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
ADD3	120	broad.mit.edu	36	10	111850570	111850570	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:111850570C>T	uc001kyt.2	+	c.169C>T	c.(169-171)CGA>TGA	p.R57*	ADD3_uc001kys.2_Nonsense_Mutation_p.R57*|ADD3_uc001kyu.1_Nonsense_Mutation_p.R57*|ADD3_uc001kyv.1_Nonsense_Mutation_p.R57*|ADD3_uc001kyw.1_Nonsense_Mutation_p.R57*	NM_016824	NP_058432	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma) isoform a	57						cytoskeleton	actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton			ovary(2)|large_intestine(1)	3		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)										0.538462	47.652179	47.685638	14	12	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	111850570	111850570	307	10	C	T	T	19	19	ADD3	T	5	1
HABP2	3026	broad.mit.edu	36	10	115338115	115338115	+	Silent	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:115338115C>T	uc001lai.2	+	c.1680C>T	c.(1678-1680)TTC>TTT	p.F560F		NM_004132	NP_004123	Q14520	HABP2_HUMAN	hyaluronan binding protein 2 preproprotein	560					cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)	2		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)										0.4	8.490527	8.579851	4	6	CC		KEEP	---	---	---	---	capture			Silent	SNP	115338115	115338115	7220	10	C	T	T	32	32	HABP2	T	2	2
SLC18A2	6571	broad.mit.edu	36	10	119003613	119003613	+	Silent	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:119003613G>C	uc001ldd.1	+	c.588G>C	c.(586-588)TCG>TCC	p.S196S	SLC18A2_uc009xyy.1_5'UTR	NM_003054	NP_003045	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine),	196	Helical; (Potential).				neurotransmitter secretion	clathrin sculpted monoamine transport vesicle membrane|integral to plasma membrane|membrane fraction	monoamine transmembrane transporter activity				0		Colorectal(252;0.19)		all cancers(201;0.029)	Alseroxylon(DB00386)|Reserpine(DB00206)|Tetrabenazine(DB04844)									0.214286	6.81738	7.872744	3	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	119003613	119003613	14922	10	G	C	C	40	40	SLC18A2	C	3	3
FAM175B	23172	broad.mit.edu	36	10	126507337	126507337	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:126507337G>A	uc001lib.2	+	c.481G>A	c.(481-483)GCT>ACT	p.A161T		NM_032182	NP_115558	Q15018	F175B_HUMAN	hypothetical protein LOC23172	161						BRISC complex	polyubiquitin binding				0														0.384615	16.173614	16.324749	5	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	126507337	126507337	5704	10	G	A	A	38	38	FAM175B	A	1	1
NCOA4	8031	broad.mit.edu	36	10	51249178	51249178	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:51249178T>G	uc009xon.1	+	c.79T>G	c.(79-81)TCC>GCC	p.S27A	PARG_uc001jih.1_Intron|NCOA4_uc001jis.2_Missense_Mutation_p.S11A|NCOA4_uc001jit.1_Missense_Mutation_p.S11A|NCOA4_uc009xoo.1_Missense_Mutation_p.S11A	NM_005437	NP_005428	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4 isoform 3	11					androgen receptor signaling pathway|male gonad development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	androgen receptor binding|transcription coactivator activity			central_nervous_system(1)|kidney(1)	2										48				0.319444	51.188014	53.280526	23	49	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51249178	51249178	10630	10	T	G	G	54	54	NCOA4	G	4	4
PIK3AP1	118788	broad.mit.edu	36	10	98459348	98459348	+	Silent	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:98459348G>A	uc001kmq.1	-	c.396C>T	c.(394-396)ACC>ACT	p.T132T		NM_152309	NP_689522	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	132						cytoplasm|plasma membrane				ovary(1)	1		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)										0.454545	16.774319	16.794047	5	6	GG		KEEP	---	---	---	---	capture			Silent	SNP	98459348	98459348	12332	10	G	A	A	35	35	PIK3AP1	A	2	2
NXF1	10482	broad.mit.edu	36	11	62320119	62320119	+	Nonsense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62320119G>A	uc009yog.1	-	c.1585C>T	c.(1585-1587)CAG>TAG	p.Q529*	NXF1_uc001nvf.1_Nonsense_Mutation_p.Q486*|NXF1_uc001nvg.1_3'UTR	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1 isoform 1	486	NTF2.				gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(1)	1														0.394737	87.13021	87.868281	30	46	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	62320119	62320119	11187	11	G	A	A	47	47	NXF1	A	5	2
PLCB3	5331	broad.mit.edu	36	11	63782996	63782996	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:63782996C>G	uc001nzb.2	+	c.1317C>G	c.(1315-1317)ATC>ATG	p.I439M	PLCB3_uc009ypg.1_Missense_Mutation_p.I439M|PLCB3_uc009yph.1_Missense_Mutation_p.I372M|PLCB3_uc009ypi.1_Missense_Mutation_p.I439M	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C, beta 3	439	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2														0.166667	6.410749	8.920659	4	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63782996	63782996	12455	11	C	G	G	31	31	PLCB3	G	3	3
SSH3	54961	broad.mit.edu	36	11	66831678	66831678	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:66831678G>C	uc001okj.1	+	c.685G>C	c.(685-687)GCC>CCC	p.A229P	SSH3_uc001okk.1_Non-coding_Transcript|SSH3_uc001okl.1_Missense_Mutation_p.A83P	NM_017857	NP_060327	Q8TE77	SSH3_HUMAN	slingshot homolog 3	229					regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton|nucleus	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)											0.5	12.856193	12.856193	5	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66831678	66831678	15702	11	G	C	C	42	42	SSH3	C	3	3
NOS1	4842	broad.mit.edu	36	12	116208338	116208338	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:116208338C>T	uc001twm.1	-	c.1244G>A	c.(1243-1245)CGG>CAG	p.R415Q		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1 (neuronal)	415					arginine catabolic process|multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|oxidation-reduction process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(2)|pancreas(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	Esophageal Squamous(162;1748 2599 51982 52956)								0.356568	401.96386	408.72647	133	240	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116208338	116208338	10944	12	C	T	T	23	23	NOS1	T	1	1
LRTM2	654429	broad.mit.edu	36	12	1814081	1814081	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:1814081G>A	uc001qjt.1	+	c.1046G>A	c.(1045-1047)CGC>CAC	p.R349H	CACNA2D4_uc001qjp.1_Intron|CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron|CACNA2D4_uc009zdr.1_Intron|LRTM2_uc001qju.1_Missense_Mutation_p.R349H|LRTM2_uc001qjv.1_Missense_Mutation_p.R111H	NM_001039029	NP_001034118	Q8N967	LRTM2_HUMAN	leucine-rich repeats and transmembrane domains	349	Cytoplasmic (Potential).					integral to membrane				large_intestine(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000834)											0.625	12.780086	12.893612	5	3	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1814081	1814081	9421	12	G	A	A	38	38	LRTM2	A	1	1
ADAMTS20	80070	broad.mit.edu	36	12	42231152	42231152	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:42231152T>G	uc001rnn.1	-	c.280A>C	c.(280-282)ACC>CCC	p.T94P		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	94						proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)					p.T94S(LS411N-Tumor)	2149				0.25	8.093278	9.002681	4	12	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42231152	42231152	267	12	T	G	G	58	58	ADAMTS20	G	4	4
KCNA5	3741	broad.mit.edu	36	12	5024477	5024477	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5024477C>G	uc001qni.1	+	c.903C>G	c.(901-903)AGC>AGG	p.S301R		NM_002234	NP_002225	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related	301						Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(2)|breast(2)	4														0.285714	6.784807	7.368978	4	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5024477	5024477	8311	12	C	G	G	27	27	KCNA5	G	3	3
DGKH	160851	broad.mit.edu	36	13	41640929	41640929	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:41640929C>G	uc001uyl.1	+	c.1342C>G	c.(1342-1344)CGA>GGA	p.R448G	DGKH_uc001uym.1_Missense_Mutation_p.R448G|DGKH_uc001uyn.1_Non-coding_Transcript|DGKH_uc001uyo.1_Missense_Mutation_p.R303G|DGKH_uc001uyp.2_Non-coding_Transcript	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	448	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)										0.156863	9.627689	15.314048	8	43	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41640929	41640929	4649	13	C	G	G	19	19	DGKH	G	3	3
