broad.mit.edu	36	7	12224673	12224673	+	Splice_Site_SNP	SNP	G	A	A			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:12224673G>A	uc003ssh.1	+	c.e3_splice_site			TMEM106B_uc003ssi.1_Splice_Site_SNP	NM_018374	NP_060844			transmembrane protein 106B							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (126;0.185)										0.1875	105.463233	128.867308	48	208	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	12224673	12224673	16551	7	G	A	A	40	40	TMEM106B	A	5	1
ATP6V0A4	50617	broad.mit.edu	36	7	138095038	138095038	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:138095038G>A	uc003vuf.1	-	c.638C>T	c.(637-639)ACG>ATG	p.T213M	ATP6V0A4_uc003vug.1_Missense_Mutation_p.T213M|ATP6V0A4_uc003vuh.1_Missense_Mutation_p.T213M	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	213	Cytoplasmic (Potential).				cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1														0.220588	109.165877	123.838498	45	159	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	138095038	138095038	1189	7	G	A	A	40	40	ATP6V0A4	A	1	1
CLU	1191	broad.mit.edu	36	8	27528157	27528157	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:27528157G>A	uc003xfz.1	-	c.59C>T	c.(58-60)ACG>ATG	p.T20M		NM_001831	NP_976084	P10909	CLUS_HUMAN	clusterin isoform 1	Error:Variant_position_missing_in_P10909_after_alignment					complement activation, classical pathway|innate immune response|lipid metabolic process|negative regulation of apoptosis|negative regulation of protein homooligomerization|platelet activation|platelet degranulation|release of cytochrome c from mitochondria|response to misfolded protein|response to virus|reverse cholesterol transport	mitochondrion|platelet alpha granule lumen|spherical high-density lipoprotein particle	misfolded protein binding			ovary(2)	2		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)								OREG0018671	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.466667	18.418325	18.433179	7	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27528157	27528157	3706	8	G	A	A	40	40	CLU	A	1	1
DENND1A	57706	broad.mit.edu	36	9	125185786	125185786	+	Missense_Mutation	SNP	A	G	G			TCGA-12-1088-01	TCGA-12-1088-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:125185786A>G	uc004bnz.1	-	c.1805T>C	c.(1804-1806)CTG>CCG	p.L602P	DENND1A_uc004bny.1_Missense_Mutation_p.L384P|DENND1A_uc010mwh.1_Missense_Mutation_p.L23P	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1	602						cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2														0.181818	22.414903	27.649119	10	45	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125185786	125185786	4605	9	A	G	G	7	7	DENND1A	G	4	4
TCEAL3	85012	broad.mit.edu	36	X	102751011	102751011	+	Silent	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:102751011C>T	uc004ekq.1	+	c.363C>T	c.(361-363)TCC>TCT	p.S121S	TCEAL3_uc004ekr.1_Silent_p.S121S|TCEAL3_uc010noq.1_Silent_p.S121S	NM_001006933	NP_116315	Q969E4	TCAL3_HUMAN	transcription elongation factor A (SII)-like 3	121					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0														0.112971	34.132145	69.408366	27	212	CC		KEEP	---	---	---	---	capture			Silent	SNP	102751011	102751011	16198	23	C	T	T	22	22	TCEAL3	T	2	2
NRK	203447	broad.mit.edu	36	X	105086247	105086247	+	Silent	SNP	A	G	G			TCGA-12-1088-01	TCGA-12-1088-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:105086247A>G	uc004emd.1	+	c.4748A>G	c.(4747-4749)TAA>TGA	p.*1583*		NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1583					protein phosphorylation		ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14										430				0.357143	16.874857	17.124875	5	9	AA		KEEP	---	---	---	---	capture			Silent	SNP	105086247	105086247	11060	23	A	G	G	13	13	NRK	G	4	4
LHFPL1	340596	broad.mit.edu	36	X	111801070	111801070	+	Missense_Mutation	SNP	G	A	A			TCGA-12-1088-01	TCGA-12-1088-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:111801070G>A	uc004epp.1	-	c.274C>T	c.(274-276)CGC>TGC	p.R92C	LHFPL1_uc004epq.1_Missense_Mutation_p.R69C|LHFPL1_uc010nqa.1_Intron|LHFPL1_uc010nqb.1_Missense_Mutation_p.R69C	NM_178175	NP_835469	Q86WI0	LHPL1_HUMAN	lipoma HMGIC fusion partner-like 1	69						integral to membrane					0														0.268293	29.309066	31.294744	11	30	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111801070	111801070	9090	23	G	A	A	38	38	LHFPL1	A	1	1