RB1	5925	broad.mit.edu	36	13	47935867	47935867	+	Splice_Site_SNP	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:47935867G>A	uc001vcb.1	+	c.e21_splice_site				NM_000321	NP_000312			retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|transcription repressor activity|ubiquitin protein ligase binding	p.?(1)		lung(93)|eye(89)|central_nervous_system(47)|bone(22)|breast(20)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|soft_tissue(8)|prostate(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	355		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)			6		568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.540541	136.706632	136.812523	40	34	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	47935867	47935867	13559	13	G	A	A	33	33	RB1	A	5	2
CHD8	57680	broad.mit.edu	36	14	20966183	20966183	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:20966183G>C	uc001was.1	-	c.449C>G	c.(448-450)GCT>GGT	p.A150G	CHD8_uc001war.1_Missense_Mutation_p.A46G	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	429					ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|chromatin assembly or disassembly|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	chromatin|MLL1 complex	ATP binding|beta-catenin binding|chromatin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding|transcription activator activity|transcription repressor activity			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)						886				0.307692	6.487137	6.920749	4	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20966183	20966183	3465	14	G	C	C	34	34	CHD8	C	3	3
EFS	10278	broad.mit.edu	36	14	22896319	22896319	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:22896319G>C	uc001wjo.1	-	c.1642C>G	c.(1642-1644)CAG>GAG	p.Q548E	EFS_uc001wjp.1_Missense_Mutation_p.Q455E	NM_005864	NP_005855	O43281	EFS_HUMAN	embryonal Fyn-associated substrate isoform 1	548					cell adhesion|intracellular signal transduction	cytoplasm	SH3 domain binding			large_intestine(1)	1	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)										0.272727	6.41763	6.931804	3	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22896319	22896319	5148	14	G	C	C	46	46	EFS	C	3	3
NPAS3	64067	broad.mit.edu	36	14	33313489	33313489	+	Splice_Site_SNP	SNP	T	A	A			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:33313489T>A	uc001wru.1	+	c.e8_splice_site			NPAS3_uc001wrt.1_Splice_Site_SNP|NPAS3_uc001wrv.1_Splice_Site_SNP|NPAS3_uc001wrs.1_Splice_Site_SNP	NM_022123	NP_071406			neuronal PAS domain protein 3 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity|transcription regulator activity			ovary(1)	1	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)										0.3	85.333417	89.264288	33	77	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	33313489	33313489	10968	14	T	A	A	57	57	NPAS3	A	5	4
SLC8A3	6547	broad.mit.edu	36	14	69587524	69587524	+	Silent	SNP	G	T	T			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:69587524G>T	uc001xly.1	-	c.2085C>A	c.(2083-2085)ACC>ACA	p.T695T	SLC8A3_uc001xlu.1_Silent_p.T52T|SLC8A3_uc001xlv.1_Silent_p.T66T|SLC8A3_uc001xlw.1_Silent_p.T692T|SLC8A3_uc001xlx.1_Silent_p.T693T|SLC8A3_uc001xlz.1_Silent_p.T689T|SLC8A3_uc010ara.1_Non-coding_Transcript|SLC8A3_uc001xma.1_Silent_p.T52T	NM_183002	NP_892114	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium	695	Cytoplasmic (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			ovary(2)|breast(2)	4				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)										0.375427	331.987869	335.97514	110	183	GG		KEEP	---	---	---	---	capture			Silent	SNP	69587524	69587524	15205	14	G	T	T	43	43	SLC8A3	T	3	3
PSEN1	5663	broad.mit.edu	36	14	72753690	72753690	+	Silent	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:72753690C>T	uc001xnr.1	+	c.1233C>T	c.(1231-1233)TTC>TTT	p.F411F	PSEN1_uc001xns.1_Silent_p.F407F|PSEN1_uc010ark.1_Silent_p.F407F|PSEN1_uc001xnt.1_Non-coding_Transcript|PSEN1_uc001xnu.1_Non-coding_Transcript	NM_000021	NP_000012	P49768	PSN1_HUMAN	presenilin 1 isoform I-467	411	Required for interaction with CTNNB1.|Helical; (Potential).				amyloid precursor protein catabolic process|anti-apoptosis|beta-amyloid metabolic process|cell-cell adhesion|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|smooth endoplasmic reticulum calcium ion homeostasis	apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|gamma-secretase complex|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum|smooth endoplasmic reticulum|Z disc	beta-catenin binding|cadherin binding|calcium channel activity|endopeptidase activity|PDZ domain binding			kidney(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075)						189				0.16	7.622731	24.628685	24	126	CC		KEEP	---	---	---	---	capture			Silent	SNP	72753690	72753690	13103	14	C	T	T	31	31	PSEN1	T	1	1
RYR3	6263	broad.mit.edu	36	15	31829768	31829768	+	Silent	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:31829768C>T	uc001zhi.1	+	c.8388C>T	c.(8386-8388)ATC>ATT	p.I2796I	RYR3_uc010bar.1_Silent_p.I2796I	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2796	4.|Cytoplasmic (By similarity).|4 X approximate repeats.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)										0.319672	107.675606	111.204137	39	83	CC		KEEP	---	---	---	---	capture			Silent	SNP	31829768	31829768	14250	15	C	T	T	29	29	RYR3	T	2	2
PLCB2	5330	broad.mit.edu	36	15	38374543	38374543	+	Missense_Mutation	SNP	G	A	A	rs61755438	unknown	TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:38374543G>A	uc001zld.1	-	c.1792C>T	c.(1792-1794)CGC>TGC	p.R598C	PLCB2_uc010bbo.1_Missense_Mutation_p.R594C	NM_004573	NP_004564	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	598	PI-PLC Y-box.				activation of phospholipase C activity|intracellular signal transduction|lipid catabolic process|phospholipid metabolic process|synaptic transmission	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(3)|breast(3)|kidney(1)|pancreas(1)	8		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)					p.R598C(HCC2157-Tumor)	1073				0.52809	138.913106	138.973538	47	42	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38374543	38374543	12454	15	G	A	A	38	38	PLCB2	A	1	1
IL16	3603	broad.mit.edu	36	15	79359041	79359041	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:79359041T>C	uc002bgh.2	+	c.952T>C	c.(952-954)TGC>CGC	p.C318R	IL16_uc002bgc.2_Non-coding_Transcript|IL16_uc010blq.1_Missense_Mutation_p.C318R|IL16_uc002bge.2_Non-coding_Transcript|IL16_uc002bgg.1_Missense_Mutation_p.C318R|IL16_uc002bgi.1_5'UTR	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	318	Interaction with GRIN2A.				immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4														0.423077	33.92125	34.055285	11	15	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79359041	79359041	7934	15	T	C	C	59	59	IL16	C	4	4
UNC45A	55898	broad.mit.edu	36	15	89292056	89292056	+	Silent	SNP	A	G	G			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:89292056A>G	uc002bqg.1	+	c.1527A>G	c.(1525-1527)GGA>GGG	p.G509G	UNC45A_uc002bqd.1_Silent_p.G494G|UNC45A_uc002bqi.1_5'Flank	NM_018671	NP_061141	Q9H3U1	UN45A_HUMAN	smooth muscle cell associated protein-1 isoform	509					cell differentiation|muscle organ development	nucleus|perinuclear region of cytoplasm	protein binding			ovary(2)	2	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)											0.32	7.06368	7.915988	8	17	AA		KEEP	---	---	---	---	capture			Silent	SNP	89292056	89292056	17546	15	A	G	G	11	11	UNC45A	G	4	4
ADAMTS17	170691	broad.mit.edu	36	15	98513002	98513002	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:98513002A>C	uc002bvv.1	-	c.1228T>G	c.(1228-1230)TCC>GCC	p.S410A	ADAMTS17_uc002bvx.1_Missense_Mutation_p.S167A	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1	410	Peptidase M12B.				proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)										0.25	6.50588	9.605931	12	36	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	98513002	98513002	263	15	A	C	C	10	10	ADAMTS17	C	4	4
CDH13	1012	broad.mit.edu	36	16	82193614	82193614	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:82193614C>G	uc002fgx.1	+	c.1015C>G	c.(1015-1017)CTG>GTG	p.L339V		NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein	339	Cadherin 2.				adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)										0.2	10.113376	12.65443	6	24	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82193614	82193614	3228	16	C	G	G	20	20	CDH13	G	3	3
SLC6A4	6532	broad.mit.edu	36	17	25560349	25560349	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:25560349G>A	uc002hey.2	-	c.1487C>T	c.(1486-1488)GCC>GTC	p.A496V	SLC6A4_uc010csg.1_Intron	NM_001045	NP_001036	P31645	SC6A4_HUMAN	solute carrier family 6 member 4	496					response to toxin|serotonin uptake|thalamus development	cytosol|endomembrane system|endosome membrane|integral to plasma membrane|membrane raft	actin filament binding|Rab GTPase binding|serotonin transmembrane transporter activity|serotonin:sodium symporter activity			ovary(1)	1					Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Doxepin(DB01142)|Duloxetine(DB00476)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Minaprine(DB00805)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phentermine(DB00191)|Protriptyline(DB00344)|Sertraline(DB01104)|Sibutramine(DB01105)|Tegaserod(DB01079)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Zimelidine(DB04832)									0.333333	12.868285	13.238153	5	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25560349	25560349	15183	17	G	A	A	42	42	SLC6A4	A	2	2