PGRMC1	10857	broad.mit.edu	36	X	118254434	118254434	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:118254434C>T	uc004erb.1	+	c.80C>T	c.(79-81)ACG>ATG	p.T27M		NM_006667	NP_006658	O00264	PGRC1_HUMAN	progesterone receptor membrane component 1	27	Helical; (Potential).					cell surface|endoplasmic reticulum membrane|integral to membrane|microsome|nucleolus	heme binding|protein binding|receptor activity|steroid binding				0														0.555556	29.550494	29.598945	10	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118254434	118254434	12229	23	C	T	T	19	19	PGRMC1	T	1	1
MAMLD1	10046	broad.mit.edu	36	X	149392702	149392702	+	Silent	SNP	T	G	G			TCGA-12-1088-01	TCGA-12-1088-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:149392702T>G	uc004fee.1	+	c.2010T>G	c.(2008-2010)CCT>CCG	p.P670P		NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	670					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)													0.094488	14.802987	56.776177	24	230	TT		KEEP	---	---	---	---	capture			Silent	SNP	149392702	149392702	9591	23	T	G	G	54	54	MAMLD1	G	4	4
FLNA	2316	broad.mit.edu	36	X	153235169	153235169	+	Missense_Mutation	SNP	A	T	T			TCGA-12-1088-01	TCGA-12-1088-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153235169A>T	uc004fkk.2	-	c.5807T>A	c.(5806-5808)GTC>GAC	p.V1936D	FLNA_uc004fki.2_5'UTR|FLNA_uc010nuu.1_Missense_Mutation_p.V1928D	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1936	Filamin 17.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	actin cytoskeleton|cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)									518				0.266667	7.494799	8.232197	4	11	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153235169	153235169	6175	23	A	T	T	10	10	FLNA	T	4	4
FLNA	2316	broad.mit.edu	36	X	153235170	153235170	+	Missense_Mutation	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153235170C>T	uc004fkk.2	-	c.5806G>A	c.(5806-5808)GTC>ATC	p.V1936I	FLNA_uc004fki.2_5'UTR|FLNA_uc010nuu.1_Missense_Mutation_p.V1928I	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1936	Filamin 17.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	actin cytoskeleton|cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)									518				0.266667	6.9923	7.731765	4	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153235170	153235170	6175	23	C	T	T	20	20	FLNA	T	2	2
CXorf22	170063	broad.mit.edu	36	X	35903795	35903795	+	Missense_Mutation	SNP	T	C	C			TCGA-12-1088-01	TCGA-12-1088-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:35903795T>C	uc004ddj.1	+	c.2557T>C	c.(2557-2559)TCT>CCT	p.S853P	CXorf22_uc010ngv.1_Non-coding_Transcript	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN	hypothetical protein LOC170063	853										large_intestine(1)|lung(1)|ovary(1)	3														0.294991	483.394318	503.677338	159	380	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35903795	35903795	4262	23	T	C	C	62	62	CXorf22	C	4	4
PRICKLE3	4007	broad.mit.edu	36	X	48919032	48919032	+	Silent	SNP	C	T	T			TCGA-12-1088-01	TCGA-12-1088-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48919032C>T	uc004dmy.1	-	c.1782G>A	c.(1780-1782)TCG>TCA	p.S594S		NM_006150	NP_006141	O43900	PRIC3_HUMAN	LIM domain only 6	594							protein binding|zinc ion binding			breast(1)	1														0.34375	29.513736	30.204466	11	21	CC		KEEP	---	---	---	---	capture			Silent	SNP	48919032	48919032	12931	23	C	T	T	27	27	PRICKLE3	T	1	1
TAF5	6877	broad.mit.edu	36	10	105123313	105123314	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:105123313_105123314delTG	uc001kwv.1	+	c.768_769delTG	c.(766-771)CATGAGfs	p.H256fs		NM_006951	NP_008882	Q15542	TAF5_HUMAN	TBP-associated factor 5	256_257					histone acetylation|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	actin cytoskeleton|transcription factor TFIID complex|transcription factor TFTC complex	promoter binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(2)	2		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)										0.57			98	74				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	105123313	105123314	16049	10	TG	-	-	51	51	TAF5	-	5	5