KRT222	125113	broad.mit.edu	36	17	36071741	36071741	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36071741G>A	uc002hvc.2	-	c.178C>T	c.(178-180)CGC>TGC	p.R60C	KRT222_uc002hvb.2_Missense_Mutation_p.R20C|KRT222_uc010cxc.1_Missense_Mutation_p.R20C	NM_152349	NP_689562	Q8N1A0	KT222_HUMAN	truncated type I keratin KA21	60	Potential.					intermediate filament	structural molecule activity	p.R60C(1)		central_nervous_system(1)	1														0.320988	71.823906	74.128358	26	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36071741	36071741	8774	17	G	A	A	40	40	KRT222	A	1	1
KRT19	3880	broad.mit.edu	36	17	36937646	36937646	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36937646T>G	uc002hxd.2	-	c.380A>C	c.(379-381)TAC>TCC	p.Y127S		NM_002276	NP_002267	P08727	K1C19_HUMAN	keratin 19	127	Linker 1.|Rod.				interspecies interaction between organisms|response to estrogen stimulus|sarcomere organization	costamere|intermediate filament	protein binding|structural constituent of cytoskeleton|structural constituent of muscle				0		Breast(137;0.00038)												0.571429	11.90059	11.93185	4	3	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36937646	36937646	8771	17	T	G	G	57	57	KRT19	G	4	4
ACLY	47	broad.mit.edu	36	17	37297388	37297388	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:37297388C>G	uc002hyi.1	-	c.2027G>C	c.(2026-2028)GGA>GCA	p.G676A	ACLY_uc002hyg.1_Missense_Mutation_p.G622A|ACLY_uc002hyh.1_Missense_Mutation_p.G612A	NM_001096	NP_001087	P53396	ACLY_HUMAN	ATP citrate lyase isoform 1	622					ATP catabolic process|cellular carbohydrate metabolic process|citrate metabolic process|coenzyme A metabolic process|energy reserve metabolic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	citrate lyase complex|cytosol|nucleus	ATP binding|ATP citrate synthase activity|citrate (pro-3S)-lyase activity|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			ovary(2)|central_nervous_system(1)	3		Breast(137;0.000143)				Colon(64;807 1396 15971 30971)								0.275862	30.441295	33.028049	16	42	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37297388	37297388	144	17	C	G	G	30	30	ACLY	G	3	3
KCNH4	23415	broad.mit.edu	36	17	37575708	37575708	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:37575708C>T	uc002hzb.1	-	c.1333G>A	c.(1333-1335)GTG>ATG	p.V445M		NM_012285	NP_036417	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H,	445					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)								0.333333	20.518195	21.034711	7	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37575708	37575708	8339	17	C	T	T	19	19	KCNH4	T	1	1
TM4SF5	9032	broad.mit.edu	36	17	4632992	4632992	+	Silent	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:4632992C>T	uc002fyw.1	+	c.492C>T	c.(490-492)GCC>GCT	p.A164A		NM_003963	NP_003954	O14894	T4S5_HUMAN	transmembrane 4 superfamily member 5	164	Helical; (Potential).					integral to plasma membrane				ovary(1)	1														0.428571	82.83756	83.148702	30	40	CC		KEEP	---	---	---	---	capture			Silent	SNP	4632992	4632992	16501	17	C	T	T	23	23	TM4SF5	T	1	1
DGKE	8526	broad.mit.edu	36	17	52267518	52267518	+	Silent	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:52267518C>T	uc002iur.1	+	c.363C>T	c.(361-363)GAC>GAT	p.D121D	DGKE_uc002ius.1_Silent_p.D121D|C17orf67_uc002iuq.1_5'Flank	NM_003647	NP_003638	P52429	DGKE_HUMAN	diacylglycerol kinase epsilon	121					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|phospholipid biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding|protein binding			breast(2)	2	Breast(9;3.59e-07)													0.176829	60.297736	76.420645	29	135	CC		KEEP	---	---	---	---	capture			Silent	SNP	52267518	52267518	4647	17	C	T	T	19	19	DGKE	T	1	1
ENGASE	64772	broad.mit.edu	36	17	74592331	74592331	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:74592331G>C	uc002jwv.1	+	c.1559G>C	c.(1558-1560)AGC>ACC	p.S520T	ENGASE_uc002jww.1_Missense_Mutation_p.S226T	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	520						cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity				0														0.206897	6.566477	8.866779	6	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74592331	74592331	5311	17	G	C	C	34	34	ENGASE	C	3	3
PFAS	5198	broad.mit.edu	36	17	8109949	8109949	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:8109949G>C	uc002gkr.1	+	c.2590G>C	c.(2590-2592)GGG>CGG	p.G864R	PFAS_uc002gks.2_5'UTR	NM_012393	NP_036525	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	864					'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)									0.272727	6.950448	8.053973	6	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8109949	8109949	12176	17	G	C	C	39	39	PFAS	C	3	3
MBD1	4152	broad.mit.edu	36	18	46054222	46054222	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:46054222G>C	uc002lem.2	-	c.1156C>G	c.(1156-1158)CTG>GTG	p.L386V	MBD1_uc002lef.2_Missense_Mutation_p.L137V|MBD1_uc010dow.1_Missense_Mutation_p.L386V|MBD1_uc002leg.2_Missense_Mutation_p.L336V|MBD1_uc002leh.2_Missense_Mutation_p.L330V|MBD1_uc002lei.2_Missense_Mutation_p.L386V|MBD1_uc002lej.2_Missense_Mutation_p.L330V|MBD1_uc002lek.2_Missense_Mutation_p.L337V|MBD1_uc002lel.2_Missense_Mutation_p.L363V|MBD1_uc002len.2_Missense_Mutation_p.L386V|MBD1_uc010dox.1_Missense_Mutation_p.L363V|MBD1_uc002leo.2_Missense_Mutation_p.L386V	NM_015846	NP_056671	Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1 isoform 1	386					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|nuclear speck	methyl-CpG binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription repressor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.307692	6.889249	7.321551	4	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46054222	46054222	9726	18	G	C	C	34	34	MBD1	C	3	3
CNDP1	84735	broad.mit.edu	36	18	70379185	70379185	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:70379185C>T	uc002llq.1	+	c.418C>T	c.(418-420)CGG>TGG	p.R140W		NM_032649	NP_116038	Q96KN2	CNDP1_HUMAN	carnosinase 1	140					proteolysis	extracellular region	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity|tripeptidase activity				0		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		Melanoma(32;1029 1042 25286 38395 44237)								0.424242	44.245448	44.41045	14	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70379185	70379185	3731	18	C	T	T	23	23	CNDP1	T	1	1
AP1M2	10053	broad.mit.edu	36	19	10553477	10553477	+	Silent	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10553477G>A	uc002mpd.1	-	c.345C>T	c.(343-345)GAC>GAT	p.D115D	AP1M2_uc002mpc.1_Silent_p.D115D	NM_005498	NP_005489	Q9Y6Q5	AP1M2_HUMAN	adaptor-related protein complex 1, mu 2 subunit	115					cellular membrane organization|post-Golgi vesicle-mediated transport|protein targeting|regulation of defense response to virus by virus|vesicle targeting|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding			ovary(2)	2			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)											0.371429	39.068118	39.575538	13	22	GG		KEEP	---	---	---	---	capture			Silent	SNP	10553477	10553477	745	19	G	A	A	40	40	AP1M2	A	1	1
BRD4	23476	broad.mit.edu	36	19	15237285	15237285	+	Silent	SNP	A	G	G			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15237285A>G	uc002nar.1	-	c.729T>C	c.(727-729)CCT>CCC	p.P243P	BRD4_uc002nas.1_Silent_p.P243P|BRD4_uc002nat.2_Silent_p.P243P|BRD4_uc002nau.2_Silent_p.P243P	NM_058243	NP_490597	O60885	BRD4_HUMAN	bromodomain-containing protein 4 isoform long	243					interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of gene-specific transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)							269				0.307692	7.089176	7.521679	4	9	AA		KEEP	---	---	---	---	capture			Silent	SNP	15237285	15237285	1535	19	A	G	G	11	11	BRD4	G	4	4
ACTN4	81	broad.mit.edu	36	19	43900467	43900467	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:43900467C>G	uc002oja.1	+	c.1204C>G	c.(1204-1206)CTG>GTG	p.L402V	ACTN4_uc010egc.1_Missense_Mutation_p.L402V	NM_004924	NP_004915	O43707	ACTN4_HUMAN	actinin, alpha 4	402	Spectrin 1.				platelet activation|platelet degranulation|positive regulation of cellular component movement|positive regulation of sodium:hydrogen antiporter activity|protein transport|regulation of apoptosis	extracellular region|nucleolus|perinuclear region of cytoplasm|platelet alpha granule lumen|protein complex|pseudopodium|ribonucleoprotein complex	actin filament binding|calcium ion binding|integrin binding|nucleoside binding|protein homodimerization activity				0	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			Colon(168;199 1940 10254 46213 46384)								0.5	8.667471	8.667471	4	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43900467	43900467	208	19	C	G	G	28	28	ACTN4	G	3	3
PLEKHA4	57664	broad.mit.edu	36	19	54062604	54062604	+	Splice_Site_SNP	SNP	A	G	G			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54062604A>G	uc002pkx.1	-	c.e2_splice_site			PLEKHA4_uc010eml.1_Splice_Site_SNP	NM_020904	NP_065955			pleckstrin homology domain containing, family A							cytoplasm|membrane	1-phosphatidylinositol binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)										0.571429	14.801198	14.832343	4	3	AA		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	54062604	54062604	12484	19	A	G	G	2	2	PLEKHA4	G	5	4
ZNF471	57573	broad.mit.edu	36	19	61728242	61728242	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61728242T>C	uc002qnh.1	+	c.994T>C	c.(994-996)TCT>CCT	p.S332P		NM_020813	NP_065864	Q9BX82	ZN471_HUMAN	zinc finger protein 471	332	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)								0.27027	21.62927	23.394852	10	27	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61728242	61728242	18524	19	T	C	C	58	58	ZNF471	C	4	4
DCST2	127579	broad.mit.edu	36	1	153270838	153270838	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153270838A>G	uc001fgm.1	-	c.575T>C	c.(574-576)CTG>CCG	p.L192P	DCST2_uc009wpb.1_Non-coding_Transcript|DCST1_uc001fgn.1_5'Flank	NM_144622	NP_653223	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	192	Cytoplasmic (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)											0.375	14.245631	14.465099	6	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153270838	153270838	4474	1	A	G	G	7	7	DCST2	G	4	4
SPTA1	6708	broad.mit.edu	36	1	156889026	156889026	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156889026C>T	uc001fst.1	-	c.3230G>A	c.(3229-3231)CGT>CAT	p.R1077H		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1077					actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.377049	140.32406	141.941026	46	76	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156889026	156889026	15630	1	C	T	T	19	19	SPTA1	T	1	1
CACNA1S	779	broad.mit.edu	36	1	199313796	199313796	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199313796C>T	uc001gvv.1	-	c.1453G>A	c.(1453-1455)GGG>AGG	p.G485R		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	485	Helical; Name=S2 of repeat II; (Potential).|II.				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)	4					Magnesium Sulfate(DB00653)|Verapamil(DB00661)									0.357333	398.356389	405.073922	134	241	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	199313796	199313796	2663	1	C	T	T	23	23	CACNA1S	T	1	1
CHIT1	1118	broad.mit.edu	36	1	201455576	201455576	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:201455576G>C	uc001gzn.2	-	c.754C>G	c.(754-756)CAG>GAG	p.Q252E	CHIT1_uc001gzm.1_Non-coding_Transcript|CHIT1_uc009xal.1_Missense_Mutation_p.Q43E|CHIT1_uc009xam.1_Non-coding_Transcript|CHIT1_uc009xan.1_Non-coding_Transcript|CHIT1_uc001gzo.2_Missense_Mutation_p.Q243E	NM_003465	NP_003456	Q13231	CHIT1_HUMAN	chitotriosidase	252					chitin catabolic process|immune response|response to bacterium	extracellular space|lysosome	cation binding|chitin binding|endochitinase activity				0												OREG0006436	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=CHIT1|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	0.285714	7.702345	8.274898	4	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	201455576	201455576	3480	1	G	C	C	46	46	CHIT1	C	3	3
MARK1	4139	broad.mit.edu	36	1	218902129	218902129	+	Nonstop_Mutation	SNP	T	G	G			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:218902129T>G	uc009xdw.1	+	c.2389T>G	c.(2389-2391)TAA>GAA	p.*797E	MARK1_uc001hmn.2_Nonstop_Mutation_p.*796E|MARK1_uc001hmm.2_Nonstop_Mutation_p.*759E|MARK1_uc001hmo.2_Nonstop_Mutation_p.*646E	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	797					intracellular protein kinase cascade|protein phosphorylation	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|central_nervous_system(2)|stomach(1)|lung(1)	7				GBM - Glioblastoma multiforme(131;0.0407)						258				0.230769	14.403818	17.862226	12	40	TT		KEEP	---	---	---	---	capture			Nonstop_Mutation	SNP	218902129	218902129	9695	1	T	G	G	57	57	MARK1	G	5	4
GRHL3	57822	broad.mit.edu	36	1	24535819	24535819	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:24535819T>C	uc001biy.1	+	c.542T>C	c.(541-543)CTC>CCC	p.L181P	GRHL3_uc001bix.1_Missense_Mutation_p.L176P|GRHL3_uc001biz.1_Missense_Mutation_p.L83P	NM_021180	NP_067003	Q8TE85	GRHL3_HUMAN	sister-of-mammalian grainyhead protein isoform	176					regulation of actin cytoskeleton organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)										0.222222	8.292186	9.569441	4	14	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24535819	24535819	7043	1	T	C	C	54	54	GRHL3	C	4	4
LRP8	7804	broad.mit.edu	36	1	53509575	53509575	+	Silent	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:53509575G>C	uc001cvi.1	-	c.1038C>G	c.(1036-1038)GGC>GGG	p.G346G	LRP8_uc001cvh.1_5'UTR|LRP8_uc001cvk.1_Silent_p.G176G|LRP8_uc001cvj.1_Silent_p.G346G|LRP8_uc001cvl.1_Silent_p.G217G|LRP8_uc001cvm.1_5'Flank	NM_004631	NP_004622	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein	346	EGF-like 1.|Extracellular (Potential).				cytokine-mediated signaling pathway|endocytosis|lipid metabolic process|platelet activation|proteolysis	caveola|integral to membrane	apolipoprotein E binding|calcium ion binding|very-low-density lipoprotein particle receptor activity				0														0.363636	9.294488	9.475365	4	7	GG		KEEP	---	---	---	---	capture			Silent	SNP	53509575	53509575	9336	1	G	C	C	34	34	LRP8	C	3	3
DMRTB1	63948	broad.mit.edu	36	1	53699847	53699847	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:53699847G>A	uc001cvq.1	+	c.691G>A	c.(691-693)GTC>ATC	p.V231I		NM_033067	NP_149056	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal,	231	Pro-rich.				regulation of transcription, DNA-dependent|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0														0.5	23.200436	23.200436	8	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53699847	53699847	4770	1	G	A	A	40	40	DMRTB1	A	1	1
WLS	79971	broad.mit.edu	36	1	68393379	68393379	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:68393379G>C	uc001dee.1	-	c.651C>G	c.(649-651)ATC>ATG	p.I217M	WLS_uc009wbf.1_Missense_Mutation_p.I174M|WLS_uc001def.1_Missense_Mutation_p.I219M|WLS_uc001deg.1_Missense_Mutation_p.I128M	NM_001002292	NP_001002292	Q5T9L3	WLS_HUMAN	G protein-coupled receptor 177 isoform 2	219	Lumenal (Potential).|Interacts with Wnt proteins (By similarity).				multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Wnt receptor signaling pathway	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	signal transducer activity				0										563				0.298539	452.7409	470.114742	143	336	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	68393379	68393379	17950	1	G	C	C	41	41	WLS	C	3	3
SLC25A33	84275	broad.mit.edu	36	1	9562833	9562833	+	Silent	SNP	T	G	G			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:9562833T>G	uc001apw.1	+	c.717T>G	c.(715-717)GCT>GCG	p.A239A	SLC25A33_uc001apx.1_Silent_p.A172A	NM_032315	NP_115691	Q9BSK2	S2533_HUMAN	mitochondrial carrier protein MGC4399	239	Solcar 3.|Helical; Name=5; (Potential).				transport	integral to membrane|mitochondrial inner membrane					0	all_lung(157;0.246)	all_epithelial(116;1.16e-18)|all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Breast(348;0.00191)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.44e-05)|Kidney(185;0.000262)|KIRC - Kidney renal clear cell carcinoma(229;0.000957)|BRCA - Breast invasive adenocarcinoma(304;0.0019)|STAD - Stomach adenocarcinoma(132;0.00355)|READ - Rectum adenocarcinoma(331;0.0419)										0.26087	15.058856	18.965222	18	51	TT		KEEP	---	---	---	---	capture			Silent	SNP	9562833	9562833	14994	1	T	G	G	55	55	SLC25A33	G	4	4
VPS16	64601	broad.mit.edu	36	20	2792691	2792691	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:2792691C>G	uc002whe.1	+	c.1573C>G	c.(1573-1575)CGA>GGA	p.R525G	PTPRA_uc002whj.1_5'Flank|VPS16_uc002whf.1_Missense_Mutation_p.R381G|VPS16_uc002whd.1_Non-coding_Transcript|VPS16_uc002whg.1_Missense_Mutation_p.R211G|VPS16_uc002whh.1_Non-coding_Transcript|VPS16_uc002whi.1_5'UTR	NM_022575	NP_072097	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 isoform 1	525					intracellular protein transport	early endosome|HOPS complex|late endosome membrane|lysosomal membrane|recycling endosome				ovary(2)|pancreas(1)	3														0.25	6.418321	7.100949	3	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2792691	2792691	17760	20	C	G	G	19	19	VPS16	G	3	3