TBC1D4	9882	broad.mit.edu	36	13	74834283	74834284	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:74834283_74834284delGG	uc001vjl.1	-	c.959_960delCC	c.(958-960)ACCfs	p.T320fs	TBC1D4_uc010aes.1_Frame_Shift_Del_p.T320fs	NM_014832	NP_055647	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	320	PID 2.					cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)	5		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)										0.55			46	38				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	74834283	74834284	16148	13	GG	-	-	39	39	TBC1D4	-	5	5
GABRA5	2558	broad.mit.edu	36	15	24771315	24771332	+	Splice_Site_Del	DEL	TCAAGGTACTGACTATTT	-	-			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:24771315_24771332delTCAAGGTACTGACTATTT	uc001zbd.1	+	c.e11_splice_site				NM_000810	NP_000801			gamma-aminobutyric acid (GABA) A receptor, alpha						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(1)	1		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.64			7	4				---	---	---	---	capture_indel			Splice_Site_Del	DEL	24771315	24771332	6415	15	TCAAGGTACTGACTATTT	-	-	50	50	GABRA5	-	5	5
ATP2A1	487	broad.mit.edu	36	16	28817214	28817215	+	Frame_Shift_Ins	INS	-	C	C			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:28817214_28817215insC	uc002dro.1	+	c.1705_1706insC	c.(1705-1707)ACCfs	p.T569fs	ATP2A1_uc002drn.1_Frame_Shift_Ins_p.T569fs|ATP2A1_uc002drp.1_Frame_Shift_Ins_p.T444fs	NM_173201	NP_775293	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, fast twitch 1 isoform	569	Cytoplasmic (By similarity).				apoptosis in response to endoplasmic reticulum stress|apoptotic mitochondrial changes|ATP biosynthetic process|calcium ion import|elevation of endoplasmic reticulum calcium ion concentration|elevation of mitochondrial calcium ion concentration|maintenance of mitochondrion location|negative regulation of striated muscle contraction|platelet activation|positive regulation of fast-twitch skeletal muscle fiber contraction|reduction of endoplasmic reticulum calcium ion concentration|relaxation of skeletal muscle|response to endoplasmic reticulum stress	calcium channel complex|endoplasmic reticulum membrane|ER-Golgi intermediate compartment|H zone|I band|microsome|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum|sarcoplasmic reticulum membrane	ATP binding|ATP binding|calcium ion binding|calcium ion binding|calcium-transporting ATPase activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.38			3	5				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	28817214	28817215	1155	16	-	C	C	6	6	ATP2A1	C	5	5
CAMKK1	84254	broad.mit.edu	36	17	3716027	3716028	+	Frame_Shift_Ins	INS	-	T	T			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:3716027_3716028insT	uc002fwv.1	-	c.1482_1483insA	c.(1480-1485)AAGCGTfs	p.K494fs	CAMKK1_uc002fwt.1_Frame_Shift_Ins_p.K456fs|CAMKK1_uc002fwu.1_Frame_Shift_Ins_p.K456fs	NM_172207	NP_757344	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase 1	456_457	Calmodulin-binding (By similarity).				protein phosphorylation|synaptic transmission	cytosol|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)						485				0.65			328	179				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	3716027	3716028	2723	17	-	T	T	38	38	CAMKK1	T	5	5
KCNH4	23415	broad.mit.edu	36	17	37575188	37575189	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:37575188_37575189delTC	uc002hzb.1	-	c.1422_1423delGA	c.(1420-1425)GTGACAfs	p.V474fs		NM_012285	NP_036417	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H,	474_475	Extracellular (Potential).				regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	two-component sensor activity|voltage-gated potassium channel activity			large_intestine(1)	1		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		NSCLC(117;707 1703 2300 21308 31858)								0.53			20	18				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	37575188	37575189	8339	17	TC	-	-	58	58	KCNH4	-	5	5