FAM83C	128876	broad.mit.edu	36	20	33343010	33343010	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33343010G>A	uc002xca.1	-	c.512C>T	c.(511-513)ACG>ATG	p.T171M	FAM83C_uc002xcb.1_De_novo_Start_OutOfFrame	NM_178468	NP_848563	Q9BQN1	FA83C_HUMAN	hypothetical protein LOC128876	171										ovary(2)	2			BRCA - Breast invasive adenocarcinoma(18;0.00252)											0.285714	16.441838	17.306864	6	15	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33343010	33343010	5861	20	G	A	A	40	40	FAM83C	A	1	1
SIGLEC1	6614	broad.mit.edu	36	20	3617237	3617237	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:3617237C>G	uc002wja.1	-	c.5100G>C	c.(5098-5100)GAG>GAC	p.E1700D	SIGLEC1_uc002wiz.2_Missense_Mutation_p.R1676T|SIGLEC1_uc002wjb.1_3'UTR	NM_023068	NP_075556	Q9BZZ2	SN_HUMAN	sialoadhesin precursor	1700	Cytoplasmic (Potential).				cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding			pancreas(4)|ovary(2)|breast(1)|central_nervous_system(1)	8														0.160714	11.632343	17.78071	9	47	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3617237	3617237	14800	20	C	G	G	32	32	SIGLEC1	G	3	3
TSHZ2	128553	broad.mit.edu	36	20	51305884	51305884	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:51305884G>A	uc002xwo.2	+	c.2480G>A	c.(2479-2481)CGC>CAC	p.R827H		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	827					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(23;0.1)											0.435644	131.68275	132.04768	44	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51305884	51305884	17175	20	G	A	A	38	38	TSHZ2	A	1	1
KRTAP6-3	337968	broad.mit.edu	36	21	30886716	30886716	+	Silent	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:30886716C>T	uc002yom.1	+	c.81C>T	c.(79-81)TAC>TAT	p.Y27Y		NM_181605	NP_853636			keratin associated protein 6-3												0														0.48	76.603991	76.620854	24	26	CC		KEEP	---	---	---	---	capture			Silent	SNP	30886716	30886716	8893	21	C	T	T	19	19	KRTAP6-3	T	1	1
MORC3	23515	broad.mit.edu	36	21	36663194	36663194	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:36663194A>G	uc002yvi.1	+	c.1658A>G	c.(1657-1659)AAT>AGT	p.N553S		NM_015358	NP_056173	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	553					cell aging|maintenance of protein location in nucleus|negative regulation of fibroblast proliferation|peptidyl-serine phosphorylation|protein stabilization	aggresome|intermediate filament cytoskeleton|PML body	ATP binding|zinc ion binding			ovary(2)	2														0.488889	76.549475	76.554284	22	23	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36663194	36663194	10094	21	A	G	G	4	4	MORC3	G	4	4
TTC3	7267	broad.mit.edu	36	21	37482668	37482668	+	Silent	SNP	A	G	G			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:37482668A>G	uc002yvz.1	+	c.4926A>G	c.(4924-4926)GTA>GTG	p.V1642V	TTC3_uc002ywa.1_Silent_p.V1642V|TTC3_uc002ywb.1_Silent_p.V1642V|TTC3_uc010gnf.1_Silent_p.V1407V|TTC3_uc002ywc.1_Silent_p.V1332V	NM_001001894	NP_003307	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1642					protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|breast(1)	3		Myeloproliferative disorder(46;0.0412)				Ovarian(38;194 1649 35661)								0.185185	7.96357	10.471438	5	22	AA		KEEP	---	---	---	---	capture			Silent	SNP	37482668	37482668	17252	21	A	G	G	16	16	TTC3	G	4	4
UPB1	51733	broad.mit.edu	36	22	23249619	23249619	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:23249619A>C	uc003aaf.1	+	c.949A>C	c.(949-951)AGC>CGC	p.S317R	UPB1_uc003aae.1_Missense_Mutation_p.S249R|UPB1_uc010gur.1_Non-coding_Transcript	NM_016327	NP_057411	Q9UBR1	BUP1_HUMAN	beta-ureidopropionase	317	CN hydrolase.				pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	beta-ureidopropionase activity|metal ion binding			ovary(2)	2	Colorectal(2;0.0339)													0.12069	6.889709	15.070731	7	51	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23249619	23249619	17561	22	A	C	C	11	11	UPB1	C	4	4
CBY1	25776	broad.mit.edu	36	22	37397040	37397040	+	Silent	SNP	T	G	G			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:37397040T>G	uc003awb.1	+	c.204T>G	c.(202-204)GGT>GGG	p.G68G	CBY1_uc003awc.1_Silent_p.G68G	NM_001002880	NP_056188	Q9Y3M2	CBY1_HUMAN	PKD2 interactor, golgi and endoplasmic reticulum	68	Minimal region for the interaction with PKD2.|Potential.				cardiac muscle cell differentiation|fat cell differentiation|negative regulation of transcription, DNA-dependent|protein localization	nuclear speck|trans-Golgi network	beta-catenin binding|identical protein binding			ovary(1)	1	Melanoma(58;0.04)													0.538462	17.818848	17.8353	7	6	TT		KEEP	---	---	---	---	capture			Silent	SNP	37397040	37397040	2844	22	T	G	G	59	59	CBY1	G	4	4
ROCK2	9475	broad.mit.edu	36	2	11278928	11278928	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:11278928G>C	uc002rbd.1	-	c.1106C>G	c.(1105-1107)GCT>GGT	p.A369G		NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein	369	AGC-kinase C-terminal.				axon guidance|cytokinesis|intracellular signal transduction|protein phosphorylation	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			skin(2)|stomach(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)					p.A369G(SHSY5Y-Tumor)|p.A369G(PECAPJ41CLONED2-Tumor)|p.A369G(OE33-Tumor)|p.A369G(SNU478-Tumor)|p.A369G(T3M4-Tumor)|p.A369G(JHH6-Tumor)|p.A369G(A172-Tumor)|p.A369G(CAS1-Tumor)|p.A369G(NCIH3255-Tumor)|p.A369G(HCC827-Tumor)|p.A369G(SNU81-Tumor)|p.A369G(PFEIFFER-Tumor)|p.A369G(KE37-Tumor)|p.A369G(HS895.T-Tumor)|p.A369G(SKM1-Tumor)|p.A369G(SNUC2A-Tumor)|p.A369G(KMRC3-Tumor)|p.A369G(SNU1040-Tumor)|p.A369G(HUH6-Tumor)|p.A369G(HH-Tumor)|p.A369G(HCT116-Tumor)|p.A369G(NCIH1944-Tumor)|p.A369G(SNU1214-Tumor)|p.A369G(NCIH1355-Tumor)|p.A369G(HLF-Tumor)|p.A369G(SNU1105-Tumor)|p.A369G(YD15-Tumor)|p.A369G(SKNSH-Tumor)|p.A369G(U266B1-Tumor)|p.A369G(SNU719-Tumor)|p.A369G(SNU245-Tumor)|p.A369G(CORL95-Tumor)|p.A369G(HS742.T-Tumor)|p.A369G(SNU213-Tumor)|p.A369G(NCIH854-Tumor)|p.A369G(HT1376-Tumor)|p.A369G(LXF289-Tumor)|p.A369G(RPMI8226-Tumor)|p.A369G(697-Tumor)|p.A369G(SKHEP1-Tumor)|p.A369G(LI7-Tumor)|p.A369G(HS604.T-Tumor)|p.A369G(SNU349-Tumor)|p.A369G(JVM3-Tumor)|p.A369G(NCIH1573-Tumor)|p.A369G(JHOM2B-Tumor)|p.A369G(MUTZ3-Tumor)|p.A369G(SBC5-Tumor)|p.A369G(C2BBE1-Tumor)|p.A369G(NCIH1793-Tumor)|p.A369G(COLO320-Tumor)|p.A369G(NCIH82-Tumor)|p.A369G(HS839.T-Tumor)|p.A369G(SW620-Tumor)|p.A369G(HS834.T-Tumor)|p.A369G(RD-Tumor)|p.A369G(MFE280-Tumor)|p.A369G(HEPG2-Tumor)|p.A369G(SNU1197-Tumor)|p.A369G(SNU46-Tumor)|p.A369G(HS766T-Tumor)|p.A369G(CAL62-Tumor)|p.A369G(HS934.T-Tumor)|p.A369G(8MGBA-Tumor)|p.A369G(TE4-Tumor)|p.A369G(OVK18-Tumor)|p.A369G(HS688A.T-Tumor)|p.A369G(SNU1-Tumor)|p.A369G(TGBC11TKB-Tumor)|p.A369G(HSC3-Tumor)|p.A369G(CAOV4-Tumor)|p.A369G(NCIH1437-Tumor)|p.A369G(HS819.T-Tumor)|p.A369G(SNUC5-Tumor)|p.A369G(ALEXANDERCELLS-Tumor)|p.A369G(COLO792-Tumor)|p.A369G(SNU308-Tumor)	587				0.235294	16.384255	18.563764	8	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11278928	11278928	13997	2	G	C	C	34	34	ROCK2	C	3	3
CFC1B	653275	broad.mit.edu	36	2	131072720	131072720	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:131072720T>C	uc002tro.1	-	c.212A>G	c.(211-213)GAG>GGG	p.E71G		NM_001079530	NP_115934	P0CG36	CFC1B_HUMAN	cripto, FRL-1, cryptic family 1B	71					gastrulation	extracellular region					0	Colorectal(110;0.1)													0.666667	15.747302	16.03069	8	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131072720	131072720	3413	2	T	C	C	54	54	CFC1B	C	4	4
SLC23A3	151295	broad.mit.edu	36	2	219735355	219735355	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219735355T>C	uc010fwb.1	-	c.1096A>G	c.(1096-1098)AGC>GGC	p.S366G	NHEJ1_uc002vjp.2_5'Flank|NHEJ1_uc002vjq.2_Non-coding_Transcript	NM_144712	NP_653313	Q6PIS1	S23A3_HUMAN	solute carrier family 23 (nucleobase	483	Extracellular (Potential).				transmembrane transport	integral to membrane	protein binding|transporter activity				0		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.230769	7.956783	10.662727	9	30	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	219735355	219735355	14961	2	T	C	C	54	54	SLC23A3	C	4	4
C2orf71	388939	broad.mit.edu	36	2	29147230	29147230	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:29147230T>G	uc002rmt.1	-	c.3402A>C	c.(3400-3402)AAA>AAC	p.K1134N		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	1134					response to stimulus|visual perception	photoreceptor outer segment					0														0.222222	7.285791	8.569374	4	14	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29147230	29147230	2279	2	T	G	G	60	60	C2orf71	G	4	4
BIRC6	57448	broad.mit.edu	36	2	32588322	32588322	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:32588322C>T	uc010ezu.1	+	c.9994C>T	c.(9994-9996)CGG>TGG	p.R3332W		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	3332					anti-apoptosis|apoptosis|post-translational protein modification	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					Pancreas(94;175 1509 16028 18060 45422)				1555				0.253165	44.561296	48.934628	20	59	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32588322	32588322	1463	2	C	T	T	19	19	BIRC6	T	1	1
MOGS	7841	broad.mit.edu	36	2	74545264	74545264	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:74545264T>C	uc010ffj.1	-	c.446A>G	c.(445-447)GAG>GGG	p.E149G	MOGS_uc010ffh.1_5'Flank|MOGS_uc010ffi.1_Missense_Mutation_p.E43G	NM_006302	NP_006293	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	149	Lumenal (Potential).				oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane|membrane fraction	mannosyl-oligosaccharide glucosidase activity				0														0.263158	7.06125	8.032892	5	14	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74545264	74545264	10088	2	T	C	C	54	54	MOGS	C	4	4
KIDINS220	57498	broad.mit.edu	36	2	8794459	8794459	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:8794459G>A	uc002qzc.1	-	c.3707C>T	c.(3706-3708)ACG>ATG	p.T1236M	KIDINS220_uc002qzb.1_Missense_Mutation_p.T90M|KIDINS220_uc002qzd.1_Missense_Mutation_p.T1137M	NM_020738	NP_065789	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate of 220 kDa	1236	Cytoplasmic (Potential).				activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)													0.404762	101.734077	102.399787	34	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8794459	8794459	8582	2	G	A	A	40	40	KIDINS220	A	1	1
PPP2R3A	5523	broad.mit.edu	36	3	137203272	137203272	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:137203272C>T	uc003eqv.1	+	c.242C>T	c.(241-243)TCG>TTG	p.S81L		NM_002718	NP_002709	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'',	81					protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(2)|pancreas(1)	3														0.382812	843.62678	852.849859	294	474	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	137203272	137203272	12824	3	C	T	T	31	31	PPP2R3A	T	1	1
IFT80	57560	broad.mit.edu	36	3	161469018	161469018	+	Silent	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:161469018C>T	uc010hwa.1	-	c.2100G>A	c.(2098-2100)AGG>AGA	p.R700R	IFT80_uc003fda.2_Non-coding_Transcript|IFT80_uc003fdb.1_Silent_p.R563R|IFT80_uc003fdd.1_Silent_p.R383R|IFT80_uc003fde.1_Silent_p.R563R|IFT80_uc010hwb.1_Silent_p.R700R	NM_020800	NP_065851	Q9P2H3	IFT80_HUMAN	WD repeat domain 56	700						cilium axoneme|microtubule basal body					0			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)											0.242718	65.023734	71.239922	25	78	CC		KEEP	---	---	---	---	capture			Silent	SNP	161469018	161469018	7865	3	C	T	T	22	22	IFT80	T	2	2
B3GNT5	84002	broad.mit.edu	36	3	184470596	184470596	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:184470596G>A	uc003flk.1	+	c.316G>A	c.(316-318)GGA>AGA	p.G106R	MCF2L2_uc003fli.1_Intron|MCF2L2_uc003flj.1_Intron|B3GNT5_uc003fll.1_Missense_Mutation_p.G106R|B3GNT5_uc003flm.1_Missense_Mutation_p.G106R|B3GNT5_uc010hxj.1_Missense_Mutation_p.G106R	NM_032047	NP_114436	Q9BYG0	B3GN5_HUMAN	UDP-GlcNAc:betaGal	106	Lumenal (Potential).				central nervous system development|glycolipid biosynthetic process|protein glycosylation	Golgi membrane|integral to membrane	beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity|galactosyltransferase activity			ovary(1)	1	all_cancers(143;8.52e-13)|Ovarian(172;0.0355)		all cancers(12;4.52e-44)|Epithelial(37;8.82e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)											0.3829	320.570545	323.801593	103	166	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	184470596	184470596	1281	3	G	A	A	39	39	B3GNT5	A	1	1
MCF2L2	23101	broad.mit.edu	36	3	184523746	184523746	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:184523746G>A	uc003fli.1	-	c.574C>T	c.(574-576)CGC>TGC	p.R192C	MCF2L2_uc003flj.1_Missense_Mutation_p.R192C|MCF2L2_uc003flp.1_Missense_Mutation_p.R227C	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor	192	CRAL-TRIO.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(1)|breast(1)	4	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)											0.401961	124.159849	125.015195	41	61	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	184523746	184523746	9769	3	G	A	A	37	37	MCF2L2	A	1	1
CNTN4	152330	broad.mit.edu	36	3	3056838	3056838	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:3056838G>A	uc003bpc.1	+	c.2281G>A	c.(2281-2283)GTG>ATG	p.V761M	CNTN4_uc003bpb.1_Missense_Mutation_p.V432M|CNTN4_uc003bpe.1_Missense_Mutation_p.V433M|CNTN4_uc003bpf.1_Missense_Mutation_p.V432M|CNTN4_uc003bpg.1_Missense_Mutation_p.V17M	NM_175607	NP_783302	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	761	Fibronectin type-III 2.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding	p.Y432Y(1)		large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)										0.358209	645.54515	656.215565	216	387	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3056838	3056838	3781	3	G	A	A	40	40	CNTN4	A	1	1
RBM6	10180	broad.mit.edu	36	3	49980097	49980097	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49980097G>A	uc003cyc.1	+	c.235G>A	c.(235-237)GAC>AAC	p.D79N	RBM6_uc010hlc.1_Intron|RBM6_uc003cyd.1_Intron|RBM6_uc003cye.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6	79					RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)										0.363636	189.709837	192.784236	68	119	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49980097	49980097	13606	3	G	A	A	33	33	RBM6	A	2	2
OR5K3	403277	broad.mit.edu	36	3	99592909	99592909	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99592909C>A	uc003dsl.1	+	c.710C>A	c.(709-711)TCT>TAT	p.S237Y		NM_001005516	NP_001005516	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K,	237	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.340599	372.646805	380.896513	125	242	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99592909	99592909	11578	3	C	A	A	32	32	OR5K3	A	3	3
ADH6	130	broad.mit.edu	36	4	100347653	100347653	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:100347653G>A	uc003huo.2	-	c.937C>T	c.(937-939)CGT>TGT	p.R313C	ADH6_uc003hup.2_Missense_Mutation_p.R313C|ADH6_uc010ile.1_Intron	NM_001102470	NP_001095940	P28332	ADH6_HUMAN	alcohol dehydrogenase 6 isoform 1	313					ethanol oxidation|response to ethanol|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|electron carrier activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)|NADH(DB00157)									0.4	382.040003	384.750039	124	186	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100347653	100347653	313	4	G	A	A	40	40	ADH6	A	1	1
UGT8	7368	broad.mit.edu	36	4	115816837	115816837	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:115816837C>T	uc003ibs.2	+	c.1570C>T	c.(1570-1572)CTC>TTC	p.L524F	UGT8_uc003ibt.2_Missense_Mutation_p.L524F	NM_001128174	NP_001121646	Q16880	CGT_HUMAN	UDP glycosyltransferase 8 (UDP-galactose	524					central nervous system development|peripheral nervous system development	integral to membrane	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity			ovary(1)	1		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)										0.279352	204.471069	215.283269	69	178	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115816837	115816837	17523	4	C	T	T	24	24	UGT8	T	2	2
ASB5	140458	broad.mit.edu	36	4	177427227	177427227	+	Silent	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:177427227C>T	uc003iuq.1	-	c.27G>A	c.(25-27)CCG>CCA	p.P9P		NM_080874	NP_543150	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box-containing protein	9					intracellular signal transduction						0		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)										0.423729	76.064703	76.364218	25	34	CC		KEEP	---	---	---	---	capture			Silent	SNP	177427227	177427227	1044	4	C	T	T	19	19	ASB5	T	1	1
PGM2	55276	broad.mit.edu	36	4	37528210	37528210	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:37528210C>A	uc003gta.1	+	c.1423C>A	c.(1423-1425)CAT>AAT	p.H475N		NM_018290	NP_060760	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	475					glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity|phosphopentomutase activity			ovary(1)	1														0.188679	10.20419	15.052639	10	43	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37528210	37528210	12221	4	C	A	A	21	21	PGM2	A	3	3
GEMIN5	25929	broad.mit.edu	36	5	154285638	154285638	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:154285638C>T	uc003lvx.2	-	c.1270G>A	c.(1270-1272)GGC>AGC	p.G424S		NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5	424	WD 8.				ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			ovary(1)|skin(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)											0.33913	116.485797	119.118942	39	76	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154285638	154285638	6599	5	C	T	T	24	24	GEMIN5	T	2	2