ZNF470	388566	broad.mit.edu	36	19	61781343	61781344	+	Frame_Shift_Del	DEL	AT	-	-			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:61781343_61781344delAT	uc002qnl.2	+	c.1734_1735delAT	c.(1732-1737)TCATATfs	p.S578fs	ZNF470_uc010etn.1_Intron	NM_001001668	NP_001001668	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	578_579	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)										0.35			92	173				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	61781343	61781344	18523	19	AT	-	-	8	8	ZNF470	-	5	5
VARS2	57176	broad.mit.edu	36	6	30995857	30995858	+	Frame_Shift_Ins	INS	-	A	A			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:30995857_30995858insA	uc003nsc.1	+	c.1178_1179insA	c.(1177-1179)GTGfs	p.V393fs	VARS2_uc010jsg.1_5'UTR	NM_020442	NP_065175	Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	393					valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4														0.31			40	87				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	30995857	30995858	17689	6	-	A	A	59	59	VARS2	A	5	5
CYB5R4	51167	broad.mit.edu	36	6	84626280	84626281	+	Frame_Shift_Ins	INS	-	G	G			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:84626280_84626281insG	uc003pkf.1	+	c.60_61insG	c.(58-63)TCCGGGfs	p.S20fs		NM_016230	NP_057314	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4	20_21					cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|oxidation-reduction process|response to antibiotic|superoxide metabolic process	endoplasmic reticulum|perinuclear region of cytoplasm	cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity			breast(2)	2		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)		Esophageal Squamous(86;1289 1332 25971 40349 52675)				343		OREG0017553	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.33			3	6				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	84626280	84626281	4294	6	-	G	G	23	23	CYB5R4	G	5	5
REPIN1	29803	broad.mit.edu	36	7	149699933	149699934	+	Frame_Shift_Ins	INS	-	C	C			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:149699933_149699934insC	uc010lpr.1	+	c.841_842insC	c.(841-843)GCCfs	p.A281fs	REPIN1_uc003whd.2_Frame_Shift_Ins_p.A213fs|REPIN1_uc010lpq.1_Frame_Shift_Ins_p.A224fs|REPIN1_uc003whc.2_Frame_Shift_Ins_p.A224fs|REPIN1_uc003whe.2_Frame_Shift_Ins_p.A224fs	NM_001099695	NP_001093165	Q9BWE0	REPI1_HUMAN	replication initiator 1 isoform 3	224					DNA replication	nuclear origin of replication recognition complex	DNA binding|zinc ion binding			pancreas(1)	1	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)											0.50			3	3				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	149699933	149699934	13696	7	-	C	C	38	38	REPIN1	C	5	5
LAS1L	81887	broad.mit.edu	36	X	64666244	64666250	+	Frame_Shift_Del	DEL	CCTCTTC	-	-			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:64666244_64666250delCCTCTTC	uc004dwa.1	-	c.748_754delGAAGAGG	c.(748-756)GAAGAGGTGfs	p.E250fs	LAS1L_uc004dwc.1_Frame_Shift_Del_p.E250fs|LAS1L_uc004dwd.1_Frame_Shift_Del_p.E208fs	NM_031206	NP_112483	Q9Y4W2	LAS1L_HUMAN	LAS1-like	250_252						MLL1 complex|nucleolus	protein binding			ovary(3)|large_intestine(1)	4														0.34			91	180				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	64666244	64666250	8959	23	CCTCTTC	-	-	18	18	LAS1L	-	5	5
MED12	9968	broad.mit.edu	36	X	70273062	70273062	+	Frame_Shift_Del	DEL	G	-	-			TCGA-12-1088-01	TCGA-12-1088-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70273062_70273062delG	uc004dyy.1	+	c.5232_5232delG	c.(5230-5232)CTGfs	p.L1744fs	MED12_uc004dyz.1_Frame_Shift_Del_p.L1744fs|MED12_uc004dza.1_Frame_Shift_Del_p.L1591fs|MED12_uc010nla.1_Frame_Shift_Del_p.L370fs	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1744	Pro-rich.|Interaction with CTNNB1 and GLI3.				androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)													0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	70273062	70273062	9817	23	G	-	-	46	46	MED12	-	5	5