MGAT1	4245	broad.mit.edu	36	5	180152555	180152555	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:180152555C>T	uc003mmg.2	-	c.23G>A	c.(22-24)GGG>GAG	p.G8E	MGAT1_uc010jlf.1_Missense_Mutation_p.G8E|MGAT1_uc010jlg.1_Missense_Mutation_p.G8E|MGAT1_uc003mmh.2_Missense_Mutation_p.G8E|MGAT1_uc010jlh.1_Missense_Mutation_p.G8E|MGAT1_uc003mmi.2_Missense_Mutation_p.G8E|MGAT1_uc010jli.1_Missense_Mutation_p.G8E	NM_002406	NP_002397	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein	8	Helical; Signal-anchor for type II membrane protein; (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity			ovary(1)	1	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.375	8.822953	8.932717	3	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	180152555	180152555	9932	5	C	T	T	22	22	MGAT1	T	2	2
ADAMTS12	81792	broad.mit.edu	36	5	33631916	33631916	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:33631916C>T	uc003jia.1	-	c.2534G>A	c.(2533-2535)CGC>CAC	p.R845H	ADAMTS12_uc010iuq.1_Missense_Mutation_p.R760H	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	845	TSP type-1 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.369748	262.748976	266.292596	88	150	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33631916	33631916	258	5	C	T	T	27	27	ADAMTS12	T	1	1
DAB2	1601	broad.mit.edu	36	5	39417430	39417430	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:39417430C>T	uc003jlx.2	-	c.1387G>A	c.(1387-1389)GTC>ATC	p.V463I	DAB2_uc003jlw.2_Missense_Mutation_p.V442I	NM_001343	NP_001334	P98082	DAB2_HUMAN	disabled homolog 2	463					cell proliferation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway, planar cell polarity pathway	clathrin coated vesicle membrane|coated pit	protein C-terminus binding			kidney(2)|skin(1)	3	all_lung(31;0.000197)		Epithelial(62;0.137)											0.426136	232.100214	232.936376	75	101	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39417430	39417430	4384	5	C	T	T	19	19	DAB2	T	1	1
RBM16	22828	broad.mit.edu	36	6	155155735	155155735	+	Silent	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:155155735C>G	uc003qqa.1	+	c.408C>G	c.(406-408)GCC>GCG	p.A136A	RBM16_uc003qpz.1_Silent_p.A136A|RBM16_uc010kji.1_Silent_p.A157A	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16	136	CID.				mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)										0.22807	7.125576	11.374899	13	44	CC		KEEP	---	---	---	---	capture			Silent	SNP	155155735	155155735	13579	6	C	G	G	23	23	RBM16	G	3	3
NOX3	50508	broad.mit.edu	36	6	155791785	155791785	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:155791785C>G	uc003qqm.1	-	c.980G>C	c.(979-981)TGC>TCC	p.C327S		NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	327	Extracellular (Potential).|FAD-binding FR-type.				oxidation-reduction process		electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)										0.208333	6.556063	8.456492	5	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	155791785	155791785	10961	6	C	G	G	25	25	NOX3	G	3	3
LHFPL5	222662	broad.mit.edu	36	6	35890499	35890499	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:35890499A>G	uc003olg.1	+	c.611A>G	c.(610-612)GAC>GGC	p.D204G		NM_182548	NP_872354	Q8TAF8	TMHS_HUMAN	lipoma HMGIC fusion partner-like 5	204						integral to membrane					0														0.210526	6.788268	8.263927	4	15	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35890499	35890499	9094	6	A	G	G	10	10	LHFPL5	G	4	4
TJAP1	93643	broad.mit.edu	36	6	43579356	43579356	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43579356C>G	uc003ovd.1	+	c.513C>G	c.(511-513)GAC>GAG	p.D171E	TJAP1_uc003ovc.1_Missense_Mutation_p.D161E|TJAP1_uc010jyp.1_Missense_Mutation_p.D130E|TJAP1_uc003ove.1_Missense_Mutation_p.D161E|TJAP1_uc003ovf.1_Missense_Mutation_p.D161E|TJAP1_uc003ovg.1_Missense_Mutation_p.D37E|TJAP1_uc003ovh.1_5'UTR|TJAP1_uc003ovi.1_Missense_Mutation_p.D37E	NM_080604	NP_542171	Q5JTD0	TJAP1_HUMAN	tight junction protein 4 (peripheral)	171	Potential.					Golgi apparatus|tight junction	protein binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)											0.214286	7.2229	9.350649	6	22	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43579356	43579356	16457	6	C	G	G	20	20	TJAP1	G	3	3
EEF1A1	1915	broad.mit.edu	36	6	74284821	74284821	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:74284821C>T	uc003phi.1	-	c.1006G>A	c.(1006-1008)GAA>AAA	p.E336K	EEF1A1_uc003phd.1_Missense_Mutation_p.E61K|EEF1A1_uc003phe.1_Missense_Mutation_p.E326K|EEF1A1_uc003phf.1_Missense_Mutation_p.E336K|EEF1A1_uc003phg.1_Missense_Mutation_p.E336K|EEF1A1_uc003phh.1_Missense_Mutation_p.E182K|EEF1A1_uc003phj.1_Missense_Mutation_p.E336K|EEF1A1_uc003phk.1_Missense_Mutation_p.E336K|EEF1A1_uc003phl.2_Intron|EEF1A1_uc003phm.1_Intron	NM_001402	NP_001393	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha	336						cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0												OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.152	35.743382	50.235411	19	106	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74284821	74284821	5110	6	C	T	T	30	30	EEF1A1	T	2	2
OR2A5	393046	broad.mit.edu	36	7	143379274	143379274	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:143379274C>A	uc003wdu.1	+	c.847C>A	c.(847-849)CCG>ACG	p.P283T		NM_012365	NP_036497	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A,	283	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0783)													0.175182	53.414217	67.047605	24	113	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143379274	143379274	11387	7	C	A	A	22	22	OR2A5	A	3	3
GIMAP1	170575	broad.mit.edu	36	7	150048367	150048367	+	Silent	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150048367G>A	uc003whp.1	+	c.366G>A	c.(364-366)GCG>GCA	p.A122A	GIMAP1_uc003whq.1_Silent_p.A114A	NM_130759	NP_570115	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	114	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.315789	47.931343	49.650808	18	39	GG		KEEP	---	---	---	---	capture			Silent	SNP	150048367	150048367	6647	7	G	A	A	38	38	GIMAP1	A	1	1
GALNTL5	168391	broad.mit.edu	36	7	151315219	151315219	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:151315219G>A	uc003wkp.1	+	c.578G>A	c.(577-579)CGG>CAG	p.R193Q	GALNTL5_uc003wkq.1_Intron|GALNTL5_uc003wkr.1_Non-coding_Transcript|GALNTL5_uc003wks.1_Non-coding_Transcript|GALNTL5_uc010lqf.1_Missense_Mutation_p.R82Q	NM_145292	NP_660335	Q7Z4T8	GLTL5_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	193	Catalytic subdomain A.|Lumenal (Potential).					Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)										0.252747	63.385863	68.434281	23	68	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151315219	151315219	6488	7	G	A	A	39	39	GALNTL5	A	1	1
CHRNA2	1135	broad.mit.edu	36	8	27375092	27375092	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:27375092G>C	uc010lur.1	-	c.1561C>G	c.(1561-1563)CTG>GTG	p.L521V	CHRNA2_uc010lus.1_Missense_Mutation_p.L323V	NM_000742	NP_000733	Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha	521	Helical; (Potential).					cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(1)	1		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Gallamine Triethiodide(DB00483)|Levallorphan(DB00504)|Mecamylamine(DB00657)|Metocurine(DB01336)|Metocurine Iodide(DB00416)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Rocuronium(DB00728)|Tubocurarine(DB01199)									0.357143	12.470051	12.722127	5	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27375092	27375092	3517	8	G	C	C	33	33	CHRNA2	C	3	3
FGFR1	2260	broad.mit.edu	36	8	38390360	38390360	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:38390360C>G	uc010lwg.1	-	c.2412G>C	c.(2410-2412)GAG>GAC	p.E804D	FGFR1_uc010lwh.1_Missense_Mutation_p.E802D|FGFR1_uc010lwi.1_Missense_Mutation_p.E713D|FGFR1_uc010lwj.1_Missense_Mutation_p.E715D|FGFR1_uc010lwk.1_Missense_Mutation_p.E794D|FGFR1_uc003xlp.1_Missense_Mutation_p.E802D|FGFR1_uc010lwf.1_Non-coding_Transcript	NM_023110	NP_075598	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1 isoform 1	804	Cytoplasmic (Potential).				axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|protein phosphorylation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|ovary(1)|breast(1)	12	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)	Melanoma(146;1153 1840 21453 21841 43625)		1		244				0.263158	9.160414	10.129765	5	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38390360	38390360	6100	8	C	G	G	28	28	FGFR1	G	3	3
KIAA0146	23514	broad.mit.edu	36	8	48788605	48788605	+	Silent	SNP	T	G	G			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:48788605T>G	uc003xqd.1	+	c.2190T>G	c.(2188-2190)GGT>GGG	p.G730G	KIAA0146_uc003xqe.1_Silent_p.G205G|KIAA0146_uc003xqf.1_Non-coding_Transcript|KIAA0146_uc010lxt.1_Silent_p.G419G|KIAA0146_uc010lxu.1_Silent_p.G229G|KIAA0146_uc003xqg.1_Non-coding_Transcript	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514	730											0		Lung NSC(58;0.175)												0.333333	6.961869	7.446255	6	12	TT		KEEP	---	---	---	---	capture			Silent	SNP	48788605	48788605	8464	8	T	G	G	58	58	KIAA0146	G	4	4
C9orf9	11092	broad.mit.edu	36	9	134749231	134749231	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:134749231A>C	uc004cbx.1	+	c.76A>C	c.(76-78)ACC>CCC	p.T26P	C9orf9_uc004cby.1_Missense_Mutation_p.T26P|C9orf9_uc004cbz.1_Missense_Mutation_p.T26P	NM_018956	NP_061829	Q96E40	CI009_HUMAN	Rsb-66 protein	26								p.?(1)			0				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|GBM - Glioblastoma multiforme(294;4.84e-07)|Epithelial(140;1.28e-06)										0.666667	9.074556	9.215626	4	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134749231	134749231	2620	9	A	C	C	6	6	C9orf9	C	4	4
KCNT1	57582	broad.mit.edu	36	9	137815712	137815712	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:137815712A>C	uc004cgn.1	+	c.2863A>C	c.(2863-2865)AAC>CAC	p.N955H	KCNT1_uc010nbf.1_Missense_Mutation_p.N910H|KCNT1_uc004cgo.1_Missense_Mutation_p.N704H	NM_020822	NP_065873	B9EGP2	B9EGP2_HUMAN	potassium channel, subfamily T, member 1	955						membrane	binding|calcium-activated potassium channel activity|catalytic activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)										0.222222	6.407504	7.68209	4	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	137815712	137815712	8396	9	A	C	C	5	5	KCNT1	C	4	4
GAS1	2619	broad.mit.edu	36	9	88750893	88750893	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:88750893C>T	uc004aox.2	-	c.622G>A	c.(622-624)GAG>AAG	p.E208K		NM_002048	NP_002039	P54826	GAS1_HUMAN	growth arrest-specific 1	208					cell cycle arrest|negative regulation of S phase of mitotic cell cycle	anchored to plasma membrane					0														0.24	14.536536	16.079798	6	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88750893	88750893	6508	9	C	T	T	29	29	GAS1	T	2	2
ZCCHC12	170261	broad.mit.edu	36	X	117843446	117843446	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:117843446G>A	uc004equ.1	+	c.211G>A	c.(211-213)GTC>ATC	p.V71I	ZCCHC12_uc010nqj.1_Missense_Mutation_p.V71I	NM_173798	NP_776159	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	71					regulation of transcription, DNA-dependent|transcription, DNA-dependent		nucleic acid binding|zinc ion binding			ovary(1)	1														0.448276	37.571072	37.638591	13	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117843446	117843446	18169	23	G	A	A	40	40	ZCCHC12	A	1	1
SLC9A6	10479	broad.mit.edu	36	X	134904785	134904785	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1037-01	TCGA-14-1037-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:134904785T>C	uc004ezk.1	+	c.500T>C	c.(499-501)GTT>GCT	p.V167A	SLC9A6_uc004ezj.1_Intron	NM_001042537	NP_001036002	Q92581	SL9A6_HUMAN	solute carrier family 9 (sodium/hydrogen	144	Helical; (Potential).				regulation of pH	early endosome membrane|endoplasmic reticulum membrane|integral to membrane|microsome|plasma membrane|recycling endosome membrane	sodium:hydrogen antiporter activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)													0.391892	91.058378	91.815729	29	45	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	134904785	134904785	15215	23	T	C	C	60	60	SLC9A6	C	4	4
TKTL1	8277	broad.mit.edu	36	X	153177460	153177460	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153177460G>T	uc004fkg.1	+	c.54G>T	c.(52-54)AGG>AGT	p.R18S	TEX28_uc004fke.1_5'Flank|TEX28_uc004fkf.1_5'Flank|TEX28_uc010nut.1_5'Flank	NM_012253	NP_036385	P51854	TKTL1_HUMAN	transketolase-like 1	18					glucose catabolic process|thiamine metabolic process	cytoplasm|nucleus	metal ion binding|transketolase activity			ovary(3)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-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)													0.487805	57.794719	57.800109	20	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153177460	153177460	16464	23	G	T	T	43	43	TKTL1	T	3	3
MAP3K15	389840	broad.mit.edu	36	X	19308260	19308260	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:19308260C>G	uc004czk.1	-	c.913G>C	c.(913-915)GCC>CCC	p.A305P	MAP3K15_uc004czj.1_Missense_Mutation_p.A265P	NM_001001671	NP_001001671	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase	830	Protein kinase.				protein phosphorylation		ATP binding|MAP kinase kinase kinase activity|metal ion binding			ovary(3)|lung(2)|skin(1)	6	Hepatocellular(33;0.183)													0.148148	16.940179	26.580806	12	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19308260	19308260	9632	23	C	G	G	25	25	MAP3K15	G	3	3
STARD8	9754	broad.mit.edu	36	X	67856926	67856926	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1037-01	TCGA-14-1037-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:67856926G>C	uc004dxb.1	+	c.1985G>C	c.(1984-1986)GGC>GCC	p.G662A	STARD8_uc004dxa.1_Missense_Mutation_p.G582A|STARD8_uc004dxc.2_Missense_Mutation_p.G582A	NM_014725	NP_055540	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain	582	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion	GTPase activator activity			breast(3)|ovary(2)|pancreas(1)	6														0.296296	12.873875	13.886791	8	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67856926	67856926	15782	23	G	C	C	42	42	STARD8	C	3	3
GDPD2	54857	broad.mit.edu	36	X	69562980	69562980	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1037-01	TCGA-14-1037-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:69562980C>G	uc004dyh.1	+	c.398C>G	c.(397-399)GCT>GGT	p.A133G	GDPD2_uc010nkx.1_Missense_Mutation_p.A133G|GDPD2_uc010nky.1_5'UTR	NM_017711	NP_060181	Q9HCC8	GDPD2_HUMAN	osteoblast differentiation promoting factor	133	Helical; (Potential).				glycerol metabolic process|lipid metabolic process	cytoplasm|cytoskeleton|integral to membrane|plasma membrane	glycerophosphodiester phosphodiesterase activity|glycerophosphoinositol inositolphosphodiesterase activity|metal ion binding			ovary(2)	2	Renal(35;0.156)													0.285714	6.687898	7.269604	4	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69562980	69562980	6592	23	C	G	G	28	28	GDPD2	G	3	3
ZNF711	7552	broad.mit.edu	36	X	84396929	84396929	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1037-01	TCGA-14-1037-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:84396929A>G	uc004eeq.1	+	c.88A>G	c.(88-90)ATG>GTG	p.M30V	ZNF711_uc004eeo.1_Missense_Mutation_p.M30V|ZNF711_uc004eep.1_Missense_Mutation_p.M30V	NM_021998	NP_068838	Q9Y462	ZN711_HUMAN	zinc finger protein 711	30					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|transcription regulator activity|zinc ion binding			ovary(3)	3														0.148148	6.569146	16.379053	12	69	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84396929	84396929	18712	23	A	G	G	4	4	ZNF711	G	4	4
PLXNC1	10154	broad.mit.edu	36	12	93197442	93197445	+	Frame_Shift_Del	DEL	TCAG	-	-			TCGA-14-1037-01	TCGA-14-1037-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:93197442_93197445delTCAG	uc001tdc.1	+	c.3661_3664delTCAG	c.(3661-3666)TCAGTCfs	p.S1221fs	PLXNC1_uc009zsv.1_5'UTR	NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1	1221_1222	Cytoplasmic (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3														0.33			35	71				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	93197442	93197445	12552	12	TCAG	-	-	62	62	PLXNC1	-	5	5
OBSCN	84033	broad.mit.edu	36	1	226534873	226534874	+	Frame_Shift_Ins	INS	-	A	A			TCGA-14-1037-01	TCGA-14-1037-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:226534873_226534874insA	uc009xez.1	+	c.7950_7951insA	c.(7948-7953)CTGAAGfs	p.L2650fs	OBSCN_uc001hsn.1_Frame_Shift_Ins_p.L2650fs|OBSCN_uc001hsp.1_Frame_Shift_Ins_p.L349fs|OBSCN_uc001hsq.1_5'UTR	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	2650_2651	Ig-like 26.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	226534873	226534874	11217	1	-	A	A	45	45	OBSCN	A	5	5
MARCKS	4082	broad.mit.edu	36	6	114287903	114287903	+	Frame_Shift_Del	DEL	A	-	-			TCGA-14-1037-01	TCGA-14-1037-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:114287903_114287903delA	uc003pvy.2	+	c.454_454delA	c.(454-456)AAAfs	p.K152fs		NM_002356	NP_002347	P29966	MARCS_HUMAN	myristoylated alanine-rich protein kinase C	152	Calmodulin-binding (PSD).				energy reserve metabolic process|regulation of insulin secretion	actin cytoskeleton|plasma membrane	actin filament binding|calmodulin binding				0		all_cancers(87;7.65e-05)|all_epithelial(87;0.000296)|all_hematologic(75;0.0172)|Colorectal(196;0.0317)|all_lung(197;0.198)		Epithelial(106;1.59e-07)|all cancers(137;9.85e-07)|OV - Ovarian serous cystadenocarcinoma(136;0.000322)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	114287903	114287903	9692	6	A	-	-	9	9	MARCKS	-	5	5
